CCP4 Bulletin Board Archive: loop building with ARP/wARP

From: Gregory Bowman
Date: 25 August 2011 14:12

Hi all,

I have a large disordered loop (33aa) for a 2.0 Å dataset for which the rest of the structure is well-defined, and phases are decent (Rwork=19.6, Rfree=24.6). I can see some broken up density at one end, but have been unable to convincingly build into into this region manually. I would like to try arp/warp to improve density or possibly extend the loop termini but have been thwarted by some technical problems and would appreciate any advice. I've installed ccp4 6.2.0 on Mac OS X (10.6.8) with fink, both as 32-bit and 64-bit to allow me to run ARP/wARP (version 7.1) from the ccp4i GUI. I've been unable to get "loopy" to work, and also the standard ARP/wARP classic.

When I run "ARP/wARP Loops" (a.k.a. loopy), I get the message in the log file: "Couldn't find any loop to build, loopy will simple copy the pdb file". The program is able to read the sequence .pir file and match it to the structure, and seems from the sequence alignment to identify the regions of the sequence for which there is no structure. I'm guessing that I'm not putting some obvious parameter into the GUI/starting script, but I don't know what that might be. The script generated from the GUI (21_loopy.def) is pasted below.

When I try to run ARP/wARP classic for loop building, I get the following message in the logfile:

QUITTING ... ARP/wARP module stopped with an error message:

REFMAC

*** Look for error message in the file:

/Users/gbowman/Greg/20_warpNtrace_refine.last.log

At the end of the warpNtrace_refine.last.log file, the program reports what seem to be close contacts. Since I don't see this in the structure, and don't have any problems or errors like this when I refine the structure with REMAC, is this from rebuilding, and is this the problem that halts REFMAC?

Thanks!

Greg

========= ========= ========= ========= ========= =========

20_warpNtrace_refine.last.log

========= ========= ========= ========= ========= =========

<snip>

Input file :restraints.pdb

NUMBER OF MONOMERS IN THE LIBRARY : 11465

with complete description : 11465

NUMBER OF MODIFICATIONS : 53

NUMBER OF LINKS : 66

I am reading libraries. Please wait.

- energy parameters

- monomer"s description (links & mod )

</FONT></B>

Number of atoms : 2463

Number of residues : 859

Number of chains : 3

I am reading library. Please wait.

mon_lib.cif

INFO: link is found (not be used) dist= 1.907 ideal_dist= 1.432

ch:AA res: 8 GLY at:CA .->ch:AA res: 50 TYR at:OH .

INFO: link is found (not be used) dist= 2.126 ideal_dist= 1.645

ch:AA res: 13 ARG at:NH1 .->ch:AA res: 54 MET at:SD .

INFO: link is found (not be used) dist= 1.820 ideal_dist= 1.462

ch:AA res: 13 ARG at:NH1 .->ch:AA res: 54 MET at:CE .

INFO: link is found (not be used) dist= 1.757 ideal_dist= 1.395

ch:AA res: 13 ARG at:NE .->ch:AA res: 119 PHE at:CD1 .

INFO: link is found (not be used) dist= 1.572 ideal_dist= 1.462

ch:AA res: 13 ARG at:NH2 .->ch:AA res: 125 LEU at:CD2 .

INFO: link is found (not be used) dist= 1.751 ideal_dist= 1.513

ch:AA res: 33 ILE at:CG2 .->ch:AA res: 39 PRO at:CG .

INFO: link is found (not be used) dist= 1.451 ideal_dist= 1.513

ch:AA res: 33 ILE at:CG2 .->ch:AA res: 39 PRO at:CD .

INFO: link is found (not be used) dist= 1.759 ideal_dist= 1.524

ch:AA res: 58 LYS at:CD .->ch:AA res: 130 LEU at:CB .

INFO: link is found (not be used) dist= 1.725 ideal_dist= 1.513

ch:AA res: 58 LYS at:CD .->ch:AA res: 130 LEU at:CD1 .

INFO: link is found (not be used) dist= 1.578 ideal_dist= 1.524

ch:AA res: 83 ARG at:CD .->ch:AA res: 101 PRO at:CG .

INFO: link is found (not be used) dist= 1.843 ideal_dist= 1.457

ch:AA res: 83 ARG at:NE .->ch:AA res: 101 PRO at:CB .

INFO: link is found (not be used) dist= 0.666 ideal_dist= 1.457

ch:AA res: 83 ARG at:NE .->ch:AA res: 101 PRO at:CG .

INFO: link is found (not be used) dist= 1.275 ideal_dist= 1.510

ch:AA res: 83 ARG at:CZ .->ch:AA res: 101 PRO at:CB .

INFO: link is found (not be used) dist= 1.102 ideal_dist= 1.510

ch:AA res: 83 ARG at:CZ .->ch:AA res: 101 PRO at:CG .

INFO: link is found (not be used) dist= 1.191 ideal_dist= 1.457

ch:AA res: 83 ARG at:NH1 .->ch:AA res: 101 PRO at:CA .

INFO: link is found (not be used) dist= 0.690 ideal_dist= 1.457

ch:AA res: 83 ARG at:NH1 .->ch:AA res: 101 PRO at:CB .

INFO: link is found (not be used) dist= 1.891 ideal_dist= 1.457

ch:AA res: 83 ARG at:NH1 .->ch:AA res: 101 PRO at:CG .

INFO: link is found (not be used) dist= 1.352 ideal_dist= 1.457

ch:AA res: 165 VAL at:CG1 .->ch:AA res: 172 TRP at:CZ3 .

INFO: link is found (not be used) dist= 1.440 ideal_dist= 1.457

ch:AA res: 165 VAL at:CG1 .->ch:AA res: 172 TRP at:CE3 .

INFO: link is found (not be used) dist= 1.367 ideal_dist= 1.320

ch:AA res: 172 TRP at:CD1 .->ch:AA res: 176 GLU at:OE1 .

INFO: link is found (not be used) dist= 1.447 ideal_dist= 1.275

ch:AA res: 172 TRP at:NE1 .->ch:AA res: 176 GLU at:OE1 .

INFO: link is found (not be used) dist= 1.760 ideal_dist= 1.360

ch:AA res: 172 TRP at:CH2 .->ch:AA res: 253 ARG at:CZ .

INFO: link is found (not be used) dist= 1.690 ideal_dist= 1.309

ch:AA res: 187 TYR at:OH .->ch:AA res: 198 ASP at:OD2 .

--------------------------------

--- title of input coord file ---

PDB_code:xxxx

PDB_name:----

PDB_date:XX-XXX-XX

--------------------------------

Number of chains : 3

Total number of monomers : 859

Number of atoms : 2463

Number of missing atoms : 0

Number of rebuilt atoms : 0

Number of unknown atoms : 0

Number of deleted atoms : 0

Number of bonds restraints : 1863

Number of angles restraints : 2492

Number of torsions restraints : 1286

Number of chiralities : 266

Number of planar groups : 318

loop_

_atom_type_symbol

_atom_type_scat_Cromer_Mann_a1

_atom_type_scat_Cromer_Mann_b1

_atom_type_scat_Cromer_Mann_a2

_atom_type_scat_Cromer_Mann_b2

_atom_type_scat_Cromer_Mann_a3

_atom_type_scat_Cromer_Mann_b3

_atom_type_scat_Cromer_Mann_a4

_atom_type_scat_Cromer_Mann_b4

_atom_type_scat_Cromer_Mann_c

N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290

C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156

S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 1.0496

O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508

========= ========= ========= ========= ========= =========

21_loopy.def

========= ========= ========= ========= ========= =========

#CCP4I VERSION CCP4Interface 2.1.0
#CCP4I SCRIPT DEF loopy
#CCP4I DATE 25 Aug 2011 08:17:34
#CCP4I USER gbowman
#CCP4I JOB_ID 21
#CCP4I PROJECT GDB210i
#CCP4I TASKNAME loopy
#CCP4I LOG_FILE 21_loopy.log
#CCP4I EDIT_SCRIPT 0
#CCP4I HTML_LOG 0
#CCP4I REMOTE 0
#CCP4I SERVER_HOST localhost
#CCP4I SERVER_PORT 4441
#CCP4I DATABASE_SERVER 0
#CCP4I DATABASE_SERVER_HOST localhost
#CCP4I DATABASE_SERVER_PORT 0

ABORT_LEVEL 8
ATOM_RADIUS 0.74
B_FACTOR 20
B_FACTOR_SIDE_CHAIN 26
CA_DISTANCE 3.8
CA_DISTANCE_ERROR 0.3
CELL_1 38.670
CELL_2 61.426
CELL_3 76.771
CELL_4 90.00
CELL_5 104.17
CELL_6 90.00
CHECK_FIRST_ANGLE 1
C_ANCHOR "A 1213"
DIR_EXT_MAP_FILENAME TEMPORARY
DIR_LOOPFIT_EXE_FILENAME "Full path.."
DIR_LOOPFIT_LOG_FILENAME TEMPORARY
DIR_MAP_FILENAME GDB210i
DIR_MAP_FROM_MTZ TEMPORARY
DIR_MESSAGE_FILENAME GDB210i
DIR_MTZ_FILENAME GDB210i
DIR_OUTPUT_PDB GDB210i
DIR_PDB_INPUT_FILENAME GDB210i
DIR_PRELOOPFIT_PDB TEMPORARY
DIR_SAVE_LOOP_NAME GDB210i
DIR_SAVE_PROP_PDB GDB210i
DIR_SEQIN,0 ""
DIR_SEQIN,1 GDB210i
DIR_STRUCTURE_TO_C "Full path.."
DIR_STRUCTURE_TO_N "Full path.."
DIR_XML_MESSAGE_FILENAME GDB210i
DUMMY_REMOVAL_THRESHOLD 0.1
EXTEND_GAP_SMALLER_THAN 5
EXTEND_REFINEMENT 0
EXT_MAP_FILENAME ""
F1 FWT
FITTARGET 1
FORCE_MIN_CAS_KEPT 1
GRID_NUMBER 378
GRID_TYPE 0
INCLUDE_ALL 1
INCLUDE_CHAINS ""
KEEP_NEG_DENS_HALFWAY 0
LIKELIHOOD_THRESHOLD -5

LOOPFIT_EXE_FILENAME /Users/gbowman/Greg/arp_warp_7.1/bin/bin-i386-Darwin/loopfit

LOOPFIT_LOG_FILENAME loopfit.log

LOOPS_TO_BUILD A1213(33)A1245

LOOP_BOTH_WAYS 1

LOOP_DENSITY_CUTOFF_NO 100

LOOP_LENGTH 33

LOOP_MAIN_CHAIN_DENS_NO 12

LOOP_OVERLAP 0

LOOP_RMS 0.5

LOOP_SEQUENCE ""

LOOP_STRUCTURE_CUTOFF_NO -1

LOOP_STRUCTURE_MIN_NO 0

LOOP_STRUCTURE_THRESHOLD -7

LOOP_TO_C 1

MAP_FILENAME ""

MAP_FROM_MTZ 160BDNAmerged2011aug09_loopy2.map

MAP_INPUT_MODE MTZ

MAX_DISTANCE_BETWEEN_ANCHORS -1.

MAX_LOOPS_AFTER_MC_PLANE 50

MAX_LOOP_LENGTH 15

MAX_NO_CAS_KEPT 5

MESSAGE_FILENAME loopy.msg

MESSAGE_LEVEL 5

MET_IS_SEL,0 0

MET_IS_SEL,1 0

MINIMAL_DISTANCE 0.45

MODE_LOOPY 0

MTZ_FILENAME 160BDNAmerged2011aug09_refmacGDB210i-215.mtz

NMOL,0 1

NMOL,1 1

NRES,0 ""

NRES,1 272

NRESMOL,0 ""

NRESMOL,1 272

NSEQFILES 1

N_ANCHOR "A 1245"

OUTPUT_PDB 2011aug24-GDB210i-renameDNA-3_loopy1.pdb

OVERLAP_REMOVAL_THRESHOLD 0.1

PDB_INPUT_FILENAME 2011aug24-GDB210i-renameDNA-3_refmac1b.pdb

PHI PHWT

PRELOOPFIT_PDB pre_loopfit.pdb

REFINEMENT 1

REMOVAL_FACTOR 1.

SAVE_BEST_NUMBER 2

SAVE_LOOPS 1

SAVE_LOOP_BASENAME 2011aug24-GDB210i-renameDNA-3_loop

SAVE_LOOP_DIR /Users/gbowman/Greg

SAVE_LOOP_NAME 2011aug24-GDB210i-renameDNA-3_loop1.pdb

SAVE_LOOP_PROP_BASE 2011aug24-GDB210i-renameDNA-3_proposed

SAVE_LOOP_PROP_DIR /Users/gbowman/Greg

SAVE_PROP_PDB 2011aug24-GDB210i-renameDNA-3_proposed1.pdb

SEQIN,0 ""

SEQIN,1 160B.pir

SHELL_THICKNESS 1

SHOW_DETAILS_DENSITY 0

SHOW_DETAILS_LIKELIHOOD 0

SHOW_PRUNING_DETAILS 0

SPACEGROUP P21

SPACEGROUP_NUMBER 4

STRUCTURE_TO_C /Users/gbowman/Greg/arp_warp_7.1/bin/bin-i386-Darwin/set_1200_2C_my_0.3b_cos_log.llh

STRUCTURE_TO_N /Users/gbowman/Greg/arp_warp_7.1/bin/bin-i386-Darwin/set_1200_2N_my_0.3b_cos_log.llh

TITLE "build 1213 loop with loopy"

USER_SETTING_MAX_NO_CAS 0

USE_PIR_FILE 1

WEIGHT_DENSITY 1.

WEIGHT_DISTANCE 1.

WEIGHT_STRUCTURE 1.

XML_MESSAGE_FILENAME loopy.xml

========= ========= ========= ========= =========

----------
From: Victor Lamzin

Dear Greg,

Try ARP/wARP 7.2, released a few days ago, which is better, more stable and should have improved flash of error messages to the log files.

ARP/wARP Loopy will not build a 33-residue loop at once, but Classic model building may get the gap shortened.

Go to www.arp-warp.org for download. In parallel, from the same page you can submit Classic protein model building for remote execution in Hamburg, which also has ARP/wARP 7.2 installed.

Please get back if problems remain.

With best regards,
Victor

CCP4 Bulletin Board Archive

Saturday, 3 September 2011

loop building with ARP/wARP

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