Mon 24 Dec 00:36:30 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vll-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:36:34 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 405 and 0 Target number of residues in the AU: 405 Target solvent content: 0.6921 Checking the provided sequence file Detected sequence length: 334 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 668 Adjusted target solvent content: 0.49 Input MTZ file: 1vll-3.8-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5344 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 76.441 3.800 Wilson plot Bfac: 112.68 7455 reflections ( 99.96 % complete ) and 0 restraints for refining 5930 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3756 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3516 (Rfree = 0.000) for 5930 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.99 4.04 Search for helices and strands: 0 residues in 0 chains, 6068 seeds are put forward NCS extension: 0 residues added, 6068 seeds are put forward Round 1: 222 peptides, 44 chains. Longest chain 13 peptides. Score 0.293 Round 2: 277 peptides, 45 chains. Longest chain 12 peptides. Score 0.415 Round 3: 304 peptides, 48 chains. Longest chain 14 peptides. Score 0.445 Round 4: 322 peptides, 50 chains. Longest chain 14 peptides. Score 0.465 Round 5: 336 peptides, 48 chains. Longest chain 17 peptides. Score 0.511 Taking the results from Round 5 Chains 48, Residues 288, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11592 restraints for refining 4831 atoms. 10479 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2764 (Rfree = 0.000) for 4831 atoms. Found 6 (26 requested) and removed 36 (13 requested) atoms. Cycle 2: After refmac, R = 0.2652 (Rfree = 0.000) for 4725 atoms. Found 8 (26 requested) and removed 32 (13 requested) atoms. Cycle 3: After refmac, R = 0.2479 (Rfree = 0.000) for 4664 atoms. Found 8 (25 requested) and removed 21 (12 requested) atoms. Cycle 4: After refmac, R = 0.2418 (Rfree = 0.000) for 4599 atoms. Found 6 (25 requested) and removed 20 (12 requested) atoms. Cycle 5: After refmac, R = 0.2355 (Rfree = 0.000) for 4560 atoms. Found 7 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.94 3.99 Search for helices and strands: 0 residues in 0 chains, 4754 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 4776 seeds are put forward Round 1: 278 peptides, 55 chains. Longest chain 11 peptides. Score 0.317 Round 2: 314 peptides, 51 chains. Longest chain 16 peptides. Score 0.439 Round 3: 305 peptides, 48 chains. Longest chain 18 peptides. Score 0.448 Round 4: 338 peptides, 47 chains. Longest chain 20 peptides. Score 0.524 Round 5: 325 peptides, 45 chains. Longest chain 20 peptides. Score 0.516 Taking the results from Round 4 Chains 51, Residues 291, Estimated correctness of the model 0.0 % 6 chains (64 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 10876 restraints for refining 4832 atoms. 9541 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2333 (Rfree = 0.000) for 4832 atoms. Found 11 (26 requested) and removed 59 (13 requested) atoms. Cycle 7: After refmac, R = 0.2273 (Rfree = 0.000) for 4746 atoms. Found 8 (26 requested) and removed 37 (13 requested) atoms. Cycle 8: After refmac, R = 0.2131 (Rfree = 0.000) for 4697 atoms. Found 9 (25 requested) and removed 25 (12 requested) atoms. Cycle 9: After refmac, R = 0.2127 (Rfree = 0.000) for 4665 atoms. Found 6 (25 requested) and removed 27 (12 requested) atoms. Cycle 10: After refmac, R = 0.1995 (Rfree = 0.000) for 4632 atoms. Found 5 (25 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.92 3.97 Search for helices and strands: 0 residues in 0 chains, 4789 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4811 seeds are put forward Round 1: 264 peptides, 47 chains. Longest chain 11 peptides. Score 0.365 Round 2: 297 peptides, 41 chains. Longest chain 22 peptides. Score 0.496 Round 3: 313 peptides, 44 chains. Longest chain 18 peptides. Score 0.501 Round 4: 337 peptides, 45 chains. Longest chain 19 peptides. Score 0.539 Round 5: 316 peptides, 42 chains. Longest chain 22 peptides. Score 0.524 Taking the results from Round 4 Chains 47, Residues 292, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 10851 restraints for refining 4832 atoms. 9615 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2317 (Rfree = 0.000) for 4832 atoms. Found 8 (26 requested) and removed 32 (13 requested) atoms. Cycle 12: After refmac, R = 0.2211 (Rfree = 0.000) for 4767 atoms. Found 10 (26 requested) and removed 28 (13 requested) atoms. Cycle 13: After refmac, R = 0.2085 (Rfree = 0.000) for 4728 atoms. Found 5 (26 requested) and removed 22 (13 requested) atoms. Cycle 14: After refmac, R = 0.2068 (Rfree = 0.000) for 4692 atoms. Found 15 (25 requested) and removed 21 (12 requested) atoms. Cycle 15: After refmac, R = 0.2009 (Rfree = 0.000) for 4668 atoms. Found 14 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.95 4.00 Search for helices and strands: 0 residues in 0 chains, 4846 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 4865 seeds are put forward Round 1: 297 peptides, 54 chains. Longest chain 15 peptides. Score 0.372 Round 2: 326 peptides, 51 chains. Longest chain 16 peptides. Score 0.464 Round 3: 324 peptides, 50 chains. Longest chain 19 peptides. Score 0.469 Round 4: 325 peptides, 44 chains. Longest chain 20 peptides. Score 0.524 Round 5: 308 peptides, 46 chains. Longest chain 18 peptides. Score 0.472 Taking the results from Round 4 Chains 48, Residues 281, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11026 restraints for refining 4832 atoms. 9852 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2563 (Rfree = 0.000) for 4832 atoms. Found 24 (26 requested) and removed 31 (13 requested) atoms. Cycle 17: After refmac, R = 0.2349 (Rfree = 0.000) for 4791 atoms. Found 20 (26 requested) and removed 26 (13 requested) atoms. Cycle 18: After refmac, R = 0.2207 (Rfree = 0.000) for 4767 atoms. Found 8 (26 requested) and removed 28 (13 requested) atoms. Cycle 19: After refmac, R = 0.2230 (Rfree = 0.000) for 4724 atoms. Found 17 (26 requested) and removed 20 (13 requested) atoms. Cycle 20: After refmac, R = 0.2043 (Rfree = 0.000) for 4709 atoms. Found 7 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.93 3.98 Search for helices and strands: 0 residues in 0 chains, 4867 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4891 seeds are put forward Round 1: 241 peptides, 47 chains. Longest chain 10 peptides. Score 0.309 Round 2: 273 peptides, 44 chains. Longest chain 17 peptides. Score 0.416 Round 3: 286 peptides, 45 chains. Longest chain 18 peptides. Score 0.435 Round 4: 283 peptides, 43 chains. Longest chain 15 peptides. Score 0.448 Round 5: 294 peptides, 44 chains. Longest chain 18 peptides. Score 0.462 Taking the results from Round 5 Chains 45, Residues 250, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11495 restraints for refining 4832 atoms. 10499 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2408 (Rfree = 0.000) for 4832 atoms. Found 20 (26 requested) and removed 24 (13 requested) atoms. Cycle 22: After refmac, R = 0.2258 (Rfree = 0.000) for 4805 atoms. Found 18 (26 requested) and removed 24 (13 requested) atoms. Cycle 23: After refmac, R = 0.2122 (Rfree = 0.000) for 4776 atoms. Found 12 (26 requested) and removed 20 (13 requested) atoms. Cycle 24: After refmac, R = 0.2037 (Rfree = 0.000) for 4759 atoms. Found 18 (26 requested) and removed 16 (13 requested) atoms. Cycle 25: After refmac, R = 0.1991 (Rfree = 0.000) for 4755 atoms. Found 25 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.91 3.96 Search for helices and strands: 0 residues in 0 chains, 4946 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4968 seeds are put forward Round 1: 246 peptides, 50 chains. Longest chain 10 peptides. Score 0.290 Round 2: 285 peptides, 52 chains. Longest chain 13 peptides. Score 0.364 Round 3: 287 peptides, 49 chains. Longest chain 14 peptides. Score 0.398 Round 4: 283 peptides, 48 chains. Longest chain 21 peptides. Score 0.399 Round 5: 301 peptides, 48 chains. Longest chain 18 peptides. Score 0.439 Taking the results from Round 5 Chains 50, Residues 253, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11265 restraints for refining 4832 atoms. 10241 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2221 (Rfree = 0.000) for 4832 atoms. Found 10 (26 requested) and removed 35 (13 requested) atoms. Cycle 27: After refmac, R = 0.2087 (Rfree = 0.000) for 4779 atoms. Found 7 (26 requested) and removed 22 (13 requested) atoms. Cycle 28: After refmac, R = 0.2171 (Rfree = 0.000) for 4745 atoms. Found 10 (26 requested) and removed 19 (13 requested) atoms. Cycle 29: After refmac, R = 0.1964 (Rfree = 0.000) for 4722 atoms. Found 8 (26 requested) and removed 21 (13 requested) atoms. Cycle 30: After refmac, R = 0.2050 (Rfree = 0.000) for 4703 atoms. Found 12 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.94 3.99 Search for helices and strands: 0 residues in 0 chains, 4870 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 4889 seeds are put forward Round 1: 214 peptides, 41 chains. Longest chain 11 peptides. Score 0.306 Round 2: 274 peptides, 45 chains. Longest chain 18 peptides. Score 0.408 Round 3: 263 peptides, 42 chains. Longest chain 13 peptides. Score 0.413 Round 4: 272 peptides, 42 chains. Longest chain 15 peptides. Score 0.433 Round 5: 275 peptides, 41 chains. Longest chain 15 peptides. Score 0.449 Taking the results from Round 5 Chains 42, Residues 234, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11302 restraints for refining 4832 atoms. 10321 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2571 (Rfree = 0.000) for 4832 atoms. Found 20 (26 requested) and removed 41 (13 requested) atoms. Cycle 32: After refmac, R = 0.2250 (Rfree = 0.000) for 4788 atoms. Found 20 (26 requested) and removed 23 (13 requested) atoms. Cycle 33: After refmac, R = 0.2227 (Rfree = 0.000) for 4777 atoms. Found 18 (26 requested) and removed 18 (13 requested) atoms. Cycle 34: After refmac, R = 0.2096 (Rfree = 0.000) for 4764 atoms. Found 17 (26 requested) and removed 23 (13 requested) atoms. Cycle 35: After refmac, R = 0.2091 (Rfree = 0.000) for 4745 atoms. Found 13 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.94 3.99 Search for helices and strands: 0 residues in 0 chains, 4883 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4901 seeds are put forward Round 1: 202 peptides, 40 chains. Longest chain 11 peptides. Score 0.285 Round 2: 220 peptides, 34 chains. Longest chain 16 peptides. Score 0.396 Round 3: 222 peptides, 36 chains. Longest chain 19 peptides. Score 0.380 Round 4: 233 peptides, 35 chains. Longest chain 19 peptides. Score 0.416 Round 5: 226 peptides, 36 chains. Longest chain 18 peptides. Score 0.389 Taking the results from Round 4 Chains 35, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11608 restraints for refining 4831 atoms. 10851 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2362 (Rfree = 0.000) for 4831 atoms. Found 18 (26 requested) and removed 38 (13 requested) atoms. Cycle 37: After refmac, R = 0.2221 (Rfree = 0.000) for 4790 atoms. Found 21 (26 requested) and removed 27 (13 requested) atoms. Cycle 38: After refmac, R = 0.1832 (Rfree = 0.000) for 4769 atoms. Found 2 (26 requested) and removed 15 (13 requested) atoms. Cycle 39: After refmac, R = 0.1707 (Rfree = 0.000) for 4752 atoms. Found 2 (26 requested) and removed 14 (13 requested) atoms. Cycle 40: After refmac, R = 0.1744 (Rfree = 0.000) for 4738 atoms. Found 0 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.96 4.01 Search for helices and strands: 0 residues in 0 chains, 4881 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4904 seeds are put forward Round 1: 213 peptides, 41 chains. Longest chain 10 peptides. Score 0.303 Round 2: 217 peptides, 36 chains. Longest chain 12 peptides. Score 0.367 Round 3: 213 peptides, 37 chains. Longest chain 12 peptides. Score 0.347 Round 4: 220 peptides, 35 chains. Longest chain 14 peptides. Score 0.385 Round 5: 223 peptides, 36 chains. Longest chain 15 peptides. Score 0.382 Taking the results from Round 4 Chains 36, Residues 185, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11809 restraints for refining 4831 atoms. 11073 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2182 (Rfree = 0.000) for 4831 atoms. Found 12 (26 requested) and removed 38 (13 requested) atoms. Cycle 42: After refmac, R = 0.2217 (Rfree = 0.000) for 4780 atoms. Found 18 (26 requested) and removed 26 (13 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2132 (Rfree = 0.000) for 4764 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 44: After refmac, R = 0.1956 (Rfree = 0.000) for 4759 atoms. Found 15 (26 requested) and removed 19 (13 requested) atoms. Cycle 45: After refmac, R = 0.2084 (Rfree = 0.000) for 4748 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.91 3.96 Search for helices and strands: 0 residues in 0 chains, 4883 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4900 seeds are put forward Round 1: 195 peptides, 36 chains. Longest chain 13 peptides. Score 0.312 Round 2: 204 peptides, 37 chains. Longest chain 10 peptides. Score 0.324 Round 3: 217 peptides, 37 chains. Longest chain 14 peptides. Score 0.357 Round 4: 197 peptides, 33 chains. Longest chain 16 peptides. Score 0.351 Round 5: 210 peptides, 32 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 178, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7455 reflections ( 99.96 % complete ) and 11493 restraints for refining 4818 atoms. 10782 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2335 (Rfree = 0.000) for 4818 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2229 (Rfree = 0.000) for 4791 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2228 (Rfree = 0.000) for 4770 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2045 (Rfree = 0.000) for 4745 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Writing output files ... TimeTaking 45.78