Mon 24 Dec 07:54:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vqs-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.8-parrot-noncs ############### 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 07:54:46 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/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.8-parrot-noncs/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 462 and 0 Target number of residues in the AU: 462 Target solvent content: 0.6326 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-3.8-parrot-noncs.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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 4640 target number of atoms Had to go as low as 0.85 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: 29.971 3.801 Wilson plot Bfac: 67.67 7192 reflections ( 99.49 % complete ) and 0 restraints for refining 5161 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3465 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3582 (Rfree = 0.000) for 5161 atoms. Found 28 (28 requested) and removed 46 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 5229 seeds are put forward NCS extension: 0 residues added, 5229 seeds are put forward Round 1: 217 peptides, 43 chains. Longest chain 9 peptides. Score 0.295 Round 2: 289 peptides, 48 chains. Longest chain 15 peptides. Score 0.421 Round 3: 324 peptides, 50 chains. Longest chain 21 peptides. Score 0.479 Round 4: 316 peptides, 44 chains. Longest chain 22 peptides. Score 0.518 Round 5: 329 peptides, 40 chains. Longest chain 26 peptides. Score 0.578 Taking the results from Round 5 Chains 40, Residues 289, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9417 restraints for refining 4195 atoms. 8301 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3025 (Rfree = 0.000) for 4195 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 2: After refmac, R = 0.2876 (Rfree = 0.000) for 4100 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. Cycle 3: After refmac, R = 0.2471 (Rfree = 0.000) for 4039 atoms. Found 8 (22 requested) and removed 25 (11 requested) atoms. Cycle 4: After refmac, R = 0.2857 (Rfree = 0.000) for 3994 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 5: After refmac, R = 0.2865 (Rfree = 0.000) for 3943 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 4068 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 4089 seeds are put forward Round 1: 297 peptides, 50 chains. Longest chain 17 peptides. Score 0.419 Round 2: 330 peptides, 49 chains. Longest chain 21 peptides. Score 0.501 Round 3: 318 peptides, 44 chains. Longest chain 16 peptides. Score 0.522 Round 4: 319 peptides, 40 chains. Longest chain 24 peptides. Score 0.559 Round 5: 321 peptides, 42 chains. Longest chain 22 peptides. Score 0.545 Taking the results from Round 4 Chains 42, Residues 279, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9223 restraints for refining 4196 atoms. 8027 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2862 (Rfree = 0.000) for 4196 atoms. Found 23 (23 requested) and removed 48 (11 requested) atoms. Cycle 7: After refmac, R = 0.2692 (Rfree = 0.000) for 4107 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2523 (Rfree = 0.000) for 4053 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 9: After refmac, R = 0.2534 (Rfree = 0.000) for 4008 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2466 (Rfree = 0.000) for 3977 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 4096 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 4113 seeds are put forward Round 1: 279 peptides, 49 chains. Longest chain 16 peptides. Score 0.387 Round 2: 297 peptides, 44 chains. Longest chain 18 peptides. Score 0.478 Round 3: 300 peptides, 40 chains. Longest chain 22 peptides. Score 0.521 Round 4: 304 peptides, 48 chains. Longest chain 18 peptides. Score 0.455 Round 5: 315 peptides, 45 chains. Longest chain 22 peptides. Score 0.506 Taking the results from Round 3 Chains 40, Residues 260, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9020 restraints for refining 4094 atoms. 7949 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2933 (Rfree = 0.000) for 4094 atoms. Found 22 (22 requested) and removed 55 (11 requested) atoms. Cycle 12: After refmac, R = 0.2707 (Rfree = 0.000) for 4022 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 13: After refmac, R = 0.2619 (Rfree = 0.000) for 3970 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 14: After refmac, R = 0.2538 (Rfree = 0.000) for 3940 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 15: After refmac, R = 0.2493 (Rfree = 0.000) for 3920 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 4063 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4077 seeds are put forward Round 1: 270 peptides, 49 chains. Longest chain 12 peptides. Score 0.365 Round 2: 293 peptides, 49 chains. Longest chain 13 peptides. Score 0.420 Round 3: 291 peptides, 44 chains. Longest chain 19 peptides. Score 0.465 Round 4: 311 peptides, 45 chains. Longest chain 20 peptides. Score 0.498 Round 5: 301 peptides, 43 chains. Longest chain 17 peptides. Score 0.496 Taking the results from Round 4 Chains 45, Residues 266, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9222 restraints for refining 4120 atoms. 8203 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2729 (Rfree = 0.000) for 4120 atoms. Found 22 (22 requested) and removed 45 (11 requested) atoms. Cycle 17: After refmac, R = 0.2485 (Rfree = 0.000) for 4067 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 18: After refmac, R = 0.2373 (Rfree = 0.000) for 4035 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 19: After refmac, R = 0.2383 (Rfree = 0.000) for 4014 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2344 (Rfree = 0.000) for 4002 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 4141 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4156 seeds are put forward Round 1: 253 peptides, 48 chains. Longest chain 14 peptides. Score 0.334 Round 2: 288 peptides, 47 chains. Longest chain 25 peptides. Score 0.428 Round 3: 281 peptides, 44 chains. Longest chain 21 peptides. Score 0.442 Round 4: 283 peptides, 37 chains. Longest chain 20 peptides. Score 0.514 Round 5: 285 peptides, 41 chains. Longest chain 18 peptides. Score 0.481 Taking the results from Round 4 Chains 37, Residues 246, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9660 restraints for refining 4197 atoms. 8713 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2679 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 38 (11 requested) atoms. Cycle 22: After refmac, R = 0.2221 (Rfree = 0.000) for 4152 atoms. Found 10 (22 requested) and removed 25 (11 requested) atoms. Cycle 23: After refmac, R = 0.2466 (Rfree = 0.000) for 4113 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 24: After refmac, R = 0.2519 (Rfree = 0.000) for 4087 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 25: After refmac, R = 0.2537 (Rfree = 0.000) for 4069 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 4165 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 4184 seeds are put forward Round 1: 242 peptides, 48 chains. Longest chain 11 peptides. Score 0.306 Round 2: 266 peptides, 48 chains. Longest chain 13 peptides. Score 0.366 Round 3: 260 peptides, 44 chains. Longest chain 13 peptides. Score 0.393 Round 4: 265 peptides, 43 chains. Longest chain 15 peptides. Score 0.416 Round 5: 280 peptides, 44 chains. Longest chain 18 peptides. Score 0.440 Taking the results from Round 5 Chains 44, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9699 restraints for refining 4193 atoms. 8799 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2954 (Rfree = 0.000) for 4193 atoms. Found 23 (23 requested) and removed 53 (11 requested) atoms. Cycle 27: After refmac, R = 0.2690 (Rfree = 0.000) for 4114 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 28: After refmac, R = 0.2198 (Rfree = 0.000) for 4072 atoms. Found 11 (22 requested) and removed 15 (11 requested) atoms. Cycle 29: After refmac, R = 0.2559 (Rfree = 0.000) for 4044 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 30: After refmac, R = 0.2754 (Rfree = 0.000) for 4022 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 4126 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 4154 seeds are put forward Round 1: 216 peptides, 44 chains. Longest chain 10 peptides. Score 0.281 Round 2: 247 peptides, 42 chains. Longest chain 16 peptides. Score 0.383 Round 3: 269 peptides, 44 chains. Longest chain 17 peptides. Score 0.415 Round 4: 255 peptides, 44 chains. Longest chain 14 peptides. Score 0.381 Round 5: 257 peptides, 40 chains. Longest chain 16 peptides. Score 0.428 Taking the results from Round 5 Chains 40, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9671 restraints for refining 4197 atoms. 8843 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2782 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 46 (11 requested) atoms. Cycle 32: After refmac, R = 0.2704 (Rfree = 0.000) for 4145 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 33: After refmac, R = 0.2707 (Rfree = 0.000) for 4096 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 34: After refmac, R = 0.2656 (Rfree = 0.000) for 4073 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 35: After refmac, R = 0.2591 (Rfree = 0.000) for 4058 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 4184 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4206 seeds are put forward Round 1: 188 peptides, 40 chains. Longest chain 12 peptides. Score 0.250 Round 2: 224 peptides, 41 chains. Longest chain 12 peptides. Score 0.336 Round 3: 231 peptides, 38 chains. Longest chain 15 peptides. Score 0.387 Round 4: 246 peptides, 39 chains. Longest chain 18 peptides. Score 0.412 Round 5: 236 peptides, 37 chains. Longest chain 17 peptides. Score 0.410 Taking the results from Round 4 Chains 39, Residues 207, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9265 restraints for refining 4081 atoms. 8476 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2698 (Rfree = 0.000) for 4081 atoms. Found 22 (22 requested) and removed 54 (11 requested) atoms. Cycle 37: After refmac, R = 0.2645 (Rfree = 0.000) for 4023 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 38: After refmac, R = 0.2567 (Rfree = 0.000) for 4002 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 39: After refmac, R = 0.2550 (Rfree = 0.000) for 3992 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 40: After refmac, R = 0.2557 (Rfree = 0.000) for 3982 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 4108 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4125 seeds are put forward Round 1: 184 peptides, 41 chains. Longest chain 14 peptides. Score 0.227 Round 2: 219 peptides, 37 chains. Longest chain 17 peptides. Score 0.368 Round 3: 227 peptides, 39 chains. Longest chain 15 peptides. Score 0.366 Round 4: 225 peptides, 41 chains. Longest chain 16 peptides. Score 0.339 Round 5: 242 peptides, 38 chains. Longest chain 15 peptides. Score 0.413 Taking the results from Round 5 Chains 38, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9527 restraints for refining 4139 atoms. 8749 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2823 (Rfree = 0.000) for 4139 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. Cycle 42: After refmac, R = 0.2759 (Rfree = 0.000) for 4080 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 43: After refmac, R = 0.2837 (Rfree = 0.000) for 4043 atoms. Found 22 (22 requested) and removed 33 (11 requested) atoms. Cycle 44: After refmac, R = 0.2736 (Rfree = 0.000) for 4007 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 45: After refmac, R = 0.2678 (Rfree = 0.000) for 3993 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 4095 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4115 seeds are put forward Round 1: 149 peptides, 34 chains. Longest chain 7 peptides. Score 0.209 Round 2: 205 peptides, 39 chains. Longest chain 13 peptides. Score 0.309 Round 3: 224 peptides, 40 chains. Longest chain 15 peptides. Score 0.347 Round 4: 224 peptides, 39 chains. Longest chain 10 peptides. Score 0.358 Round 5: 225 peptides, 39 chains. Longest chain 9 peptides. Score 0.361 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vqs-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7192 reflections ( 99.49 % complete ) and 9247 restraints for refining 4049 atoms. 8542 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2814 (Rfree = 0.000) for 4049 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2718 (Rfree = 0.000) for 4005 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2590 (Rfree = 0.000) for 3977 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2636 (Rfree = 0.000) for 3953 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Writing output files ... TimeTaking 54.17