Mon 24 Dec 00:29:00 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 1vp7-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.2-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/1vp7-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.2-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 00:29:05 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/1vp7-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.2-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 595 and 0 Target number of residues in the AU: 595 Target solvent content: 0.5294 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 600 Adjusted target solvent content: 0.53 Input MTZ file: 1vp7-3.2-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.60 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: 207.138 3.200 Wilson plot Bfac: 30.03 12229 reflections ( 99.72 % complete ) and 0 restraints for refining 5291 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3036 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2608 (Rfree = 0.000) for 5291 atoms. Found 47 (47 requested) and removed 41 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.65 2.55 Search for helices and strands: 0 residues in 0 chains, 5402 seeds are put forward NCS extension: 0 residues added, 5402 seeds are put forward Round 1: 276 peptides, 34 chains. Longest chain 23 peptides. Score 0.527 Round 2: 328 peptides, 32 chains. Longest chain 27 peptides. Score 0.640 Round 3: 342 peptides, 32 chains. Longest chain 33 peptides. Score 0.662 Round 4: 359 peptides, 31 chains. Longest chain 33 peptides. Score 0.695 Round 5: 360 peptides, 29 chains. Longest chain 36 peptides. Score 0.710 Taking the results from Round 5 Chains 29, Residues 331, Estimated correctness of the model 67.3 % 7 chains (178 residues) have been docked in sequence Building loops using Loopy2018 29 chains (331 residues) following loop building 7 chains (178 residues) in sequence following loop building ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 6927 restraints for refining 4229 atoms. 4934 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2903 (Rfree = 0.000) for 4229 atoms. Found 38 (38 requested) and removed 65 (19 requested) atoms. Cycle 2: After refmac, R = 0.2735 (Rfree = 0.000) for 4122 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. Cycle 3: After refmac, R = 0.2577 (Rfree = 0.000) for 4095 atoms. Found 30 (36 requested) and removed 31 (18 requested) atoms. Cycle 4: After refmac, R = 0.2488 (Rfree = 0.000) for 4073 atoms. Found 26 (34 requested) and removed 21 (18 requested) atoms. Cycle 5: After refmac, R = 0.2403 (Rfree = 0.000) for 4056 atoms. Found 21 (33 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.67 2.57 Search for helices and strands: 0 residues in 0 chains, 4165 seeds are put forward NCS extension: 15 residues added (10 deleted due to clashes), 4180 seeds are put forward Round 1: 336 peptides, 32 chains. Longest chain 43 peptides. Score 0.653 Round 2: 357 peptides, 28 chains. Longest chain 37 peptides. Score 0.713 Round 3: 362 peptides, 30 chains. Longest chain 30 peptides. Score 0.706 Round 4: 368 peptides, 27 chains. Longest chain 51 peptides. Score 0.734 Round 5: 335 peptides, 33 chains. Longest chain 25 peptides. Score 0.644 Taking the results from Round 4 Chains 28, Residues 341, Estimated correctness of the model 72.1 % 5 chains (160 residues) have been docked in sequence Building loops using Loopy2018 28 chains (341 residues) following loop building 5 chains (160 residues) in sequence following loop building ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7020 restraints for refining 4150 atoms. 5078 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2965 (Rfree = 0.000) for 4150 atoms. Found 33 (33 requested) and removed 65 (18 requested) atoms. Cycle 7: After refmac, R = 0.2725 (Rfree = 0.000) for 4081 atoms. Found 32 (32 requested) and removed 37 (18 requested) atoms. Cycle 8: After refmac, R = 0.2564 (Rfree = 0.000) for 4061 atoms. Found 17 (31 requested) and removed 25 (18 requested) atoms. Cycle 9: After refmac, R = 0.2481 (Rfree = 0.000) for 4039 atoms. Found 13 (30 requested) and removed 19 (18 requested) atoms. Cycle 10: After refmac, R = 0.2446 (Rfree = 0.000) for 4019 atoms. Found 11 (30 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.64 2.54 Search for helices and strands: 0 residues in 0 chains, 4139 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 4175 seeds are put forward Round 1: 334 peptides, 33 chains. Longest chain 24 peptides. Score 0.642 Round 2: 347 peptides, 25 chains. Longest chain 38 peptides. Score 0.719 Round 3: 344 peptides, 29 chains. Longest chain 33 peptides. Score 0.687 Round 4: 336 peptides, 29 chains. Longest chain 42 peptides. Score 0.675 Round 5: 337 peptides, 33 chains. Longest chain 25 peptides. Score 0.647 Taking the results from Round 2 Chains 27, Residues 322, Estimated correctness of the model 69.1 % 7 chains (161 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 C and 54 C Built loop between residues 59 E and 68 E 24 chains (333 residues) following loop building 5 chains (175 residues) in sequence following loop building ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 6632 restraints for refining 4089 atoms. 4654 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2792 (Rfree = 0.000) for 4089 atoms. Found 29 (29 requested) and removed 54 (18 requested) atoms. Cycle 12: After refmac, R = 0.2624 (Rfree = 0.000) for 4046 atoms. Found 26 (28 requested) and removed 27 (18 requested) atoms. Cycle 13: After refmac, R = 0.2516 (Rfree = 0.000) for 4030 atoms. Found 21 (27 requested) and removed 31 (18 requested) atoms. Cycle 14: After refmac, R = 0.2411 (Rfree = 0.000) for 4008 atoms. Found 15 (27 requested) and removed 31 (18 requested) atoms. Cycle 15: After refmac, R = 0.2394 (Rfree = 0.000) for 3981 atoms. Found 18 (25 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.62 2.52 Search for helices and strands: 0 residues in 0 chains, 4097 seeds are put forward NCS extension: 24 residues added (23 deleted due to clashes), 4121 seeds are put forward Round 1: 340 peptides, 26 chains. Longest chain 57 peptides. Score 0.703 Round 2: 344 peptides, 27 chains. Longest chain 40 peptides. Score 0.701 Round 3: 346 peptides, 26 chains. Longest chain 38 peptides. Score 0.711 Round 4: 331 peptides, 32 chains. Longest chain 29 peptides. Score 0.645 Round 5: 347 peptides, 28 chains. Longest chain 39 peptides. Score 0.699 Taking the results from Round 3 Chains 28, Residues 320, Estimated correctness of the model 67.5 % 7 chains (141 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 B and 65 B 27 chains (325 residues) following loop building 6 chains (146 residues) in sequence following loop building ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 6858 restraints for refining 4040 atoms. 5035 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2835 (Rfree = 0.000) for 4040 atoms. Found 25 (25 requested) and removed 48 (18 requested) atoms. Cycle 17: After refmac, R = 0.2662 (Rfree = 0.000) for 4005 atoms. Found 24 (24 requested) and removed 35 (18 requested) atoms. Cycle 18: After refmac, R = 0.2592 (Rfree = 0.000) for 3983 atoms. Found 18 (23 requested) and removed 21 (17 requested) atoms. Cycle 19: After refmac, R = 0.2565 (Rfree = 0.000) for 3974 atoms. Found 11 (22 requested) and removed 21 (17 requested) atoms. Cycle 20: After refmac, R = 0.2534 (Rfree = 0.000) for 3961 atoms. Found 8 (22 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.67 2.57 Search for helices and strands: 0 residues in 0 chains, 4060 seeds are put forward NCS extension: 46 residues added (15 deleted due to clashes), 4106 seeds are put forward Round 1: 337 peptides, 31 chains. Longest chain 39 peptides. Score 0.662 Round 2: 342 peptides, 30 chains. Longest chain 45 peptides. Score 0.677 Round 3: 321 peptides, 34 chains. Longest chain 32 peptides. Score 0.612 Round 4: 342 peptides, 35 chains. Longest chain 30 peptides. Score 0.639 Round 5: 340 peptides, 31 chains. Longest chain 23 peptides. Score 0.667 Taking the results from Round 2 Chains 31, Residues 312, Estimated correctness of the model 60.1 % 5 chains (149 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7129 restraints for refining 4069 atoms. 5341 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2813 (Rfree = 0.000) for 4069 atoms. Found 22 (22 requested) and removed 55 (18 requested) atoms. Cycle 22: After refmac, R = 0.2663 (Rfree = 0.000) for 4025 atoms. Found 18 (22 requested) and removed 26 (18 requested) atoms. Cycle 23: After refmac, R = 0.2605 (Rfree = 0.000) for 4010 atoms. Found 16 (22 requested) and removed 21 (18 requested) atoms. Cycle 24: After refmac, R = 0.2586 (Rfree = 0.000) for 3996 atoms. Found 12 (21 requested) and removed 18 (17 requested) atoms. Cycle 25: After refmac, R = 0.2573 (Rfree = 0.000) for 3988 atoms. Found 6 (21 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.65 2.55 Search for helices and strands: 0 residues in 0 chains, 4086 seeds are put forward NCS extension: 57 residues added (10 deleted due to clashes), 4143 seeds are put forward Round 1: 306 peptides, 34 chains. Longest chain 29 peptides. Score 0.585 Round 2: 325 peptides, 31 chains. Longest chain 34 peptides. Score 0.643 Round 3: 334 peptides, 28 chains. Longest chain 35 peptides. Score 0.680 Round 4: 329 peptides, 30 chains. Longest chain 29 peptides. Score 0.657 Round 5: 337 peptides, 36 chains. Longest chain 28 peptides. Score 0.623 Taking the results from Round 3 Chains 31, Residues 306, Estimated correctness of the model 60.8 % 7 chains (153 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 6958 restraints for refining 4049 atoms. 5183 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2779 (Rfree = 0.000) for 4049 atoms. Found 22 (22 requested) and removed 33 (18 requested) atoms. Cycle 27: After refmac, R = 0.2651 (Rfree = 0.000) for 4025 atoms. Found 22 (22 requested) and removed 23 (18 requested) atoms. Cycle 28: After refmac, R = 0.2588 (Rfree = 0.000) for 4016 atoms. Found 16 (22 requested) and removed 20 (18 requested) atoms. Cycle 29: After refmac, R = 0.2534 (Rfree = 0.000) for 4000 atoms. Found 16 (22 requested) and removed 18 (18 requested) atoms. Cycle 30: After refmac, R = 0.2516 (Rfree = 0.000) for 3994 atoms. Found 14 (21 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.60 2.50 Search for helices and strands: 0 residues in 0 chains, 4066 seeds are put forward NCS extension: 0 residues added, 4066 seeds are put forward Round 1: 315 peptides, 32 chains. Longest chain 40 peptides. Score 0.618 Round 2: 317 peptides, 31 chains. Longest chain 32 peptides. Score 0.629 Round 3: 336 peptides, 33 chains. Longest chain 27 peptides. Score 0.645 Round 4: 330 peptides, 35 chains. Longest chain 24 peptides. Score 0.620 Round 5: 317 peptides, 34 chains. Longest chain 31 peptides. Score 0.605 Taking the results from Round 3 Chains 35, Residues 303, Estimated correctness of the model 52.6 % 6 chains (112 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7323 restraints for refining 4052 atoms. 5703 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2805 (Rfree = 0.000) for 4052 atoms. Found 22 (22 requested) and removed 47 (18 requested) atoms. Cycle 32: After refmac, R = 0.2638 (Rfree = 0.000) for 4013 atoms. Found 22 (22 requested) and removed 21 (18 requested) atoms. Cycle 33: After refmac, R = 0.2569 (Rfree = 0.000) for 4006 atoms. Found 14 (22 requested) and removed 18 (18 requested) atoms. Cycle 34: After refmac, R = 0.2535 (Rfree = 0.000) for 3996 atoms. Found 12 (21 requested) and removed 18 (17 requested) atoms. Cycle 35: After refmac, R = 0.2505 (Rfree = 0.000) for 3987 atoms. Found 8 (21 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.58 2.48 Search for helices and strands: 0 residues in 0 chains, 4126 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 4140 seeds are put forward Round 1: 292 peptides, 31 chains. Longest chain 19 peptides. Score 0.585 Round 2: 320 peptides, 28 chains. Longest chain 33 peptides. Score 0.658 Round 3: 320 peptides, 27 chains. Longest chain 46 peptides. Score 0.666 Round 4: 307 peptides, 28 chains. Longest chain 58 peptides. Score 0.637 Round 5: 290 peptides, 32 chains. Longest chain 29 peptides. Score 0.573 Taking the results from Round 3 Chains 28, Residues 293, Estimated correctness of the model 57.6 % 6 chains (118 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7195 restraints for refining 4039 atoms. 5586 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2703 (Rfree = 0.000) for 4039 atoms. Found 22 (22 requested) and removed 40 (18 requested) atoms. Cycle 37: After refmac, R = 0.2560 (Rfree = 0.000) for 4013 atoms. Found 18 (22 requested) and removed 22 (18 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2501 (Rfree = 0.000) for 4001 atoms. Found 9 (21 requested) and removed 20 (17 requested) atoms. Cycle 39: After refmac, R = 0.2464 (Rfree = 0.000) for 3985 atoms. Found 5 (21 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.2439 (Rfree = 0.000) for 3968 atoms. Found 3 (21 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.57 2.47 Search for helices and strands: 0 residues in 0 chains, 4087 seeds are put forward NCS extension: 0 residues added, 4087 seeds are put forward Round 1: 294 peptides, 28 chains. Longest chain 29 peptides. Score 0.615 Round 2: 323 peptides, 33 chains. Longest chain 29 peptides. Score 0.624 Round 3: 325 peptides, 26 chains. Longest chain 47 peptides. Score 0.681 Round 4: 310 peptides, 31 chains. Longest chain 22 peptides. Score 0.617 Round 5: 315 peptides, 34 chains. Longest chain 24 peptides. Score 0.601 Taking the results from Round 3 Chains 28, Residues 299, Estimated correctness of the model 61.0 % 7 chains (160 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 6681 restraints for refining 4072 atoms. 4887 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2694 (Rfree = 0.000) for 4072 atoms. Found 22 (22 requested) and removed 37 (18 requested) atoms. Cycle 42: After refmac, R = 0.2542 (Rfree = 0.000) for 4042 atoms. Found 22 (22 requested) and removed 21 (18 requested) atoms. Cycle 43: After refmac, R = 0.2465 (Rfree = 0.000) for 4035 atoms. Found 11 (22 requested) and removed 20 (18 requested) atoms. Cycle 44: After refmac, R = 0.2436 (Rfree = 0.000) for 4021 atoms. Found 13 (22 requested) and removed 19 (18 requested) atoms. Cycle 45: After refmac, R = 0.2423 (Rfree = 0.000) for 4011 atoms. Found 9 (22 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.61 2.51 Search for helices and strands: 0 residues in 0 chains, 4098 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 4136 seeds are put forward Round 1: 294 peptides, 32 chains. Longest chain 51 peptides. Score 0.580 Round 2: 313 peptides, 25 chains. Longest chain 34 peptides. Score 0.670 Round 3: 310 peptides, 29 chains. Longest chain 34 peptides. Score 0.634 Round 4: 294 peptides, 26 chains. Longest chain 25 peptides. Score 0.631 Round 5: 294 peptides, 33 chains. Longest chain 26 peptides. Score 0.572 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 288, Estimated correctness of the model 58.5 % 7 chains (150 residues) have been docked in sequence Sequence coverage is 51 % Consider running further cycles of model building using 1vp7-3_warpNtrace.pdb as input Building loops using Loopy2018 25 chains (288 residues) following loop building 7 chains (150 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12229 reflections ( 99.72 % complete ) and 6895 restraints for refining 4051 atoms. 5193 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2586 (Rfree = 0.000) for 4051 atoms. Found 0 (22 requested) and removed 6 (18 requested) atoms. Cycle 47: After refmac, R = 0.2490 (Rfree = 0.000) for 4029 atoms. Found 0 (22 requested) and removed 4 (18 requested) atoms. Cycle 48: After refmac, R = 0.2497 (Rfree = 0.000) for 4016 atoms. Found 0 (22 requested) and removed 4 (18 requested) atoms. Cycle 49: After refmac, R = 0.2460 (Rfree = 0.000) for 4007 atoms. TimeTaking 80.92