null Sun 23 Dec 22:23:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vmg-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:12 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/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.8-parrot-hancs/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 95 and 0 Target number of residues in the AU: 95 Target solvent content: 0.6628 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 95 Adjusted target solvent content: 0.66 Input MTZ file: 1vmg-3.8-parrot-hancs.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: 98 Cell parameters: 79.748 79.748 95.906 90.000 90.000 90.000 Input sequence file: 1vmg-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 760 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 Loops will be built when appropriate and at the last cycle Resolution range: 61.319 3.804 Wilson plot Bfac: 86.02 1670 reflections ( 99.52 % complete ) and 0 restraints for refining 843 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3444 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3881 (Rfree = 0.000) for 843 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.97 3.18 Search for helices and strands: 0 residues in 0 chains, 865 seeds are put forward Round 1: 22 peptides, 4 chains. Longest chain 8 peptides. Score 0.268 Round 2: 34 peptides, 4 chains. Longest chain 11 peptides. Score 0.420 Round 3: 32 peptides, 3 chains. Longest chain 18 peptides. Score 0.454 Round 4: 31 peptides, 4 chains. Longest chain 11 peptides. Score 0.386 Round 5: 30 peptides, 3 chains. Longest chain 19 peptides. Score 0.432 Taking the results from Round 3 Chains 3, Residues 29, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1670 reflections ( 99.52 % complete ) and 1680 restraints for refining 686 atoms. 1567 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3809 (Rfree = 0.000) for 686 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 2: After refmac, R = 0.3546 (Rfree = 0.000) for 665 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 3: After refmac, R = 0.3481 (Rfree = 0.000) for 656 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 4: After refmac, R = 0.3395 (Rfree = 0.000) for 638 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 5: After refmac, R = 0.3353 (Rfree = 0.000) for 623 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 2.99 Search for helices and strands: 0 residues in 0 chains, 663 seeds are put forward Round 1: 34 peptides, 4 chains. Longest chain 14 peptides. Score 0.420 Round 2: 34 peptides, 3 chains. Longest chain 24 peptides. Score 0.475 Round 3: 35 peptides, 3 chains. Longest chain 25 peptides. Score 0.485 Round 4: 40 peptides, 5 chains. Longest chain 16 peptides. Score 0.433 Round 5: 37 peptides, 5 chains. Longest chain 14 peptides. Score 0.400 Taking the results from Round 3 Chains 3, Residues 32, Estimated correctness of the model 0.0 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 1670 reflections ( 99.52 % complete ) and 1124 restraints for refining 669 atoms. 881 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3573 (Rfree = 0.000) for 669 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 7: After refmac, R = 0.3321 (Rfree = 0.000) for 656 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 8: After refmac, R = 0.3218 (Rfree = 0.000) for 636 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 9: After refmac, R = 0.3146 (Rfree = 0.000) for 623 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 10: After refmac, R = 0.3007 (Rfree = 0.000) for 616 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 2.85 Search for helices and strands: 0 residues in 0 chains, 661 seeds are put forward Round 1: 38 peptides, 7 chains. Longest chain 8 peptides. Score 0.304 Round 2: 43 peptides, 6 chains. Longest chain 13 peptides. Score 0.415 Round 3: 51 peptides, 6 chains. Longest chain 14 peptides. Score 0.497 Round 4: 47 peptides, 7 chains. Longest chain 9 peptides. Score 0.408 Round 5: 46 peptides, 5 chains. Longest chain 14 peptides. Score 0.495 Taking the results from Round 3 Chains 6, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1670 reflections ( 99.52 % complete ) and 1506 restraints for refining 671 atoms. 1332 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3489 (Rfree = 0.000) for 671 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 12: After refmac, R = 0.3367 (Rfree = 0.000) for 651 atoms. Found 3 (3 requested) and removed 75 (1 requested) atoms. Cycle 13: After refmac, R = 0.3789 (Rfree = 0.000) for 560 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 14: After refmac, R = 0.3581 (Rfree = 0.000) for 544 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 15: After refmac, R = 0.3769 (Rfree = 0.000) for 532 atoms. Found 2 (2 requested) and removed 31 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 2.96 Search for helices and strands: 0 residues in 0 chains, 532 seeds are put forward Round 1: 27 peptides, 6 chains. Longest chain 6 peptides. Score 0.213 Round 2: 30 peptides, 4 chains. Longest chain 10 peptides. Score 0.374 Round 3: 30 peptides, 5 chains. Longest chain 9 peptides. Score 0.315 Round 4: 39 peptides, 6 chains. Longest chain 11 peptides. Score 0.370 Round 5: 37 peptides, 5 chains. Longest chain 11 peptides. Score 0.400 Taking the results from Round 5 Chains 5, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1670 reflections ( 99.52 % complete ) and 1093 restraints for refining 500 atoms. 970 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 16: After refmac, R = 0.4288 (Rfree = 0.000) for 500 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 17: After refmac, R = 0.4091 (Rfree = 0.000) for 489 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 18: After refmac, R = 0.4085 (Rfree = 0.000) for 474 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 19: After refmac, R = 0.3845 (Rfree = 0.000) for 470 atoms. Found 2 (2 requested) and removed 34 (1 requested) atoms. Cycle 20: After refmac, R = 0.3874 (Rfree = 0.000) for 431 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 2.97 Search for helices and strands: 0 residues in 0 chains, 455 seeds are put forward Round 1: 42 peptides, 6 chains. Longest chain 11 peptides. Score 0.404 Round 2: 40 peptides, 4 chains. Longest chain 22 peptides. Score 0.484 Round 3: 40 peptides, 5 chains. Longest chain 19 peptides. Score 0.433 Round 4: 37 peptides, 4 chains. Longest chain 11 peptides. Score 0.453 Round 5: 38 peptides, 4 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 2 Chains 4, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1670 reflections ( 99.52 % complete ) and 1060 restraints for refining 512 atoms. 920 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3778 (Rfree = 0.000) for 512 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 22: After refmac, R = 0.3861 (Rfree = 0.000) for 504 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 23: After refmac, R = 0.3602 (Rfree = 0.000) for 495 atoms. Found 2 (2 requested) and removed 15 (1 requested) atoms. Cycle 24: After refmac, R = 0.3623 (Rfree = 0.000) for 472 atoms. Found 2 (2 requested) and removed 7 (1 requested) atoms. Cycle 25: After refmac, R = 0.3416 (Rfree = 0.000) for 455 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 2.93 Search for helices and strands: 0 residues in 0 chains, 475 seeds are put forward Round 1: 31 peptides, 6 chains. Longest chain 6 peptides. Score 0.270 Round 2: 40 peptides, 5 chains. Longest chain 14 peptides. Score 0.433 Round 3: 41 peptides, 6 chains. Longest chain 9 peptides. Score 0.392 Round 4: 35 peptides, 4 chains. Longest chain 15 peptides. Score 0.431 Round 5: 39 peptides, 4 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 5 Chains 4, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1670 reflections ( 99.52 % complete ) and 966 restraints for refining 485 atoms. 830 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.4071 (Rfree = 0.000) for 485 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 27: After refmac, R = 0.3780 (Rfree = 0.000) for 478 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 28: After refmac, R = 0.3768 (Rfree = 0.000) for 473 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 29: After refmac, R = 0.3734 (Rfree = 0.000) for 467 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 30: After refmac, R = 0.3685 (Rfree = 0.000) for 464 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.04 Search for helices and strands: 0 residues in 0 chains, 494 seeds are put forward Round 1: 33 peptides, 4 chains. Longest chain 11 peptides. Score 0.409 Round 2: 38 peptides, 4 chains. Longest chain 15 peptides. Score 0.463 Round 3: 39 peptides, 4 chains. Longest chain 17 peptides. Score 0.474 Round 4: 33 peptides, 4 chains. Longest chain 16 peptides. Score 0.409 Round 5: 37 peptides, 5 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 3 Chains 4, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1670 reflections ( 99.52 % complete ) and 1112 restraints for refining 523 atoms. 976 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3714 (Rfree = 0.000) for 523 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 32: After refmac, R = 0.3534 (Rfree = 0.000) for 510 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 33: After refmac, R = 0.3779 (Rfree = 0.000) for 500 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 34: After refmac, R = 0.3503 (Rfree = 0.000) for 496 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. Cycle 35: After refmac, R = 0.3280 (Rfree = 0.000) for 483 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 2.99 Search for helices and strands: 0 residues in 0 chains, 513 seeds are put forward Round 1: 32 peptides, 4 chains. Longest chain 12 peptides. Score 0.398 Round 2: 33 peptides, 4 chains. Longest chain 15 peptides. Score 0.409 Round 3: 37 peptides, 5 chains. Longest chain 10 peptides. Score 0.400 Round 4: 35 peptides, 3 chains. Longest chain 22 peptides. Score 0.485 Round 5: 40 peptides, 4 chains. Longest chain 20 peptides. Score 0.484 Taking the results from Round 4 Chains 3, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1670 reflections ( 99.52 % complete ) and 1209 restraints for refining 555 atoms. 1084 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.4010 (Rfree = 0.000) for 555 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 37: After refmac, R = 0.3731 (Rfree = 0.000) for 541 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 38: After refmac, R = 0.3758 (Rfree = 0.000) for 533 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. Cycle 39: After refmac, R = 0.3778 (Rfree = 0.000) for 522 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 40: After refmac, R = 0.3817 (Rfree = 0.000) for 515 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 2.97 Search for helices and strands: 0 residues in 0 chains, 545 seeds are put forward Round 1: 29 peptides, 4 chains. Longest chain 16 peptides. Score 0.362 Round 2: 38 peptides, 5 chains. Longest chain 12 peptides. Score 0.411 Round 3: 38 peptides, 5 chains. Longest chain 11 peptides. Score 0.411 Round 4: 43 peptides, 6 chains. Longest chain 11 peptides. Score 0.415 Round 5: 40 peptides, 4 chains. Longest chain 21 peptides. Score 0.484 Taking the results from Round 5 Chains 4, Residues 36, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 1670 reflections ( 99.52 % complete ) and 1008 restraints for refining 611 atoms. 772 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3786 (Rfree = 0.000) for 611 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 42: After refmac, R = 0.3525 (Rfree = 0.000) for 586 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 43: After refmac, R = 0.3728 (Rfree = 0.000) for 564 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 44: After refmac, R = 0.3475 (Rfree = 0.000) for 555 atoms. Found 3 (3 requested) and removed 15 (1 requested) atoms. Cycle 45: After refmac, R = 0.3632 (Rfree = 0.000) for 531 atoms. Found 2 (2 requested) and removed 9 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 2.98 Search for helices and strands: 0 residues in 0 chains, 558 seeds are put forward Round 1: 26 peptides, 4 chains. Longest chain 10 peptides. Score 0.324 Round 2: 35 peptides, 5 chains. Longest chain 16 peptides. Score 0.377 Round 3: 34 peptides, 6 chains. Longest chain 7 peptides. Score 0.309 Round 4: 36 peptides, 6 chains. Longest chain 9 peptides. Score 0.334 Round 5: 36 peptides, 6 chains. Longest chain 11 peptides. Score 0.334 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 30, 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 1vmg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1670 reflections ( 99.52 % complete ) and 1097 restraints for refining 518 atoms. 982 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3839 (Rfree = 0.000) for 518 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.3826 (Rfree = 0.000) for 507 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.3835 (Rfree = 0.000) for 496 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.3728 (Rfree = 0.000) for 487 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:43:58 GMT 2018 Job finished. TimeTaking 20.93 Used memory is bytes: 13986528