Sun 23 Dec 23:47:52 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 1vr5-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-4.0-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/1vr5-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-4.0-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 ============================================================ Sun 23 Dec 23:47:57 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/1vr5-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-4.0-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 971 and 0 Target number of residues in the AU: 971 Target solvent content: 0.6646 Checking the provided sequence file Detected sequence length: 547 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1094 Adjusted target solvent content: 0.62 Input MTZ file: 1vr5-4.0-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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8752 target number of atoms Had to go as low as 0.95 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: 115.780 4.000 Wilson plot Bfac: 88.19 13747 reflections ( 99.52 % complete ) and 0 restraints for refining 9712 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3282 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3080 (Rfree = 0.000) for 9712 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.19 Search for helices and strands: 0 residues in 0 chains, 9883 seeds are put forward NCS extension: 0 residues added, 9883 seeds are put forward Round 1: 552 peptides, 96 chains. Longest chain 13 peptides. Score 0.368 Round 2: 655 peptides, 92 chains. Longest chain 23 peptides. Score 0.490 Round 3: 675 peptides, 84 chains. Longest chain 24 peptides. Score 0.540 Round 4: 697 peptides, 81 chains. Longest chain 26 peptides. Score 0.570 Round 5: 711 peptides, 77 chains. Longest chain 31 peptides. Score 0.596 Taking the results from Round 5 Chains 85, Residues 634, Estimated correctness of the model 0.0 % 10 chains (120 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 16187 restraints for refining 7900 atoms. 13253 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2476 (Rfree = 0.000) for 7900 atoms. Found 37 (37 requested) and removed 58 (18 requested) atoms. Cycle 2: After refmac, R = 0.2347 (Rfree = 0.000) for 7780 atoms. Found 31 (37 requested) and removed 52 (18 requested) atoms. Cycle 3: After refmac, R = 0.2262 (Rfree = 0.000) for 7706 atoms. Found 16 (36 requested) and removed 56 (18 requested) atoms. Cycle 4: After refmac, R = 0.1996 (Rfree = 0.000) for 7626 atoms. Found 11 (36 requested) and removed 29 (18 requested) atoms. Cycle 5: After refmac, R = 0.1971 (Rfree = 0.000) for 7591 atoms. Found 10 (36 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.23 Search for helices and strands: 0 residues in 0 chains, 7839 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 7855 seeds are put forward Round 1: 639 peptides, 94 chains. Longest chain 24 peptides. Score 0.466 Round 2: 692 peptides, 80 chains. Longest chain 21 peptides. Score 0.570 Round 3: 721 peptides, 85 chains. Longest chain 21 peptides. Score 0.575 Round 4: 695 peptides, 78 chains. Longest chain 25 peptides. Score 0.580 Round 5: 691 peptides, 72 chains. Longest chain 31 peptides. Score 0.599 Taking the results from Round 5 Chains 79, Residues 619, Estimated correctness of the model 0.0 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 16951 restraints for refining 7902 atoms. 14309 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2779 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 46 (18 requested) atoms. Cycle 7: After refmac, R = 0.2305 (Rfree = 0.000) for 7766 atoms. Found 29 (37 requested) and removed 34 (18 requested) atoms. Cycle 8: After refmac, R = 0.2246 (Rfree = 0.000) for 7679 atoms. Found 21 (36 requested) and removed 34 (18 requested) atoms. Cycle 9: After refmac, R = 0.2190 (Rfree = 0.000) for 7627 atoms. Found 29 (36 requested) and removed 34 (18 requested) atoms. Cycle 10: After refmac, R = 0.2156 (Rfree = 0.000) for 7602 atoms. Found 18 (36 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.19 Search for helices and strands: 0 residues in 0 chains, 7839 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 7859 seeds are put forward Round 1: 588 peptides, 99 chains. Longest chain 19 peptides. Score 0.393 Round 2: 673 peptides, 90 chains. Longest chain 27 peptides. Score 0.514 Round 3: 692 peptides, 82 chains. Longest chain 23 peptides. Score 0.562 Round 4: 675 peptides, 77 chains. Longest chain 18 peptides. Score 0.567 Round 5: 672 peptides, 83 chains. Longest chain 29 peptides. Score 0.541 Taking the results from Round 4 Chains 81, Residues 598, Estimated correctness of the model 0.0 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17322 restraints for refining 7901 atoms. 14840 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2418 (Rfree = 0.000) for 7901 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. Cycle 12: After refmac, R = 0.2106 (Rfree = 0.000) for 7846 atoms. Found 23 (37 requested) and removed 37 (18 requested) atoms. Cycle 13: After refmac, R = 0.2012 (Rfree = 0.000) for 7808 atoms. Found 15 (37 requested) and removed 60 (18 requested) atoms. Cycle 14: After refmac, R = 0.2029 (Rfree = 0.000) for 7750 atoms. Found 10 (36 requested) and removed 24 (18 requested) atoms. Cycle 15: After refmac, R = 0.1961 (Rfree = 0.000) for 7719 atoms. Found 13 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.20 Search for helices and strands: 0 residues in 0 chains, 7958 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 7983 seeds are put forward Round 1: 563 peptides, 91 chains. Longest chain 15 peptides. Score 0.403 Round 2: 619 peptides, 87 chains. Longest chain 17 peptides. Score 0.477 Round 3: 631 peptides, 84 chains. Longest chain 19 peptides. Score 0.501 Round 4: 644 peptides, 80 chains. Longest chain 20 peptides. Score 0.529 Round 5: 634 peptides, 81 chains. Longest chain 21 peptides. Score 0.516 Taking the results from Round 4 Chains 84, Residues 564, Estimated correctness of the model 0.0 % 6 chains (58 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17264 restraints for refining 7900 atoms. 14839 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2171 (Rfree = 0.000) for 7900 atoms. Found 23 (37 requested) and removed 72 (18 requested) atoms. Cycle 17: After refmac, R = 0.1970 (Rfree = 0.000) for 7772 atoms. Found 21 (37 requested) and removed 26 (18 requested) atoms. Cycle 18: After refmac, R = 0.1917 (Rfree = 0.000) for 7736 atoms. Found 19 (36 requested) and removed 25 (18 requested) atoms. Cycle 19: After refmac, R = 0.1879 (Rfree = 0.000) for 7715 atoms. Found 12 (36 requested) and removed 26 (18 requested) atoms. Cycle 20: After refmac, R = 0.1824 (Rfree = 0.000) for 7691 atoms. Found 20 (36 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 3.19 Search for helices and strands: 0 residues in 0 chains, 7951 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 7976 seeds are put forward Round 1: 555 peptides, 93 chains. Longest chain 17 peptides. Score 0.386 Round 2: 580 peptides, 81 chains. Longest chain 19 peptides. Score 0.465 Round 3: 605 peptides, 76 chains. Longest chain 21 peptides. Score 0.510 Round 4: 638 peptides, 83 chains. Longest chain 20 peptides. Score 0.511 Round 5: 638 peptides, 84 chains. Longest chain 25 peptides. Score 0.507 Taking the results from Round 4 Chains 86, Residues 555, Estimated correctness of the model 0.0 % 7 chains (58 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17268 restraints for refining 7902 atoms. 14897 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2230 (Rfree = 0.000) for 7902 atoms. Found 33 (37 requested) and removed 33 (18 requested) atoms. Cycle 22: After refmac, R = 0.2049 (Rfree = 0.000) for 7836 atoms. Found 31 (37 requested) and removed 37 (18 requested) atoms. Cycle 23: After refmac, R = 0.1987 (Rfree = 0.000) for 7801 atoms. Found 17 (37 requested) and removed 29 (18 requested) atoms. Cycle 24: After refmac, R = 0.1954 (Rfree = 0.000) for 7774 atoms. Found 21 (37 requested) and removed 26 (18 requested) atoms. Cycle 25: After refmac, R = 0.1880 (Rfree = 0.000) for 7755 atoms. Found 15 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.21 Search for helices and strands: 0 residues in 0 chains, 7928 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 7956 seeds are put forward Round 1: 582 peptides, 100 chains. Longest chain 13 peptides. Score 0.382 Round 2: 604 peptides, 84 chains. Longest chain 19 peptides. Score 0.475 Round 3: 612 peptides, 88 chains. Longest chain 20 peptides. Score 0.466 Round 4: 605 peptides, 82 chains. Longest chain 18 peptides. Score 0.485 Round 5: 636 peptides, 84 chains. Longest chain 18 peptides. Score 0.505 Taking the results from Round 5 Chains 89, Residues 552, Estimated correctness of the model 0.0 % 7 chains (58 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17180 restraints for refining 7902 atoms. 14823 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2741 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 39 (18 requested) atoms. Cycle 27: After refmac, R = 0.2693 (Rfree = 0.000) for 7767 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. Cycle 28: After refmac, R = 0.2704 (Rfree = 0.000) for 7675 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. Cycle 29: After refmac, R = 0.2445 (Rfree = 0.000) for 7583 atoms. Found 36 (36 requested) and removed 37 (18 requested) atoms. Cycle 30: After refmac, R = 0.2096 (Rfree = 0.000) for 7542 atoms. Found 35 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.18 Search for helices and strands: 0 residues in 0 chains, 7760 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7774 seeds are put forward Round 1: 507 peptides, 94 chains. Longest chain 13 peptides. Score 0.328 Round 2: 570 peptides, 90 chains. Longest chain 15 peptides. Score 0.415 Round 3: 577 peptides, 88 chains. Longest chain 28 peptides. Score 0.431 Round 4: 603 peptides, 84 chains. Longest chain 20 peptides. Score 0.474 Round 5: 596 peptides, 80 chains. Longest chain 21 peptides. Score 0.485 Taking the results from Round 5 Chains 84, Residues 516, Estimated correctness of the model 0.0 % 5 chains (54 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17477 restraints for refining 7902 atoms. 15264 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2793 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 62 (18 requested) atoms. Cycle 32: After refmac, R = 0.2263 (Rfree = 0.000) for 7793 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. Cycle 33: After refmac, R = 0.2109 (Rfree = 0.000) for 7757 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 34: After refmac, R = 0.2103 (Rfree = 0.000) for 7749 atoms. Found 35 (36 requested) and removed 40 (18 requested) atoms. Cycle 35: After refmac, R = 0.1854 (Rfree = 0.000) for 7729 atoms. Found 20 (36 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.18 Search for helices and strands: 0 residues in 0 chains, 7952 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7969 seeds are put forward Round 1: 536 peptides, 100 chains. Longest chain 12 peptides. Score 0.332 Round 2: 599 peptides, 87 chains. Longest chain 17 peptides. Score 0.458 Round 3: 603 peptides, 89 chains. Longest chain 21 peptides. Score 0.453 Round 4: 584 peptides, 87 chains. Longest chain 23 peptides. Score 0.443 Round 5: 595 peptides, 89 chains. Longest chain 16 peptides. Score 0.445 Taking the results from Round 2 Chains 89, Residues 512, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17559 restraints for refining 7901 atoms. 15465 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2253 (Rfree = 0.000) for 7901 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. Cycle 37: After refmac, R = 0.2029 (Rfree = 0.000) for 7841 atoms. Found 34 (37 requested) and removed 31 (18 requested) atoms. Cycle 38: After refmac, R = 0.1959 (Rfree = 0.000) for 7810 atoms. Found 37 (37 requested) and removed 26 (18 requested) atoms. Cycle 39: After refmac, R = 0.1936 (Rfree = 0.000) for 7791 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. Cycle 40: After refmac, R = 0.1913 (Rfree = 0.000) for 7787 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.19 Search for helices and strands: 0 residues in 0 chains, 8029 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 8050 seeds are put forward Round 1: 457 peptides, 91 chains. Longest chain 10 peptides. Score 0.285 Round 2: 526 peptides, 85 chains. Longest chain 22 peptides. Score 0.392 Round 3: 525 peptides, 87 chains. Longest chain 14 peptides. Score 0.382 Round 4: 534 peptides, 80 chains. Longest chain 19 peptides. Score 0.424 Round 5: 540 peptides, 79 chains. Longest chain 13 peptides. Score 0.435 Taking the results from Round 5 Chains 79, Residues 461, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13747 reflections ( 99.52 % complete ) and 18368 restraints for refining 7902 atoms. 16603 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2130 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 42: After refmac, R = 0.2046 (Rfree = 0.000) for 7873 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. Cycle 43: After refmac, R = 0.2044 (Rfree = 0.000) for 7853 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. Cycle 44: After refmac, R = 0.1957 (Rfree = 0.000) for 7845 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. Cycle 45: After refmac, R = 0.1949 (Rfree = 0.000) for 7838 atoms. Found 37 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.21 Search for helices and strands: 0 residues in 0 chains, 8090 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8105 seeds are put forward Round 1: 456 peptides, 89 chains. Longest chain 17 peptides. Score 0.294 Round 2: 528 peptides, 87 chains. Longest chain 18 peptides. Score 0.385 Round 3: 552 peptides, 82 chains. Longest chain 18 peptides. Score 0.433 Round 4: 543 peptides, 81 chains. Longest chain 18 peptides. Score 0.428 Round 5: 527 peptides, 78 chains. Longest chain 19 peptides. Score 0.426 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 83, Residues 470, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vr5-4_warpNtrace.pdb as input Building loops using Loopy2018 83 chains (470 residues) following loop building 3 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13747 reflections ( 99.52 % complete ) and 17913 restraints for refining 7903 atoms. 16021 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2110 (Rfree = 0.000) for 7903 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2009 (Rfree = 0.000) for 7828 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.1935 (Rfree = 0.000) for 7778 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1661 (Rfree = 0.000) for 7735 atoms. TimeTaking 97.53