Mon 24 Dec 01:08:04 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 1vr5-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.8-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/1vr5-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.8-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 01:08:09 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/1vr5-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.8-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 995 and 0 Target number of residues in the AU: 995 Target solvent content: 0.6563 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: 1vr5-3.8-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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-3.8-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 3.800 Wilson plot Bfac: 82.25 15989 reflections ( 99.57 % complete ) and 0 restraints for refining 9666 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3242 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3148 (Rfree = 0.000) for 9666 atoms. Found 53 (53 requested) and removed 36 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.12 Search for helices and strands: 0 residues in 0 chains, 9858 seeds are put forward NCS extension: 0 residues added, 9858 seeds are put forward Round 1: 575 peptides, 102 chains. Longest chain 15 peptides. Score 0.365 Round 2: 690 peptides, 90 chains. Longest chain 27 peptides. Score 0.529 Round 3: 717 peptides, 89 chains. Longest chain 26 peptides. Score 0.556 Round 4: 748 peptides, 84 chains. Longest chain 24 peptides. Score 0.600 Round 5: 756 peptides, 79 chains. Longest chain 27 peptides. Score 0.624 Taking the results from Round 5 Chains 83, Residues 677, Estimated correctness of the model 9.7 % 5 chains (54 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16612 restraints for refining 7913 atoms. 13781 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2424 (Rfree = 0.000) for 7913 atoms. Found 43 (43 requested) and removed 53 (21 requested) atoms. Cycle 2: After refmac, R = 0.2259 (Rfree = 0.000) for 7798 atoms. Found 43 (43 requested) and removed 53 (21 requested) atoms. Cycle 3: After refmac, R = 0.2153 (Rfree = 0.000) for 7728 atoms. Found 36 (42 requested) and removed 38 (21 requested) atoms. Cycle 4: After refmac, R = 0.2060 (Rfree = 0.000) for 7691 atoms. Found 26 (42 requested) and removed 52 (21 requested) atoms. Cycle 5: After refmac, R = 0.2006 (Rfree = 0.000) for 7647 atoms. Found 39 (42 requested) and removed 35 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.02 Search for helices and strands: 0 residues in 0 chains, 8008 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 8038 seeds are put forward Round 1: 648 peptides, 90 chains. Longest chain 17 peptides. Score 0.491 Round 2: 711 peptides, 87 chains. Longest chain 20 peptides. Score 0.559 Round 3: 725 peptides, 80 chains. Longest chain 25 peptides. Score 0.596 Round 4: 742 peptides, 77 chains. Longest chain 31 peptides. Score 0.620 Round 5: 754 peptides, 72 chains. Longest chain 38 peptides. Score 0.646 Taking the results from Round 5 Chains 82, Residues 682, Estimated correctness of the model 19.1 % 7 chains (123 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 15738 restraints for refining 7915 atoms. 12559 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2426 (Rfree = 0.000) for 7915 atoms. Found 43 (43 requested) and removed 61 (21 requested) atoms. Cycle 7: After refmac, R = 0.2426 (Rfree = 0.000) for 7819 atoms. Found 43 (43 requested) and removed 52 (21 requested) atoms. Cycle 8: After refmac, R = 0.2285 (Rfree = 0.000) for 7753 atoms. Found 42 (42 requested) and removed 43 (21 requested) atoms. Cycle 9: After refmac, R = 0.2177 (Rfree = 0.000) for 7706 atoms. Found 30 (42 requested) and removed 41 (21 requested) atoms. Cycle 10: After refmac, R = 0.2298 (Rfree = 0.000) for 7666 atoms. Found 42 (42 requested) and removed 44 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.08 Search for helices and strands: 0 residues in 0 chains, 7900 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 7919 seeds are put forward Round 1: 688 peptides, 104 chains. Longest chain 15 peptides. Score 0.470 Round 2: 761 peptides, 84 chains. Longest chain 22 peptides. Score 0.610 Round 3: 748 peptides, 86 chains. Longest chain 20 peptides. Score 0.593 Round 4: 755 peptides, 74 chains. Longest chain 36 peptides. Score 0.640 Round 5: 746 peptides, 84 chains. Longest chain 26 peptides. Score 0.598 Taking the results from Round 4 Chains 80, Residues 681, Estimated correctness of the model 16.6 % 7 chains (98 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 15989 reflections ( 99.57 % complete ) and 16076 restraints for refining 7914 atoms. 12997 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2352 (Rfree = 0.000) for 7914 atoms. Found 43 (43 requested) and removed 45 (21 requested) atoms. Cycle 12: After refmac, R = 0.2201 (Rfree = 0.000) for 7856 atoms. Found 43 (43 requested) and removed 44 (21 requested) atoms. Cycle 13: After refmac, R = 0.2074 (Rfree = 0.000) for 7823 atoms. Found 43 (43 requested) and removed 30 (21 requested) atoms. Cycle 14: After refmac, R = 0.1989 (Rfree = 0.000) for 7811 atoms. Found 37 (43 requested) and removed 32 (21 requested) atoms. Cycle 15: After refmac, R = 0.1870 (Rfree = 0.000) for 7808 atoms. Found 24 (42 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.08 Search for helices and strands: 0 residues in 0 chains, 8052 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 8082 seeds are put forward Round 1: 668 peptides, 95 chains. Longest chain 19 peptides. Score 0.489 Round 2: 713 peptides, 85 chains. Longest chain 34 peptides. Score 0.568 Round 3: 719 peptides, 84 chains. Longest chain 42 peptides. Score 0.577 Round 4: 744 peptides, 82 chains. Longest chain 25 peptides. Score 0.604 Round 5: 714 peptides, 84 chains. Longest chain 22 peptides. Score 0.573 Taking the results from Round 4 Chains 90, Residues 662, Estimated correctness of the model 0.7 % 9 chains (117 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 15989 reflections ( 99.57 % complete ) and 15892 restraints for refining 7916 atoms. 12834 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2289 (Rfree = 0.000) for 7916 atoms. Found 38 (43 requested) and removed 56 (21 requested) atoms. Cycle 17: After refmac, R = 0.2141 (Rfree = 0.000) for 7836 atoms. Found 25 (43 requested) and removed 37 (21 requested) atoms. Cycle 18: After refmac, R = 0.2039 (Rfree = 0.000) for 7804 atoms. Found 28 (43 requested) and removed 35 (21 requested) atoms. Cycle 19: After refmac, R = 0.1982 (Rfree = 0.000) for 7790 atoms. Found 34 (42 requested) and removed 34 (21 requested) atoms. Cycle 20: After refmac, R = 0.1875 (Rfree = 0.000) for 7779 atoms. Found 27 (42 requested) and removed 38 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.08 Search for helices and strands: 0 residues in 0 chains, 8012 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8028 seeds are put forward Round 1: 643 peptides, 93 chains. Longest chain 17 peptides. Score 0.474 Round 2: 691 peptides, 81 chains. Longest chain 33 peptides. Score 0.565 Round 3: 689 peptides, 80 chains. Longest chain 36 peptides. Score 0.567 Round 4: 690 peptides, 81 chains. Longest chain 27 peptides. Score 0.564 Round 5: 666 peptides, 84 chains. Longest chain 25 peptides. Score 0.532 Taking the results from Round 3 Chains 85, Residues 609, Estimated correctness of the model 0.0 % 5 chains (82 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16536 restraints for refining 7914 atoms. 13797 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2371 (Rfree = 0.000) for 7914 atoms. Found 43 (43 requested) and removed 61 (21 requested) atoms. Cycle 22: After refmac, R = 0.2114 (Rfree = 0.000) for 7831 atoms. Found 32 (43 requested) and removed 36 (21 requested) atoms. Cycle 23: After refmac, R = 0.2003 (Rfree = 0.000) for 7796 atoms. Found 22 (43 requested) and removed 27 (21 requested) atoms. Cycle 24: After refmac, R = 0.1921 (Rfree = 0.000) for 7776 atoms. Found 21 (42 requested) and removed 30 (21 requested) atoms. Cycle 25: After refmac, R = 0.1870 (Rfree = 0.000) for 7750 atoms. Found 18 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.06 Search for helices and strands: 0 residues in 0 chains, 7959 seeds are put forward NCS extension: 48 residues added (4 deleted due to clashes), 8007 seeds are put forward Round 1: 611 peptides, 100 chains. Longest chain 15 peptides. Score 0.412 Round 2: 649 peptides, 88 chains. Longest chain 24 peptides. Score 0.501 Round 3: 689 peptides, 85 chains. Longest chain 22 peptides. Score 0.548 Round 4: 674 peptides, 91 chains. Longest chain 24 peptides. Score 0.511 Round 5: 679 peptides, 85 chains. Longest chain 26 peptides. Score 0.539 Taking the results from Round 3 Chains 92, Residues 604, Estimated correctness of the model 0.0 % 9 chains (69 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16998 restraints for refining 7912 atoms. 14432 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2258 (Rfree = 0.000) for 7912 atoms. Found 43 (43 requested) and removed 40 (21 requested) atoms. Cycle 27: After refmac, R = 0.2177 (Rfree = 0.000) for 7857 atoms. Found 43 (43 requested) and removed 39 (21 requested) atoms. Cycle 28: After refmac, R = 0.2049 (Rfree = 0.000) for 7847 atoms. Found 43 (43 requested) and removed 40 (21 requested) atoms. Cycle 29: After refmac, R = 0.1970 (Rfree = 0.000) for 7833 atoms. Found 28 (43 requested) and removed 43 (21 requested) atoms. Cycle 30: After refmac, R = 0.1952 (Rfree = 0.000) for 7808 atoms. Found 25 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.06 Search for helices and strands: 0 residues in 0 chains, 8023 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 8048 seeds are put forward Round 1: 588 peptides, 90 chains. Longest chain 19 peptides. Score 0.433 Round 2: 636 peptides, 86 chains. Longest chain 20 peptides. Score 0.497 Round 3: 657 peptides, 81 chains. Longest chain 21 peptides. Score 0.536 Round 4: 640 peptides, 82 chains. Longest chain 20 peptides. Score 0.517 Round 5: 639 peptides, 85 chains. Longest chain 19 peptides. Score 0.504 Taking the results from Round 3 Chains 83, Residues 576, Estimated correctness of the model 0.0 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 17128 restraints for refining 7915 atoms. 14713 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2280 (Rfree = 0.000) for 7915 atoms. Found 29 (43 requested) and removed 38 (21 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2125 (Rfree = 0.000) for 7857 atoms. Found 28 (43 requested) and removed 32 (21 requested) atoms. Cycle 33: After refmac, R = 0.2082 (Rfree = 0.000) for 7828 atoms. Found 30 (43 requested) and removed 35 (21 requested) atoms. Cycle 34: After refmac, R = 0.2028 (Rfree = 0.000) for 7806 atoms. Found 36 (43 requested) and removed 32 (21 requested) atoms. Cycle 35: After refmac, R = 0.2005 (Rfree = 0.000) for 7787 atoms. Found 37 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.07 Search for helices and strands: 0 residues in 0 chains, 8035 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 8059 seeds are put forward Round 1: 519 peptides, 90 chains. Longest chain 19 peptides. Score 0.361 Round 2: 613 peptides, 87 chains. Longest chain 17 peptides. Score 0.471 Round 3: 644 peptides, 87 chains. Longest chain 33 peptides. Score 0.500 Round 4: 626 peptides, 77 chains. Longest chain 22 peptides. Score 0.525 Round 5: 639 peptides, 85 chains. Longest chain 24 peptides. Score 0.504 Taking the results from Round 4 Chains 80, Residues 549, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 17727 restraints for refining 7914 atoms. 15481 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2258 (Rfree = 0.000) for 7914 atoms. Found 43 (43 requested) and removed 31 (21 requested) atoms. Cycle 37: After refmac, R = 0.2146 (Rfree = 0.000) for 7871 atoms. Found 43 (43 requested) and removed 31 (21 requested) atoms. Cycle 38: After refmac, R = 0.2017 (Rfree = 0.000) for 7852 atoms. Found 37 (43 requested) and removed 29 (21 requested) atoms. Cycle 39: After refmac, R = 0.1993 (Rfree = 0.000) for 7834 atoms. Found 43 (43 requested) and removed 32 (21 requested) atoms. Cycle 40: After refmac, R = 0.1910 (Rfree = 0.000) for 7834 atoms. Found 24 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 8085 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 8101 seeds are put forward Round 1: 536 peptides, 94 chains. Longest chain 22 peptides. Score 0.361 Round 2: 596 peptides, 84 chains. Longest chain 20 peptides. Score 0.468 Round 3: 589 peptides, 81 chains. Longest chain 23 peptides. Score 0.474 Round 4: 571 peptides, 74 chains. Longest chain 21 peptides. Score 0.487 Round 5: 599 peptides, 82 chains. Longest chain 25 peptides. Score 0.479 Taking the results from Round 4 Chains 79, Residues 497, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 17953 restraints for refining 7913 atoms. 15891 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2139 (Rfree = 0.000) for 7913 atoms. Found 43 (43 requested) and removed 36 (21 requested) atoms. Cycle 42: After refmac, R = 0.2028 (Rfree = 0.000) for 7883 atoms. Found 31 (43 requested) and removed 26 (21 requested) atoms. Cycle 43: After refmac, R = 0.1929 (Rfree = 0.000) for 7866 atoms. Found 15 (43 requested) and removed 28 (21 requested) atoms. Cycle 44: After refmac, R = 0.1895 (Rfree = 0.000) for 7841 atoms. Found 14 (43 requested) and removed 24 (21 requested) atoms. Cycle 45: After refmac, R = 0.1902 (Rfree = 0.000) for 7821 atoms. Found 29 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.06 Search for helices and strands: 0 residues in 0 chains, 8038 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 8052 seeds are put forward Round 1: 477 peptides, 83 chains. Longest chain 15 peptides. Score 0.348 Round 2: 546 peptides, 82 chains. Longest chain 25 peptides. Score 0.427 Round 3: 552 peptides, 79 chains. Longest chain 30 peptides. Score 0.447 Round 4: 590 peptides, 87 chains. Longest chain 21 peptides. Score 0.449 Round 5: 573 peptides, 86 chains. Longest chain 20 peptides. Score 0.436 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 88, Residues 503, Estimated correctness of the model 0.0 % 3 chains (34 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 88 chains (503 residues) following loop building 3 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15989 reflections ( 99.57 % complete ) and 17839 restraints for refining 7913 atoms. 15760 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2073 (Rfree = 0.000) for 7913 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.1968 (Rfree = 0.000) for 7854 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.1967 (Rfree = 0.000) for 7811 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.1918 (Rfree = 0.000) for 7784 atoms. TimeTaking 102.18