null Tue 25 Dec 19:27:57 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 1vr5-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.8-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/1vr5-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.8-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 ============================================================ Tue 25 Dec 19:28:07 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/1vr5-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.8-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 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-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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-3.8-parrot-hancs.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 9673 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3222 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3030 (Rfree = 0.000) for 9673 atoms. Found 53 (53 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.09 Search for helices and strands: 0 residues in 0 chains, 9860 seeds are put forward NCS extension: 0 residues added, 9860 seeds are put forward Round 1: 590 peptides, 98 chains. Longest chain 16 peptides. Score 0.399 Round 2: 717 peptides, 86 chains. Longest chain 26 peptides. Score 0.568 Round 3: 732 peptides, 89 chains. Longest chain 27 peptides. Score 0.569 Round 4: 749 peptides, 82 chains. Longest chain 25 peptides. Score 0.608 Round 5: 766 peptides, 78 chains. Longest chain 27 peptides. Score 0.634 Taking the results from Round 5 Chains 91, Residues 688, Estimated correctness of the model 14.1 % 10 chains (128 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 15282 restraints for refining 7912 atoms. 12076 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2526 (Rfree = 0.000) for 7912 atoms. Found 43 (43 requested) and removed 79 (21 requested) atoms. Cycle 2: After refmac, R = 0.2353 (Rfree = 0.000) for 7764 atoms. Found 31 (43 requested) and removed 48 (21 requested) atoms. Cycle 3: After refmac, R = 0.2262 (Rfree = 0.000) for 7709 atoms. Found 29 (42 requested) and removed 32 (21 requested) atoms. Cycle 4: After refmac, R = 0.2177 (Rfree = 0.000) for 7667 atoms. Found 21 (42 requested) and removed 37 (21 requested) atoms. Cycle 5: After refmac, R = 0.2098 (Rfree = 0.000) for 7639 atoms. Found 24 (42 requested) and removed 34 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 7869 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 7894 seeds are put forward Round 1: 716 peptides, 108 chains. Longest chain 16 peptides. Score 0.480 Round 2: 728 peptides, 81 chains. Longest chain 27 peptides. Score 0.595 Round 3: 795 peptides, 80 chains. Longest chain 30 peptides. Score 0.648 Round 4: 765 peptides, 84 chains. Longest chain 29 peptides. Score 0.613 Round 5: 783 peptides, 81 chains. Longest chain 29 peptides. Score 0.636 Taking the results from Round 3 Chains 86, Residues 715, Estimated correctness of the model 20.0 % 6 chains (84 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 15880 restraints for refining 7916 atoms. 12775 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2233 (Rfree = 0.000) for 7916 atoms. Found 43 (43 requested) and removed 47 (21 requested) atoms. Cycle 7: After refmac, R = 0.2005 (Rfree = 0.000) for 7862 atoms. Found 24 (43 requested) and removed 34 (21 requested) atoms. Cycle 8: After refmac, R = 0.1870 (Rfree = 0.000) for 7827 atoms. Found 12 (43 requested) and removed 31 (21 requested) atoms. Cycle 9: After refmac, R = 0.1786 (Rfree = 0.000) for 7782 atoms. Found 10 (42 requested) and removed 31 (21 requested) atoms. Cycle 10: After refmac, R = 0.1733 (Rfree = 0.000) for 7748 atoms. Found 10 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.08 Search for helices and strands: 0 residues in 0 chains, 7977 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7997 seeds are put forward Round 1: 713 peptides, 96 chains. Longest chain 19 peptides. Score 0.526 Round 2: 760 peptides, 81 chains. Longest chain 28 peptides. Score 0.620 Round 3: 748 peptides, 84 chains. Longest chain 28 peptides. Score 0.600 Round 4: 759 peptides, 78 chains. Longest chain 32 peptides. Score 0.629 Round 5: 754 peptides, 82 chains. Longest chain 28 peptides. Score 0.612 Taking the results from Round 4 Chains 83, Residues 681, Estimated correctness of the model 11.9 % 10 chains (158 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 15407 restraints for refining 7916 atoms. 12106 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2342 (Rfree = 0.000) for 7916 atoms. Found 42 (43 requested) and removed 87 (21 requested) atoms. Cycle 12: After refmac, R = 0.2118 (Rfree = 0.000) for 7799 atoms. Found 34 (43 requested) and removed 31 (21 requested) atoms. Cycle 13: After refmac, R = 0.2044 (Rfree = 0.000) for 7768 atoms. Found 12 (42 requested) and removed 32 (21 requested) atoms. Cycle 14: After refmac, R = 0.1982 (Rfree = 0.000) for 7740 atoms. Found 9 (42 requested) and removed 32 (21 requested) atoms. Cycle 15: After refmac, R = 0.1941 (Rfree = 0.000) for 7710 atoms. Found 13 (42 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.08 Search for helices and strands: 0 residues in 0 chains, 7920 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7934 seeds are put forward Round 1: 707 peptides, 105 chains. Longest chain 19 peptides. Score 0.484 Round 2: 731 peptides, 82 chains. Longest chain 27 peptides. Score 0.594 Round 3: 743 peptides, 96 chains. Longest chain 21 peptides. Score 0.551 Round 4: 733 peptides, 85 chains. Longest chain 28 peptides. Score 0.584 Round 5: 737 peptides, 85 chains. Longest chain 30 peptides. Score 0.588 Taking the results from Round 2 Chains 91, Residues 649, Estimated correctness of the model 0.0 % 12 chains (144 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 15775 restraints for refining 7916 atoms. 12684 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2219 (Rfree = 0.000) for 7916 atoms. Found 42 (43 requested) and removed 54 (21 requested) atoms. Cycle 17: After refmac, R = 0.2147 (Rfree = 0.000) for 7852 atoms. Found 32 (43 requested) and removed 37 (21 requested) atoms. Cycle 18: After refmac, R = 0.2031 (Rfree = 0.000) for 7832 atoms. Found 26 (43 requested) and removed 28 (21 requested) atoms. Cycle 19: After refmac, R = 0.1984 (Rfree = 0.000) for 7809 atoms. Found 26 (43 requested) and removed 26 (21 requested) atoms. Cycle 20: After refmac, R = 0.1941 (Rfree = 0.000) for 7791 atoms. Found 24 (42 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.06 Search for helices and strands: 0 residues in 0 chains, 8026 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 8046 seeds are put forward Round 1: 657 peptides, 98 chains. Longest chain 15 peptides. Score 0.466 Round 2: 684 peptides, 85 chains. Longest chain 22 peptides. Score 0.544 Round 3: 704 peptides, 88 chains. Longest chain 20 peptides. Score 0.549 Round 4: 699 peptides, 87 chains. Longest chain 22 peptides. Score 0.549 Round 5: 695 peptides, 82 chains. Longest chain 24 peptides. Score 0.565 Taking the results from Round 5 Chains 88, Residues 613, Estimated correctness of the model 0.0 % 6 chains (66 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16795 restraints for refining 7916 atoms. 14139 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2207 (Rfree = 0.000) for 7916 atoms. Found 43 (43 requested) and removed 43 (21 requested) atoms. Cycle 22: After refmac, R = 0.2002 (Rfree = 0.000) for 7862 atoms. Found 17 (43 requested) and removed 40 (21 requested) atoms. Cycle 23: After refmac, R = 0.1920 (Rfree = 0.000) for 7813 atoms. Found 20 (43 requested) and removed 38 (21 requested) atoms. Cycle 24: After refmac, R = 0.1875 (Rfree = 0.000) for 7780 atoms. Found 19 (42 requested) and removed 27 (21 requested) atoms. Cycle 25: After refmac, R = 0.1805 (Rfree = 0.000) for 7758 atoms. Found 15 (42 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.07 Search for helices and strands: 0 residues in 0 chains, 8009 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 8029 seeds are put forward Round 1: 629 peptides, 105 chains. Longest chain 14 peptides. Score 0.408 Round 2: 690 peptides, 86 chains. Longest chain 21 peptides. Score 0.545 Round 3: 702 peptides, 92 chains. Longest chain 17 peptides. Score 0.532 Round 4: 693 peptides, 84 chains. Longest chain 20 peptides. Score 0.555 Round 5: 680 peptides, 85 chains. Longest chain 25 peptides. Score 0.540 Taking the results from Round 4 Chains 94, Residues 609, Estimated correctness of the model 0.0 % 9 chains (98 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16459 restraints for refining 7915 atoms. 13707 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2284 (Rfree = 0.000) for 7915 atoms. Found 43 (43 requested) and removed 34 (21 requested) atoms. Cycle 27: After refmac, R = 0.2136 (Rfree = 0.000) for 7884 atoms. Found 40 (43 requested) and removed 34 (21 requested) atoms. Cycle 28: After refmac, R = 0.1942 (Rfree = 0.000) for 7845 atoms. Found 27 (43 requested) and removed 41 (21 requested) atoms. Cycle 29: After refmac, R = 0.1908 (Rfree = 0.000) for 7814 atoms. Found 17 (43 requested) and removed 28 (21 requested) atoms. Cycle 30: After refmac, R = 0.1898 (Rfree = 0.000) for 7789 atoms. Found 6 (42 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.09 Search for helices and strands: 0 residues in 0 chains, 8046 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 8059 seeds are put forward Round 1: 587 peptides, 100 chains. Longest chain 20 peptides. Score 0.387 Round 2: 658 peptides, 89 chains. Longest chain 23 peptides. Score 0.505 Round 3: 656 peptides, 84 chains. Longest chain 24 peptides. Score 0.523 Round 4: 655 peptides, 87 chains. Longest chain 21 peptides. Score 0.510 Round 5: 668 peptides, 89 chains. Longest chain 19 peptides. Score 0.514 Taking the results from Round 3 Chains 91, Residues 572, Estimated correctness of the model 0.0 % 7 chains (85 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16686 restraints for refining 7916 atoms. 14156 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2224 (Rfree = 0.000) for 7916 atoms. Found 43 (43 requested) and removed 34 (21 requested) atoms. Cycle 32: After refmac, R = 0.2061 (Rfree = 0.000) for 7875 atoms. Found 21 (43 requested) and removed 37 (21 requested) atoms. Cycle 33: After refmac, R = 0.1990 (Rfree = 0.000) for 7831 atoms. Found 27 (43 requested) and removed 32 (21 requested) atoms. Cycle 34: After refmac, R = 0.1916 (Rfree = 0.000) for 7815 atoms. Found 19 (43 requested) and removed 28 (21 requested) atoms. Cycle 35: After refmac, R = 0.1907 (Rfree = 0.000) for 7802 atoms. Found 25 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 3.08 Search for helices and strands: 0 residues in 0 chains, 8070 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 8092 seeds are put forward Round 1: 562 peptides, 92 chains. Longest chain 14 peptides. Score 0.398 Round 2: 619 peptides, 92 chains. Longest chain 19 peptides. Score 0.455 Round 3: 665 peptides, 86 chains. Longest chain 20 peptides. Score 0.523 Round 4: 626 peptides, 87 chains. Longest chain 20 peptides. Score 0.483 Round 5: 633 peptides, 84 chains. Longest chain 32 peptides. Score 0.503 Taking the results from Round 3 Chains 89, Residues 579, Estimated correctness of the model 0.0 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 17144 restraints for refining 7915 atoms. 14670 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2189 (Rfree = 0.000) for 7915 atoms. Found 36 (43 requested) and removed 29 (21 requested) atoms. Cycle 37: After refmac, R = 0.2049 (Rfree = 0.000) for 7893 atoms. Found 22 (43 requested) and removed 30 (21 requested) atoms. Cycle 38: After refmac, R = 0.2076 (Rfree = 0.000) for 7867 atoms. Found 34 (43 requested) and removed 32 (21 requested) atoms. Cycle 39: After refmac, R = 0.1931 (Rfree = 0.000) for 7857 atoms. Found 24 (43 requested) and removed 28 (21 requested) atoms. Cycle 40: After refmac, R = 0.1970 (Rfree = 0.000) for 7831 atoms. Found 34 (43 requested) and removed 30 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.04 Search for helices and strands: 0 residues in 0 chains, 8088 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 8103 seeds are put forward Round 1: 565 peptides, 94 chains. Longest chain 18 peptides. Score 0.392 Round 2: 619 peptides, 84 chains. Longest chain 18 peptides. Score 0.490 Round 3: 611 peptides, 82 chains. Longest chain 17 peptides. Score 0.491 Round 4: 627 peptides, 80 chains. Longest chain 26 peptides. Score 0.514 Round 5: 614 peptides, 75 chains. Longest chain 19 peptides. Score 0.523 Taking the results from Round 5 Chains 77, Residues 539, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 17806 restraints for refining 7915 atoms. 15577 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2136 (Rfree = 0.000) for 7915 atoms. Found 34 (43 requested) and removed 35 (21 requested) atoms. Cycle 42: After refmac, R = 0.2080 (Rfree = 0.000) for 7875 atoms. Found 35 (43 requested) and removed 27 (21 requested) atoms. Cycle 43: After refmac, R = 0.1993 (Rfree = 0.000) for 7862 atoms. Found 43 (43 requested) and removed 33 (21 requested) atoms. Cycle 44: After refmac, R = 0.1915 (Rfree = 0.000) for 7856 atoms. Found 24 (43 requested) and removed 26 (21 requested) atoms. Cycle 45: After refmac, R = 0.1736 (Rfree = 0.000) for 7844 atoms. Found 5 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.09 Search for helices and strands: 0 residues in 0 chains, 8117 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8132 seeds are put forward Round 1: 509 peptides, 93 chains. Longest chain 12 peptides. Score 0.335 Round 2: 565 peptides, 86 chains. Longest chain 19 peptides. Score 0.428 Round 3: 563 peptides, 87 chains. Longest chain 19 peptides. Score 0.421 Round 4: 589 peptides, 89 chains. Longest chain 28 peptides. Score 0.439 Round 5: 566 peptides, 78 chains. Longest chain 20 peptides. Score 0.465 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 79, Residues 488, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 79 chains (488 residues) following loop building 2 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15989 reflections ( 99.57 % complete ) and 18101 restraints for refining 7915 atoms. 16118 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2170 (Rfree = 0.000) for 7915 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.2213 (Rfree = 0.000) for 7866 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2129 (Rfree = 0.000) for 7829 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2034 (Rfree = 0.000) for 7791 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:26:44 GMT 2018 Job finished. TimeTaking 118.78 Used memory is bytes: 13921128