null Mon 24 Dec 07:58:40 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr5-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-noncs ############### 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 07:58:44 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-noncs/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 1039 and 0 Target number of residues in the AU: 1039 Target solvent content: 0.6411 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: 1vr5-3.4-parrot-noncs.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: 1vr5-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 8752 target number of atoms Had to go as low as 0.90 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 3.400 Wilson plot Bfac: 72.71 22185 reflections ( 99.66 % complete ) and 0 restraints for refining 9764 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3160 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3005 (Rfree = 0.000) for 9764 atoms. Found 73 (73 requested) and removed 58 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 2.89 Search for helices and strands: 0 residues in 0 chains, 9972 seeds are put forward NCS extension: 0 residues added, 9972 seeds are put forward Round 1: 676 peptides, 105 chains. Longest chain 23 peptides. Score 0.455 Round 2: 787 peptides, 96 chains. Longest chain 26 peptides. Score 0.587 Round 3: 794 peptides, 85 chains. Longest chain 26 peptides. Score 0.631 Round 4: 803 peptides, 88 chains. Longest chain 27 peptides. Score 0.627 Round 5: 812 peptides, 82 chains. Longest chain 30 peptides. Score 0.654 Taking the results from Round 5 Chains 88, Residues 730, Estimated correctness of the model 45.3 % 11 chains (165 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15187 restraints for refining 8079 atoms. 11609 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2597 (Rfree = 0.000) for 8079 atoms. Found 61 (61 requested) and removed 81 (30 requested) atoms. Cycle 2: After refmac, R = 0.2430 (Rfree = 0.000) for 7934 atoms. Found 60 (60 requested) and removed 41 (30 requested) atoms. Cycle 3: After refmac, R = 0.2312 (Rfree = 0.000) for 7886 atoms. Found 49 (60 requested) and removed 40 (30 requested) atoms. Cycle 4: After refmac, R = 0.2211 (Rfree = 0.000) for 7865 atoms. Found 30 (59 requested) and removed 39 (29 requested) atoms. Cycle 5: After refmac, R = 0.2135 (Rfree = 0.000) for 7839 atoms. Found 28 (59 requested) and removed 38 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 2.84 Search for helices and strands: 0 residues in 0 chains, 8053 seeds are put forward NCS extension: 11 residues added (14 deleted due to clashes), 8064 seeds are put forward Round 1: 781 peptides, 92 chains. Longest chain 32 peptides. Score 0.597 Round 2: 807 peptides, 84 chains. Longest chain 31 peptides. Score 0.643 Round 3: 844 peptides, 76 chains. Longest chain 50 peptides. Score 0.693 Round 4: 822 peptides, 71 chains. Longest chain 41 peptides. Score 0.695 Round 5: 837 peptides, 69 chains. Longest chain 60 peptides. Score 0.710 Taking the results from Round 5 Chains 79, Residues 768, Estimated correctness of the model 60.4 % 12 chains (242 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 499 A and 509 A 77 chains (771 residues) following loop building 11 chains (251 residues) in sequence following loop building ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 13695 restraints for refining 7957 atoms. 9606 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2505 (Rfree = 0.000) for 7957 atoms. Found 60 (60 requested) and removed 61 (30 requested) atoms. Cycle 7: After refmac, R = 0.2242 (Rfree = 0.000) for 7903 atoms. Found 38 (59 requested) and removed 44 (30 requested) atoms. Cycle 8: After refmac, R = 0.2159 (Rfree = 0.000) for 7866 atoms. Found 22 (57 requested) and removed 36 (29 requested) atoms. Cycle 9: After refmac, R = 0.2111 (Rfree = 0.000) for 7842 atoms. Found 15 (55 requested) and removed 33 (29 requested) atoms. Cycle 10: After refmac, R = 0.2108 (Rfree = 0.000) for 7819 atoms. Found 11 (54 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 2.85 Search for helices and strands: 0 residues in 0 chains, 8024 seeds are put forward NCS extension: 44 residues added (33 deleted due to clashes), 8068 seeds are put forward Round 1: 757 peptides, 87 chains. Longest chain 26 peptides. Score 0.596 Round 2: 813 peptides, 70 chains. Longest chain 46 peptides. Score 0.692 Round 3: 807 peptides, 77 chains. Longest chain 39 peptides. Score 0.666 Round 4: 806 peptides, 79 chains. Longest chain 47 peptides. Score 0.659 Round 5: 831 peptides, 73 chains. Longest chain 47 peptides. Score 0.694 Taking the results from Round 5 Chains 85, Residues 758, Estimated correctness of the model 56.3 % 14 chains (219 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14239 restraints for refining 7957 atoms. 10307 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2438 (Rfree = 0.000) for 7957 atoms. Found 54 (54 requested) and removed 54 (30 requested) atoms. Cycle 12: After refmac, R = 0.2253 (Rfree = 0.000) for 7906 atoms. Found 35 (54 requested) and removed 41 (30 requested) atoms. Cycle 13: After refmac, R = 0.2178 (Rfree = 0.000) for 7881 atoms. Found 29 (53 requested) and removed 36 (29 requested) atoms. Cycle 14: After refmac, R = 0.2112 (Rfree = 0.000) for 7847 atoms. Found 28 (53 requested) and removed 37 (29 requested) atoms. Cycle 15: After refmac, R = 0.2084 (Rfree = 0.000) for 7819 atoms. Found 22 (53 requested) and removed 34 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.81 Search for helices and strands: 0 residues in 0 chains, 8001 seeds are put forward NCS extension: 31 residues added (9 deleted due to clashes), 8032 seeds are put forward Round 1: 762 peptides, 93 chains. Longest chain 22 peptides. Score 0.578 Round 2: 798 peptides, 74 chains. Longest chain 33 peptides. Score 0.670 Round 3: 823 peptides, 74 chains. Longest chain 33 peptides. Score 0.686 Round 4: 816 peptides, 73 chains. Longest chain 38 peptides. Score 0.685 Round 5: 832 peptides, 81 chains. Longest chain 36 peptides. Score 0.670 Taking the results from Round 3 Chains 79, Residues 749, Estimated correctness of the model 54.2 % 11 chains (179 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14795 restraints for refining 7958 atoms. 11063 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2425 (Rfree = 0.000) for 7958 atoms. Found 54 (54 requested) and removed 50 (30 requested) atoms. Cycle 17: After refmac, R = 0.2320 (Rfree = 0.000) for 7937 atoms. Found 31 (54 requested) and removed 40 (30 requested) atoms. Cycle 18: After refmac, R = 0.2247 (Rfree = 0.000) for 7913 atoms. Found 27 (53 requested) and removed 32 (29 requested) atoms. Cycle 19: After refmac, R = 0.2194 (Rfree = 0.000) for 7895 atoms. Found 25 (53 requested) and removed 32 (29 requested) atoms. Cycle 20: After refmac, R = 0.2121 (Rfree = 0.000) for 7873 atoms. Found 29 (53 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 2.85 Search for helices and strands: 0 residues in 0 chains, 8065 seeds are put forward NCS extension: 24 residues added (19 deleted due to clashes), 8089 seeds are put forward Round 1: 740 peptides, 91 chains. Longest chain 31 peptides. Score 0.568 Round 2: 806 peptides, 86 chains. Longest chain 27 peptides. Score 0.636 Round 3: 798 peptides, 81 chains. Longest chain 27 peptides. Score 0.647 Round 4: 799 peptides, 84 chains. Longest chain 29 peptides. Score 0.638 Round 5: 785 peptides, 79 chains. Longest chain 32 peptides. Score 0.645 Taking the results from Round 3 Chains 86, Residues 717, Estimated correctness of the model 43.3 % 9 chains (118 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15679 restraints for refining 7958 atoms. 12332 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2445 (Rfree = 0.000) for 7958 atoms. Found 54 (54 requested) and removed 47 (30 requested) atoms. Cycle 22: After refmac, R = 0.2419 (Rfree = 0.000) for 7946 atoms. Found 44 (54 requested) and removed 36 (30 requested) atoms. Cycle 23: After refmac, R = 0.2218 (Rfree = 0.000) for 7936 atoms. Found 25 (54 requested) and removed 35 (30 requested) atoms. Cycle 24: After refmac, R = 0.2233 (Rfree = 0.000) for 7906 atoms. Found 34 (53 requested) and removed 31 (29 requested) atoms. Cycle 25: After refmac, R = 0.2223 (Rfree = 0.000) for 7898 atoms. Found 38 (53 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 2.82 Search for helices and strands: 0 residues in 0 chains, 8131 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 8143 seeds are put forward Round 1: 717 peptides, 95 chains. Longest chain 23 peptides. Score 0.533 Round 2: 751 peptides, 81 chains. Longest chain 30 peptides. Score 0.613 Round 3: 757 peptides, 82 chains. Longest chain 29 peptides. Score 0.614 Round 4: 767 peptides, 75 chains. Longest chain 30 peptides. Score 0.645 Round 5: 804 peptides, 83 chains. Longest chain 36 peptides. Score 0.645 Taking the results from Round 5 Chains 92, Residues 721, Estimated correctness of the model 42.7 % 11 chains (134 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15373 restraints for refining 7957 atoms. 11987 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2458 (Rfree = 0.000) for 7957 atoms. Found 54 (54 requested) and removed 46 (30 requested) atoms. Cycle 27: After refmac, R = 0.2297 (Rfree = 0.000) for 7926 atoms. Found 27 (54 requested) and removed 38 (30 requested) atoms. Cycle 28: After refmac, R = 0.2192 (Rfree = 0.000) for 7898 atoms. Found 28 (53 requested) and removed 35 (29 requested) atoms. Cycle 29: After refmac, R = 0.2127 (Rfree = 0.000) for 7880 atoms. Found 18 (53 requested) and removed 32 (29 requested) atoms. Cycle 30: After refmac, R = 0.2085 (Rfree = 0.000) for 7859 atoms. Found 31 (53 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 2.81 Search for helices and strands: 0 residues in 0 chains, 8091 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 8118 seeds are put forward Round 1: 725 peptides, 89 chains. Longest chain 22 peptides. Score 0.563 Round 2: 759 peptides, 77 chains. Longest chain 51 peptides. Score 0.633 Round 3: 782 peptides, 73 chains. Longest chain 32 peptides. Score 0.662 Round 4: 754 peptides, 81 chains. Longest chain 28 peptides. Score 0.615 Round 5: 774 peptides, 82 chains. Longest chain 36 peptides. Score 0.626 Taking the results from Round 3 Chains 79, Residues 709, Estimated correctness of the model 47.6 % 8 chains (129 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15489 restraints for refining 7958 atoms. 12119 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2305 (Rfree = 0.000) for 7958 atoms. Found 54 (54 requested) and removed 45 (30 requested) atoms. Cycle 32: After refmac, R = 0.2195 (Rfree = 0.000) for 7942 atoms. Found 41 (54 requested) and removed 36 (30 requested) atoms. Cycle 33: After refmac, R = 0.2133 (Rfree = 0.000) for 7930 atoms. Found 29 (53 requested) and removed 35 (29 requested) atoms. Cycle 34: After refmac, R = 0.2087 (Rfree = 0.000) for 7913 atoms. Found 26 (53 requested) and removed 32 (29 requested) atoms. Cycle 35: After refmac, R = 0.2075 (Rfree = 0.000) for 7895 atoms. Found 28 (53 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 2.82 Search for helices and strands: 0 residues in 0 chains, 8085 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8103 seeds are put forward Round 1: 703 peptides, 91 chains. Longest chain 21 peptides. Score 0.537 Round 2: 748 peptides, 81 chains. Longest chain 25 peptides. Score 0.611 Round 3: 775 peptides, 78 chains. Longest chain 43 peptides. Score 0.641 Round 4: 752 peptides, 78 chains. Longest chain 28 peptides. Score 0.624 Round 5: 787 peptides, 77 chains. Longest chain 33 peptides. Score 0.653 Taking the results from Round 5 Chains 84, Residues 710, Estimated correctness of the model 45.0 % 10 chains (157 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15371 restraints for refining 7957 atoms. 11913 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2597 (Rfree = 0.000) for 7957 atoms. Found 54 (54 requested) and removed 44 (30 requested) atoms. Cycle 37: After refmac, R = 0.2407 (Rfree = 0.000) for 7930 atoms. Found 54 (54 requested) and removed 42 (30 requested) atoms. Cycle 38: After refmac, R = 0.2302 (Rfree = 0.000) for 7917 atoms. Found 24 (53 requested) and removed 36 (29 requested) atoms. Cycle 39: After refmac, R = 0.2142 (Rfree = 0.000) for 7889 atoms. Found 22 (53 requested) and removed 35 (29 requested) atoms. Cycle 40: After refmac, R = 0.2142 (Rfree = 0.000) for 7861 atoms. Found 24 (53 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 8052 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 8073 seeds are put forward Round 1: 687 peptides, 87 chains. Longest chain 25 peptides. Score 0.538 Round 2: 742 peptides, 77 chains. Longest chain 25 peptides. Score 0.620 Round 3: 766 peptides, 78 chains. Longest chain 32 peptides. Score 0.634 Round 4: 755 peptides, 75 chains. Longest chain 33 peptides. Score 0.637 Round 5: 747 peptides, 82 chains. Longest chain 34 peptides. Score 0.606 Taking the results from Round 4 Chains 84, Residues 680, Estimated correctness of the model 40.3 % 7 chains (95 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 16084 restraints for refining 7957 atoms. 13035 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2423 (Rfree = 0.000) for 7957 atoms. Found 53 (54 requested) and removed 51 (30 requested) atoms. Cycle 42: After refmac, R = 0.2367 (Rfree = 0.000) for 7917 atoms. Found 41 (54 requested) and removed 40 (30 requested) atoms. Cycle 43: After refmac, R = 0.2135 (Rfree = 0.000) for 7895 atoms. Found 35 (53 requested) and removed 34 (29 requested) atoms. Cycle 44: After refmac, R = 0.2001 (Rfree = 0.000) for 7883 atoms. Found 18 (53 requested) and removed 32 (29 requested) atoms. Cycle 45: After refmac, R = 0.2034 (Rfree = 0.000) for 7859 atoms. Found 22 (53 requested) and removed 34 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 2.84 Search for helices and strands: 0 residues in 0 chains, 8053 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 8084 seeds are put forward Round 1: 662 peptides, 92 chains. Longest chain 30 peptides. Score 0.496 Round 2: 727 peptides, 86 chains. Longest chain 32 peptides. Score 0.576 Round 3: 734 peptides, 85 chains. Longest chain 28 peptides. Score 0.585 Round 4: 710 peptides, 86 chains. Longest chain 41 peptides. Score 0.562 Round 5: 726 peptides, 91 chains. Longest chain 23 peptides. Score 0.556 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 86, Residues 649, Estimated correctness of the model 23.7 % 4 chains (47 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 86 chains (649 residues) following loop building 4 chains (47 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22185 reflections ( 99.66 % complete ) and 16871 restraints for refining 7958 atoms. 14158 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2263 (Rfree = 0.000) for 7958 atoms. Found 0 (54 requested) and removed 30 (30 requested) atoms. Cycle 47: After refmac, R = 0.2323 (Rfree = 0.000) for 7913 atoms. Found 0 (53 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.2200 (Rfree = 0.000) for 7865 atoms. Found 0 (53 requested) and removed 29 (29 requested) atoms. Cycle 49: After refmac, R = 0.2165 (Rfree = 0.000) for 7818 atoms. Found 0 (53 requested) and removed 29 (29 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:31:55 GMT 2018 Job finished. TimeTaking 93.25 Used memory is bytes: 14021888