Mon 24 Dec 07:41:55 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 1vkm-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-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/1vkm-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-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 07:41:59 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/1vkm-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-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 1218 and 0 Target number of residues in the AU: 1218 Target solvent content: 0.6080 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-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: 19 Cell parameters: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.55 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: 75.160 3.400 Wilson plot Bfac: 55.91 23836 reflections ( 99.97 % complete ) and 0 restraints for refining 15872 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3097 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2995 (Rfree = 0.000) for 15872 atoms. Found 106 (119 requested) and removed 196 (59 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.48 Search for helices and strands: 0 residues in 0 chains, 16094 seeds are put forward NCS extension: 0 residues added, 16094 seeds are put forward Round 1: 628 peptides, 131 chains. Longest chain 10 peptides. Score 0.282 Round 2: 815 peptides, 140 chains. Longest chain 18 peptides. Score 0.429 Round 3: 932 peptides, 148 chains. Longest chain 26 peptides. Score 0.500 Round 4: 962 peptides, 143 chains. Longest chain 24 peptides. Score 0.542 Round 5: 985 peptides, 143 chains. Longest chain 29 peptides. Score 0.559 Taking the results from Round 5 Chains 152, Residues 842, Estimated correctness of the model 14.7 % 10 chains (85 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 28999 restraints for refining 12960 atoms. 25567 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2490 (Rfree = 0.000) for 12960 atoms. Found 66 (97 requested) and removed 114 (48 requested) atoms. Cycle 2: After refmac, R = 0.2396 (Rfree = 0.000) for 12759 atoms. Found 53 (97 requested) and removed 86 (48 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2317 (Rfree = 0.000) for 12655 atoms. Found 61 (96 requested) and removed 82 (48 requested) atoms. Cycle 4: After refmac, R = 0.2233 (Rfree = 0.000) for 12601 atoms. Found 52 (95 requested) and removed 76 (47 requested) atoms. Cycle 5: After refmac, R = 0.1995 (Rfree = 0.000) for 12542 atoms. Found 21 (94 requested) and removed 67 (47 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 12984 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 12996 seeds are put forward Round 1: 844 peptides, 147 chains. Longest chain 15 peptides. Score 0.428 Round 2: 964 peptides, 143 chains. Longest chain 20 peptides. Score 0.543 Round 3: 982 peptides, 141 chains. Longest chain 21 peptides. Score 0.563 Round 4: 980 peptides, 140 chains. Longest chain 17 peptides. Score 0.565 Round 5: 994 peptides, 144 chains. Longest chain 18 peptides. Score 0.563 Taking the results from Round 4 Chains 144, Residues 840, Estimated correctness of the model 16.8 % 10 chains (74 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29338 restraints for refining 12868 atoms. 25911 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2377 (Rfree = 0.000) for 12868 atoms. Found 41 (97 requested) and removed 130 (48 requested) atoms. Cycle 7: After refmac, R = 0.2316 (Rfree = 0.000) for 12707 atoms. Found 40 (96 requested) and removed 92 (48 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2243 (Rfree = 0.000) for 12614 atoms. Found 23 (95 requested) and removed 90 (47 requested) atoms. Cycle 9: After refmac, R = 0.2213 (Rfree = 0.000) for 12527 atoms. Found 19 (94 requested) and removed 83 (47 requested) atoms. Cycle 10: After refmac, R = 0.2186 (Rfree = 0.000) for 12444 atoms. Found 15 (94 requested) and removed 75 (47 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 3.42 Search for helices and strands: 0 residues in 0 chains, 12777 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 12793 seeds are put forward Round 1: 840 peptides, 149 chains. Longest chain 14 peptides. Score 0.417 Round 2: 921 peptides, 131 chains. Longest chain 22 peptides. Score 0.551 Round 3: 956 peptides, 137 chains. Longest chain 17 peptides. Score 0.557 Round 4: 919 peptides, 134 chains. Longest chain 20 peptides. Score 0.539 Round 5: 962 peptides, 136 chains. Longest chain 23 peptides. Score 0.565 Taking the results from Round 5 Chains 144, Residues 826, Estimated correctness of the model 16.8 % 7 chains (63 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29343 restraints for refining 12962 atoms. 26023 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2261 (Rfree = 0.000) for 12962 atoms. Found 37 (97 requested) and removed 120 (48 requested) atoms. Cycle 12: After refmac, R = 0.2250 (Rfree = 0.000) for 12830 atoms. Found 34 (97 requested) and removed 89 (48 requested) atoms. Cycle 13: After refmac, R = 0.2159 (Rfree = 0.000) for 12737 atoms. Found 34 (96 requested) and removed 80 (48 requested) atoms. Cycle 14: After refmac, R = 0.2082 (Rfree = 0.000) for 12667 atoms. Found 30 (95 requested) and removed 69 (47 requested) atoms. Cycle 15: After refmac, R = 0.2109 (Rfree = 0.000) for 12610 atoms. Found 31 (95 requested) and removed 75 (47 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 12983 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 13004 seeds are put forward Round 1: 774 peptides, 141 chains. Longest chain 12 peptides. Score 0.387 Round 2: 872 peptides, 134 chains. Longest chain 25 peptides. Score 0.501 Round 3: 894 peptides, 132 chains. Longest chain 18 peptides. Score 0.526 Round 4: 888 peptides, 127 chains. Longest chain 21 peptides. Score 0.539 Round 5: 910 peptides, 125 chains. Longest chain 21 peptides. Score 0.562 Taking the results from Round 5 Chains 131, Residues 785, Estimated correctness of the model 15.8 % 9 chains (94 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29031 restraints for refining 12960 atoms. 25703 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2279 (Rfree = 0.000) for 12960 atoms. Found 43 (97 requested) and removed 126 (48 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2217 (Rfree = 0.000) for 12838 atoms. Found 31 (97 requested) and removed 71 (48 requested) atoms. Cycle 18: After refmac, R = 0.2252 (Rfree = 0.000) for 12782 atoms. Found 24 (96 requested) and removed 72 (48 requested) atoms. Cycle 19: After refmac, R = 0.2182 (Rfree = 0.000) for 12726 atoms. Found 27 (96 requested) and removed 75 (48 requested) atoms. Cycle 20: After refmac, R = 0.2200 (Rfree = 0.000) for 12671 atoms. Found 28 (95 requested) and removed 79 (47 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.43 Search for helices and strands: 0 residues in 0 chains, 13029 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 13043 seeds are put forward Round 1: 770 peptides, 138 chains. Longest chain 13 peptides. Score 0.395 Round 2: 882 peptides, 140 chains. Longest chain 16 peptides. Score 0.487 Round 3: 881 peptides, 127 chains. Longest chain 22 peptides. Score 0.533 Round 4: 866 peptides, 132 chains. Longest chain 21 peptides. Score 0.503 Round 5: 881 peptides, 128 chains. Longest chain 20 peptides. Score 0.530 Taking the results from Round 3 Chains 133, Residues 754, Estimated correctness of the model 5.3 % 11 chains (93 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 28996 restraints for refining 12960 atoms. 25848 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2182 (Rfree = 0.000) for 12960 atoms. Found 34 (97 requested) and removed 85 (48 requested) atoms. Cycle 22: After refmac, R = 0.2152 (Rfree = 0.000) for 12876 atoms. Found 22 (97 requested) and removed 67 (48 requested) atoms. Cycle 23: After refmac, R = 0.2104 (Rfree = 0.000) for 12814 atoms. Found 22 (96 requested) and removed 65 (48 requested) atoms. Cycle 24: After refmac, R = 0.2056 (Rfree = 0.000) for 12756 atoms. Found 23 (96 requested) and removed 56 (48 requested) atoms. Cycle 25: After refmac, R = 0.2011 (Rfree = 0.000) for 12711 atoms. Found 20 (96 requested) and removed 61 (48 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 3.43 Search for helices and strands: 0 residues in 0 chains, 13046 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 13076 seeds are put forward Round 1: 708 peptides, 133 chains. Longest chain 15 peptides. Score 0.356 Round 2: 803 peptides, 124 chains. Longest chain 16 peptides. Score 0.479 Round 3: 837 peptides, 132 chains. Longest chain 18 peptides. Score 0.479 Round 4: 845 peptides, 127 chains. Longest chain 19 peptides. Score 0.504 Round 5: 847 peptides, 128 chains. Longest chain 15 peptides. Score 0.502 Taking the results from Round 4 Chains 131, Residues 718, Estimated correctness of the model 0.0 % 8 chains (42 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29961 restraints for refining 12962 atoms. 27136 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2110 (Rfree = 0.000) for 12962 atoms. Found 45 (97 requested) and removed 77 (48 requested) atoms. Cycle 27: After refmac, R = 0.2070 (Rfree = 0.000) for 12890 atoms. Found 47 (97 requested) and removed 68 (48 requested) atoms. Cycle 28: After refmac, R = 0.2093 (Rfree = 0.000) for 12854 atoms. Found 42 (97 requested) and removed 63 (48 requested) atoms. Cycle 29: After refmac, R = 0.2033 (Rfree = 0.000) for 12811 atoms. Found 46 (96 requested) and removed 73 (48 requested) atoms. Cycle 30: After refmac, R = 0.1788 (Rfree = 0.000) for 12770 atoms. Found 15 (96 requested) and removed 50 (48 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 13116 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 13136 seeds are put forward Round 1: 682 peptides, 130 chains. Longest chain 13 peptides. Score 0.342 Round 2: 805 peptides, 134 chains. Longest chain 18 peptides. Score 0.443 Round 3: 782 peptides, 124 chains. Longest chain 16 peptides. Score 0.461 Round 4: 819 peptides, 126 chains. Longest chain 17 peptides. Score 0.486 Round 5: 780 peptides, 124 chains. Longest chain 25 peptides. Score 0.459 Taking the results from Round 4 Chains 126, Residues 693, Estimated correctness of the model 0.0 % 7 chains (35 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 30046 restraints for refining 12961 atoms. 27317 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2100 (Rfree = 0.000) for 12961 atoms. Found 57 (97 requested) and removed 83 (48 requested) atoms. Cycle 32: After refmac, R = 0.2062 (Rfree = 0.000) for 12906 atoms. Found 47 (97 requested) and removed 61 (48 requested) atoms. Cycle 33: After refmac, R = 0.2056 (Rfree = 0.000) for 12883 atoms. Found 52 (97 requested) and removed 60 (48 requested) atoms. Cycle 34: After refmac, R = 0.2014 (Rfree = 0.000) for 12866 atoms. Found 48 (97 requested) and removed 57 (48 requested) atoms. Cycle 35: After refmac, R = 0.1996 (Rfree = 0.000) for 12849 atoms. Found 46 (97 requested) and removed 55 (48 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.43 Search for helices and strands: 0 residues in 0 chains, 13215 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 13233 seeds are put forward Round 1: 649 peptides, 127 chains. Longest chain 12 peptides. Score 0.322 Round 2: 730 peptides, 127 chains. Longest chain 16 peptides. Score 0.402 Round 3: 731 peptides, 127 chains. Longest chain 16 peptides. Score 0.403 Round 4: 706 peptides, 115 chains. Longest chain 16 peptides. Score 0.428 Round 5: 740 peptides, 122 chains. Longest chain 19 peptides. Score 0.431 Taking the results from Round 5 Chains 123, Residues 618, Estimated correctness of the model 0.0 % 7 chains (40 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29994 restraints for refining 12962 atoms. 27544 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2046 (Rfree = 0.000) for 12962 atoms. Found 47 (97 requested) and removed 67 (48 requested) atoms. Cycle 37: After refmac, R = 0.1969 (Rfree = 0.000) for 12916 atoms. Found 40 (97 requested) and removed 59 (48 requested) atoms. Cycle 38: After refmac, R = 0.1966 (Rfree = 0.000) for 12884 atoms. Found 44 (97 requested) and removed 60 (48 requested) atoms. Cycle 39: After refmac, R = 0.1921 (Rfree = 0.000) for 12863 atoms. Found 40 (97 requested) and removed 55 (48 requested) atoms. Cycle 40: After refmac, R = 0.1918 (Rfree = 0.000) for 12837 atoms. Found 24 (97 requested) and removed 56 (48 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 13159 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 13183 seeds are put forward Round 1: 631 peptides, 124 chains. Longest chain 10 peptides. Score 0.316 Round 2: 695 peptides, 119 chains. Longest chain 16 peptides. Score 0.401 Round 3: 702 peptides, 116 chains. Longest chain 16 peptides. Score 0.420 Round 4: 716 peptides, 119 chains. Longest chain 16 peptides. Score 0.421 Round 5: 717 peptides, 118 chains. Longest chain 17 peptides. Score 0.426 Taking the results from Round 5 Chains 118, Residues 599, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 30485 restraints for refining 12960 atoms. 28164 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2052 (Rfree = 0.000) for 12960 atoms. Found 44 (97 requested) and removed 67 (48 requested) atoms. Cycle 42: After refmac, R = 0.1993 (Rfree = 0.000) for 12913 atoms. Found 22 (97 requested) and removed 56 (48 requested) atoms. Cycle 43: After refmac, R = 0.1958 (Rfree = 0.000) for 12854 atoms. Found 26 (97 requested) and removed 52 (48 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1903 (Rfree = 0.000) for 12822 atoms. Found 24 (96 requested) and removed 54 (48 requested) atoms. Cycle 45: After refmac, R = 0.1883 (Rfree = 0.000) for 12784 atoms. Found 25 (96 requested) and removed 54 (48 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 13091 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 13109 seeds are put forward Round 1: 612 peptides, 120 chains. Longest chain 10 peptides. Score 0.314 Round 2: 687 peptides, 119 chains. Longest chain 13 peptides. Score 0.394 Round 3: 705 peptides, 119 chains. Longest chain 13 peptides. Score 0.411 Round 4: 704 peptides, 115 chains. Longest chain 13 peptides. Score 0.426 Round 5: 701 peptides, 112 chains. Longest chain 15 peptides. Score 0.435 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 113, Residues 589, Estimated correctness of the model 0.0 % 5 chains (26 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 113 chains (589 residues) following loop building 5 chains (26 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23836 reflections ( 99.97 % complete ) and 30301 restraints for refining 12961 atoms. 28004 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2019 (Rfree = 0.000) for 12961 atoms. Found 0 (97 requested) and removed 48 (48 requested) atoms. Cycle 47: After refmac, R = 0.1932 (Rfree = 0.000) for 12897 atoms. Found 0 (97 requested) and removed 48 (48 requested) atoms. Cycle 48: After refmac, R = 0.1908 (Rfree = 0.000) for 12834 atoms. Found 0 (97 requested) and removed 48 (48 requested) atoms. Cycle 49: After refmac, R = 0.1859 (Rfree = 0.000) for 12774 atoms. TimeTaking 130.05