null Sun 23 Dec 22:22:49 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 1vkm-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-3.4-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/1vkm-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-3.4-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 ============================================================ Sun 23 Dec 22:22:58 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/1vkm-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-3.4-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 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-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: 19 Cell parameters: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.60 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 15780 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.2958 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2825 (Rfree = 0.000) for 15780 atoms. Found 113 (119 requested) and removed 199 (59 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.49 Search for helices and strands: 0 residues in 0 chains, 16063 seeds are put forward NCS extension: 0 residues added, 16063 seeds are put forward Round 1: 741 peptides, 142 chains. Longest chain 15 peptides. Score 0.351 Round 2: 961 peptides, 149 chains. Longest chain 21 peptides. Score 0.520 Round 3: 1050 peptides, 150 chains. Longest chain 24 peptides. Score 0.584 Round 4: 1067 peptides, 136 chains. Longest chain 24 peptides. Score 0.638 Round 5: 1105 peptides, 134 chains. Longest chain 22 peptides. Score 0.667 Taking the results from Round 5 Chains 142, Residues 971, Estimated correctness of the model 49.0 % 9 chains (78 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 28363 restraints for refining 12957 atoms. 24396 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2408 (Rfree = 0.000) for 12957 atoms. Found 54 (97 requested) and removed 110 (48 requested) atoms. Cycle 2: After refmac, R = 0.2281 (Rfree = 0.000) for 12713 atoms. Found 51 (97 requested) and removed 69 (48 requested) atoms. Cycle 3: After refmac, R = 0.2276 (Rfree = 0.000) for 12603 atoms. Found 38 (95 requested) and removed 74 (47 requested) atoms. Cycle 4: After refmac, R = 0.2218 (Rfree = 0.000) for 12528 atoms. Found 37 (94 requested) and removed 81 (47 requested) atoms. Cycle 5: After refmac, R = 0.1991 (Rfree = 0.000) for 12448 atoms. Found 23 (94 requested) and removed 58 (47 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.43 Search for helices and strands: 0 residues in 0 chains, 12848 seeds are put forward NCS extension: 5 residues added (11 deleted due to clashes), 12853 seeds are put forward Round 1: 963 peptides, 143 chains. Longest chain 21 peptides. Score 0.542 Round 2: 1071 peptides, 139 chains. Longest chain 24 peptides. Score 0.632 Round 3: 1100 peptides, 137 chains. Longest chain 23 peptides. Score 0.656 Round 4: 1122 peptides, 136 chains. Longest chain 23 peptides. Score 0.672 Round 5: 1096 peptides, 136 chains. Longest chain 27 peptides. Score 0.656 Taking the results from Round 4 Chains 142, Residues 986, Estimated correctness of the model 50.4 % 13 chains (145 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 27925 restraints for refining 12959 atoms. 23645 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2314 (Rfree = 0.000) for 12959 atoms. Found 68 (97 requested) and removed 114 (48 requested) atoms. Cycle 7: After refmac, R = 0.2205 (Rfree = 0.000) for 12849 atoms. Found 44 (97 requested) and removed 95 (48 requested) atoms. Cycle 8: After refmac, R = 0.2143 (Rfree = 0.000) for 12766 atoms. Found 24 (96 requested) and removed 72 (48 requested) atoms. Cycle 9: After refmac, R = 0.2090 (Rfree = 0.000) for 12696 atoms. Found 29 (96 requested) and removed 73 (48 requested) atoms. Cycle 10: After refmac, R = 0.2082 (Rfree = 0.000) for 12638 atoms. Found 26 (95 requested) and removed 68 (47 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.46 Search for helices and strands: 0 residues in 0 chains, 13076 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 13094 seeds are put forward Round 1: 916 peptides, 140 chains. Longest chain 19 peptides. Score 0.516 Round 2: 1031 peptides, 130 chains. Longest chain 32 peptides. Score 0.632 Round 3: 1065 peptides, 132 chains. Longest chain 22 peptides. Score 0.648 Round 4: 1058 peptides, 133 chains. Longest chain 28 peptides. Score 0.641 Round 5: 1079 peptides, 127 chains. Longest chain 25 peptides. Score 0.670 Taking the results from Round 5 Chains 130, Residues 952, Estimated correctness of the model 49.8 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29048 restraints for refining 12960 atoms. 25297 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2252 (Rfree = 0.000) for 12960 atoms. Found 54 (97 requested) and removed 92 (48 requested) atoms. Cycle 12: After refmac, R = 0.2150 (Rfree = 0.000) for 12892 atoms. Found 32 (97 requested) and removed 68 (48 requested) atoms. Cycle 13: After refmac, R = 0.2101 (Rfree = 0.000) for 12837 atoms. Found 39 (97 requested) and removed 87 (48 requested) atoms. Cycle 14: After refmac, R = 0.2071 (Rfree = 0.000) for 12769 atoms. Found 25 (96 requested) and removed 68 (48 requested) atoms. Cycle 15: After refmac, R = 0.2033 (Rfree = 0.000) for 12717 atoms. Found 26 (96 requested) and removed 61 (48 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 13094 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 13114 seeds are put forward Round 1: 904 peptides, 147 chains. Longest chain 25 peptides. Score 0.481 Round 2: 1026 peptides, 126 chains. Longest chain 25 peptides. Score 0.640 Round 3: 1010 peptides, 138 chains. Longest chain 25 peptides. Score 0.593 Round 4: 1032 peptides, 127 chains. Longest chain 25 peptides. Score 0.641 Round 5: 1020 peptides, 127 chains. Longest chain 26 peptides. Score 0.634 Taking the results from Round 4 Chains 129, Residues 905, Estimated correctness of the model 41.5 % 10 chains (86 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 28746 restraints for refining 12961 atoms. 25013 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2220 (Rfree = 0.000) for 12961 atoms. Found 51 (97 requested) and removed 89 (48 requested) atoms. Cycle 17: After refmac, R = 0.2088 (Rfree = 0.000) for 12891 atoms. Found 33 (97 requested) and removed 66 (48 requested) atoms. Cycle 18: After refmac, R = 0.2007 (Rfree = 0.000) for 12831 atoms. Found 50 (97 requested) and removed 65 (48 requested) atoms. Cycle 19: After refmac, R = 0.2002 (Rfree = 0.000) for 12802 atoms. Found 39 (96 requested) and removed 59 (48 requested) atoms. Cycle 20: After refmac, R = 0.1921 (Rfree = 0.000) for 12772 atoms. Found 23 (96 requested) and removed 54 (48 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 13141 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 13154 seeds are put forward Round 1: 886 peptides, 149 chains. Longest chain 21 peptides. Score 0.458 Round 2: 981 peptides, 142 chains. Longest chain 24 peptides. Score 0.559 Round 3: 982 peptides, 137 chains. Longest chain 26 peptides. Score 0.576 Round 4: 985 peptides, 130 chains. Longest chain 21 peptides. Score 0.601 Round 5: 958 peptides, 135 chains. Longest chain 21 peptides. Score 0.565 Taking the results from Round 4 Chains 133, Residues 855, Estimated correctness of the model 29.0 % 7 chains (66 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 28884 restraints for refining 12961 atoms. 25403 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2144 (Rfree = 0.000) for 12961 atoms. Found 41 (97 requested) and removed 74 (48 requested) atoms. Cycle 22: After refmac, R = 0.2047 (Rfree = 0.000) for 12900 atoms. Found 44 (97 requested) and removed 64 (48 requested) atoms. Cycle 23: After refmac, R = 0.1979 (Rfree = 0.000) for 12866 atoms. Found 36 (97 requested) and removed 63 (48 requested) atoms. Cycle 24: After refmac, R = 0.1973 (Rfree = 0.000) for 12826 atoms. Found 50 (96 requested) and removed 54 (48 requested) atoms. Cycle 25: After refmac, R = 0.1923 (Rfree = 0.000) for 12818 atoms. Found 26 (96 requested) and removed 52 (48 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 13168 seeds are put forward NCS extension: 10 residues added (7 deleted due to clashes), 13178 seeds are put forward Round 1: 836 peptides, 150 chains. Longest chain 21 peptides. Score 0.409 Round 2: 941 peptides, 139 chains. Longest chain 23 peptides. Score 0.539 Round 3: 960 peptides, 140 chains. Longest chain 24 peptides. Score 0.550 Round 4: 929 peptides, 134 chains. Longest chain 30 peptides. Score 0.547 Round 5: 925 peptides, 129 chains. Longest chain 23 peptides. Score 0.560 Taking the results from Round 5 Chains 131, Residues 796, Estimated correctness of the model 15.1 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29404 restraints for refining 12960 atoms. 26233 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2134 (Rfree = 0.000) for 12960 atoms. Found 60 (97 requested) and removed 58 (48 requested) atoms. Cycle 27: After refmac, R = 0.2042 (Rfree = 0.000) for 12924 atoms. Found 38 (97 requested) and removed 63 (48 requested) atoms. Cycle 28: After refmac, R = 0.1967 (Rfree = 0.000) for 12877 atoms. Found 30 (97 requested) and removed 56 (48 requested) atoms. Cycle 29: After refmac, R = 0.1903 (Rfree = 0.000) for 12844 atoms. Found 45 (97 requested) and removed 58 (48 requested) atoms. Cycle 30: After refmac, R = 0.1851 (Rfree = 0.000) for 12823 atoms. Found 26 (96 requested) and removed 58 (48 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 13198 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 13213 seeds are put forward Round 1: 749 peptides, 130 chains. Longest chain 16 peptides. Score 0.407 Round 2: 878 peptides, 139 chains. Longest chain 22 peptides. Score 0.488 Round 3: 857 peptides, 134 chains. Longest chain 18 peptides. Score 0.488 Round 4: 890 peptides, 130 chains. Longest chain 22 peptides. Score 0.530 Round 5: 882 peptides, 132 chains. Longest chain 22 peptides. Score 0.516 Taking the results from Round 4 Chains 134, Residues 760, Estimated correctness of the model 4.2 % 9 chains (67 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29273 restraints for refining 12961 atoms. 26165 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1992 (Rfree = 0.000) for 12961 atoms. Found 53 (97 requested) and removed 60 (48 requested) atoms. Cycle 32: After refmac, R = 0.1903 (Rfree = 0.000) for 12920 atoms. Found 33 (97 requested) and removed 56 (48 requested) atoms. Cycle 33: After refmac, R = 0.1930 (Rfree = 0.000) for 12882 atoms. Found 39 (97 requested) and removed 58 (48 requested) atoms. Cycle 34: After refmac, R = 0.1862 (Rfree = 0.000) for 12859 atoms. Found 37 (97 requested) and removed 55 (48 requested) atoms. Cycle 35: After refmac, R = 0.1889 (Rfree = 0.000) for 12832 atoms. Found 40 (96 requested) and removed 55 (48 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 13207 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 13222 seeds are put forward Round 1: 728 peptides, 136 chains. Longest chain 17 peptides. Score 0.363 Round 2: 810 peptides, 131 chains. Longest chain 21 peptides. Score 0.459 Round 3: 821 peptides, 127 chains. Longest chain 17 peptides. Score 0.484 Round 4: 836 peptides, 128 chains. Longest chain 24 peptides. Score 0.493 Round 5: 844 peptides, 122 chains. Longest chain 19 peptides. Score 0.521 Taking the results from Round 5 Chains 125, Residues 722, Estimated correctness of the model 0.8 % 5 chains (50 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29418 restraints for refining 12961 atoms. 26494 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2025 (Rfree = 0.000) for 12961 atoms. Found 49 (97 requested) and removed 70 (48 requested) atoms. Cycle 37: After refmac, R = 0.1955 (Rfree = 0.000) for 12915 atoms. Found 24 (97 requested) and removed 60 (48 requested) atoms. Cycle 38: After refmac, R = 0.1966 (Rfree = 0.000) for 12868 atoms. Found 37 (97 requested) and removed 62 (48 requested) atoms. Cycle 39: After refmac, R = 0.1893 (Rfree = 0.000) for 12833 atoms. Found 41 (96 requested) and removed 54 (48 requested) atoms. Cycle 40: After refmac, R = 0.1903 (Rfree = 0.000) for 12812 atoms. Found 35 (96 requested) and removed 53 (48 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 13172 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 13194 seeds are put forward Round 1: 701 peptides, 127 chains. Longest chain 17 peptides. Score 0.374 Round 2: 772 peptides, 111 chains. Longest chain 20 peptides. Score 0.502 Round 3: 801 peptides, 118 chains. Longest chain 23 peptides. Score 0.500 Round 4: 801 peptides, 114 chains. Longest chain 26 peptides. Score 0.515 Round 5: 804 peptides, 114 chains. Longest chain 22 peptides. Score 0.517 Taking the results from Round 5 Chains 115, Residues 690, Estimated correctness of the model 0.0 % 9 chains (43 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29721 restraints for refining 12962 atoms. 26964 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2065 (Rfree = 0.000) for 12962 atoms. Found 41 (97 requested) and removed 67 (48 requested) atoms. Cycle 42: After refmac, R = 0.2056 (Rfree = 0.000) for 12910 atoms. Found 42 (97 requested) and removed 65 (48 requested) atoms. Cycle 43: After refmac, R = 0.2016 (Rfree = 0.000) for 12878 atoms. Found 34 (97 requested) and removed 66 (48 requested) atoms. Cycle 44: After refmac, R = 0.1978 (Rfree = 0.000) for 12842 atoms. Found 27 (96 requested) and removed 57 (48 requested) atoms. Cycle 45: After refmac, R = 0.1968 (Rfree = 0.000) for 12805 atoms. Found 37 (96 requested) and removed 55 (48 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 13139 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 13162 seeds are put forward Round 1: 669 peptides, 126 chains. Longest chain 15 peptides. Score 0.346 Round 2: 753 peptides, 121 chains. Longest chain 17 peptides. Score 0.447 Round 3: 781 peptides, 120 chains. Longest chain 19 peptides. Score 0.476 Round 4: 764 peptides, 115 chains. Longest chain 18 peptides. Score 0.480 Round 5: 762 peptides, 118 chains. Longest chain 20 peptides. Score 0.467 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 116, Residues 649, Estimated correctness of the model 0.0 % 6 chains (48 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 116 chains (649 residues) following loop building 6 chains (48 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23836 reflections ( 99.97 % complete ) and 29505 restraints for refining 12962 atoms. 26885 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1996 (Rfree = 0.000) for 12962 atoms. Found 0 (97 requested) and removed 48 (48 requested) atoms. Cycle 47: After refmac, R = 0.1927 (Rfree = 0.000) for 12894 atoms. Found 0 (97 requested) and removed 48 (48 requested) atoms. Cycle 48: After refmac, R = 0.1956 (Rfree = 0.000) for 12828 atoms. Found 0 (96 requested) and removed 48 (48 requested) atoms. Cycle 49: After refmac, R = 0.1892 (Rfree = 0.000) for 12767 atoms. Found 0 (96 requested) and removed 48 (48 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:54:05 GMT 2018 Job finished. TimeTaking 151.27 Used memory is bytes: 8500456