null Mon 24 Dec 00:45:55 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 1vkm-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.4-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/1vkm-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.4-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 00:46:00 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/1vkm-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.4-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 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-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: 19 Cell parameters: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.4-parrot-mrncs.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 15825 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.2965 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2889 (Rfree = 0.000) for 15825 atoms. Found 88 (119 requested) and removed 173 (59 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.49 Search for helices and strands: 0 residues in 0 chains, 16097 seeds are put forward NCS extension: 0 residues added, 16097 seeds are put forward Round 1: 767 peptides, 154 chains. Longest chain 11 peptides. Score 0.327 Round 2: 1003 peptides, 166 chains. Longest chain 19 peptides. Score 0.495 Round 3: 1045 peptides, 154 chains. Longest chain 22 peptides. Score 0.568 Round 4: 1065 peptides, 143 chains. Longest chain 27 peptides. Score 0.616 Round 5: 1116 peptides, 136 chains. Longest chain 35 peptides. Score 0.668 Taking the results from Round 5 Chains 141, Residues 980, Estimated correctness of the model 49.3 % 12 chains (156 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 27354 restraints for refining 12959 atoms. 23069 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2444 (Rfree = 0.000) for 12959 atoms. Found 76 (97 requested) and removed 106 (48 requested) atoms. Cycle 2: After refmac, R = 0.2344 (Rfree = 0.000) for 12755 atoms. Found 44 (97 requested) and removed 78 (48 requested) atoms. Cycle 3: After refmac, R = 0.2305 (Rfree = 0.000) for 12640 atoms. Found 33 (96 requested) and removed 73 (48 requested) atoms. Cycle 4: After refmac, R = 0.2228 (Rfree = 0.000) for 12556 atoms. Found 27 (95 requested) and removed 76 (47 requested) atoms. Cycle 5: After refmac, R = 0.2219 (Rfree = 0.000) for 12452 atoms. Found 30 (94 requested) and removed 66 (47 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.43 Search for helices and strands: 0 residues in 0 chains, 12873 seeds are put forward NCS extension: 15 residues added (10 deleted due to clashes), 12888 seeds are put forward Round 1: 963 peptides, 158 chains. Longest chain 21 peptides. Score 0.490 Round 2: 1048 peptides, 141 chains. Longest chain 27 peptides. Score 0.611 Round 3: 1043 peptides, 140 chains. Longest chain 31 peptides. Score 0.610 Round 4: 1081 peptides, 133 chains. Longest chain 25 peptides. Score 0.655 Round 5: 1069 peptides, 130 chains. Longest chain 33 peptides. Score 0.656 Taking the results from Round 5 Chains 134, Residues 939, Estimated correctness of the model 45.9 % 8 chains (122 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 28189 restraints for refining 12884 atoms. 24151 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2446 (Rfree = 0.000) for 12884 atoms. Found 50 (97 requested) and removed 114 (48 requested) atoms. Cycle 7: After refmac, R = 0.2347 (Rfree = 0.000) for 12764 atoms. Found 27 (96 requested) and removed 67 (48 requested) atoms. Cycle 8: After refmac, R = 0.2372 (Rfree = 0.000) for 12702 atoms. Found 36 (96 requested) and removed 77 (48 requested) atoms. Cycle 9: After refmac, R = 0.2295 (Rfree = 0.000) for 12636 atoms. Found 35 (95 requested) and removed 76 (47 requested) atoms. Cycle 10: After refmac, R = 0.2261 (Rfree = 0.000) for 12581 atoms. Found 34 (95 requested) and removed 68 (47 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.47 Search for helices and strands: 0 residues in 0 chains, 12963 seeds are put forward NCS extension: 29 residues added (9 deleted due to clashes), 12992 seeds are put forward Round 1: 951 peptides, 159 chains. Longest chain 19 peptides. Score 0.477 Round 2: 1037 peptides, 140 chains. Longest chain 23 peptides. Score 0.606 Round 3: 1061 peptides, 134 chains. Longest chain 35 peptides. Score 0.640 Round 4: 1064 peptides, 134 chains. Longest chain 24 peptides. Score 0.642 Round 5: 1078 peptides, 128 chains. Longest chain 25 peptides. Score 0.667 Taking the results from Round 5 Chains 135, Residues 950, Estimated correctness of the model 49.0 % 10 chains (100 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 28444 restraints for refining 12961 atoms. 24481 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2308 (Rfree = 0.000) for 12961 atoms. Found 53 (97 requested) and removed 107 (48 requested) atoms. Cycle 12: After refmac, R = 0.2206 (Rfree = 0.000) for 12861 atoms. Found 50 (97 requested) and removed 68 (48 requested) atoms. Cycle 13: After refmac, R = 0.2183 (Rfree = 0.000) for 12824 atoms. Found 51 (96 requested) and removed 78 (48 requested) atoms. Cycle 14: After refmac, R = 0.2127 (Rfree = 0.000) for 12781 atoms. Found 40 (96 requested) and removed 69 (48 requested) atoms. Cycle 15: After refmac, R = 0.1927 (Rfree = 0.000) for 12730 atoms. Found 11 (96 requested) and removed 59 (48 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 13110 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 13125 seeds are put forward Round 1: 932 peptides, 156 chains. Longest chain 16 peptides. Score 0.472 Round 2: 985 peptides, 138 chains. Longest chain 19 peptides. Score 0.575 Round 3: 1027 peptides, 135 chains. Longest chain 26 peptides. Score 0.614 Round 4: 1033 peptides, 128 chains. Longest chain 22 peptides. Score 0.639 Round 5: 980 peptides, 132 chains. Longest chain 26 peptides. Score 0.591 Taking the results from Round 4 Chains 132, Residues 905, Estimated correctness of the model 40.9 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29098 restraints for refining 12960 atoms. 25448 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2241 (Rfree = 0.000) for 12960 atoms. Found 68 (97 requested) and removed 78 (48 requested) atoms. Cycle 17: After refmac, R = 0.2123 (Rfree = 0.000) for 12921 atoms. Found 27 (97 requested) and removed 69 (48 requested) atoms. Cycle 18: After refmac, R = 0.2147 (Rfree = 0.000) for 12864 atoms. Found 37 (97 requested) and removed 68 (48 requested) atoms. Cycle 19: After refmac, R = 0.2146 (Rfree = 0.000) for 12815 atoms. Found 47 (96 requested) and removed 66 (48 requested) atoms. Cycle 20: After refmac, R = 0.1891 (Rfree = 0.000) for 12784 atoms. Found 18 (96 requested) and removed 53 (48 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.46 Search for helices and strands: 0 residues in 0 chains, 13156 seeds are put forward NCS extension: 10 residues added (7 deleted due to clashes), 13166 seeds are put forward Round 1: 847 peptides, 140 chains. Longest chain 24 peptides. Score 0.457 Round 2: 938 peptides, 130 chains. Longest chain 24 peptides. Score 0.567 Round 3: 971 peptides, 134 chains. Longest chain 23 peptides. Score 0.578 Round 4: 946 peptides, 127 chains. Longest chain 27 peptides. Score 0.583 Round 5: 943 peptides, 128 chains. Longest chain 24 peptides. Score 0.577 Taking the results from Round 4 Chains 130, Residues 819, Estimated correctness of the model 23.0 % 7 chains (78 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29262 restraints for refining 12962 atoms. 25867 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2218 (Rfree = 0.000) for 12962 atoms. Found 74 (97 requested) and removed 74 (48 requested) atoms. Cycle 22: After refmac, R = 0.2171 (Rfree = 0.000) for 12943 atoms. Found 60 (97 requested) and removed 65 (48 requested) atoms. Cycle 23: After refmac, R = 0.2089 (Rfree = 0.000) for 12907 atoms. Found 53 (97 requested) and removed 55 (48 requested) atoms. Cycle 24: After refmac, R = 0.2097 (Rfree = 0.000) for 12888 atoms. Found 56 (97 requested) and removed 56 (48 requested) atoms. Cycle 25: After refmac, R = 0.2030 (Rfree = 0.000) for 12881 atoms. Found 45 (97 requested) and removed 57 (48 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 13245 seeds are put forward NCS extension: 31 residues added (6 deleted due to clashes), 13276 seeds are put forward Round 1: 803 peptides, 143 chains. Longest chain 14 peptides. Score 0.406 Round 2: 927 peptides, 137 chains. Longest chain 20 peptides. Score 0.535 Round 3: 950 peptides, 133 chains. Longest chain 22 peptides. Score 0.566 Round 4: 936 peptides, 131 chains. Longest chain 28 peptides. Score 0.562 Round 5: 938 peptides, 126 chains. Longest chain 22 peptides. Score 0.580 Taking the results from Round 5 Chains 126, Residues 812, Estimated correctness of the model 22.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29545 restraints for refining 12961 atoms. 26329 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2264 (Rfree = 0.000) for 12961 atoms. Found 51 (97 requested) and removed 75 (48 requested) atoms. Cycle 27: After refmac, R = 0.2203 (Rfree = 0.000) for 12903 atoms. Found 68 (97 requested) and removed 62 (48 requested) atoms. Cycle 28: After refmac, R = 0.1988 (Rfree = 0.000) for 12895 atoms. Found 28 (97 requested) and removed 54 (48 requested) atoms. Cycle 29: After refmac, R = 0.1968 (Rfree = 0.000) for 12856 atoms. Found 17 (97 requested) and removed 52 (48 requested) atoms. Cycle 30: After refmac, R = 0.1980 (Rfree = 0.000) for 12820 atoms. Found 9 (96 requested) and removed 54 (48 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.46 Search for helices and strands: 0 residues in 0 chains, 13152 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 13167 seeds are put forward Round 1: 769 peptides, 143 chains. Longest chain 15 peptides. Score 0.374 Round 2: 848 peptides, 128 chains. Longest chain 23 peptides. Score 0.503 Round 3: 859 peptides, 129 chains. Longest chain 21 peptides. Score 0.508 Round 4: 827 peptides, 120 chains. Longest chain 18 peptides. Score 0.514 Round 5: 844 peptides, 121 chains. Longest chain 27 peptides. Score 0.525 Taking the results from Round 5 Chains 123, Residues 723, Estimated correctness of the model 2.3 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29996 restraints for refining 12961 atoms. 27069 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2132 (Rfree = 0.000) for 12961 atoms. Found 44 (97 requested) and removed 58 (48 requested) atoms. Cycle 32: After refmac, R = 0.2063 (Rfree = 0.000) for 12924 atoms. Found 59 (97 requested) and removed 61 (48 requested) atoms. Cycle 33: After refmac, R = 0.2051 (Rfree = 0.000) for 12906 atoms. Found 66 (97 requested) and removed 64 (48 requested) atoms. Cycle 34: After refmac, R = 0.1808 (Rfree = 0.000) for 12893 atoms. Found 30 (97 requested) and removed 60 (48 requested) atoms. Cycle 35: After refmac, R = 0.1876 (Rfree = 0.000) for 12846 atoms. Found 20 (97 requested) and removed 54 (48 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 13188 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 13218 seeds are put forward Round 1: 680 peptides, 129 chains. Longest chain 13 peptides. Score 0.345 Round 2: 822 peptides, 126 chains. Longest chain 17 peptides. Score 0.488 Round 3: 799 peptides, 116 chains. Longest chain 18 peptides. Score 0.506 Round 4: 788 peptides, 118 chains. Longest chain 20 peptides. Score 0.489 Round 5: 784 peptides, 115 chains. Longest chain 19 peptides. Score 0.497 Taking the results from Round 3 Chains 117, Residues 683, Estimated correctness of the model 0.0 % 6 chains (40 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29772 restraints for refining 12961 atoms. 27025 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2108 (Rfree = 0.000) for 12961 atoms. Found 41 (97 requested) and removed 63 (48 requested) atoms. Cycle 37: After refmac, R = 0.2147 (Rfree = 0.000) for 12912 atoms. Found 64 (97 requested) and removed 60 (48 requested) atoms. Cycle 38: After refmac, R = 0.2073 (Rfree = 0.000) for 12904 atoms. Found 54 (97 requested) and removed 58 (48 requested) atoms. Cycle 39: After refmac, R = 0.1828 (Rfree = 0.000) for 12891 atoms. Found 17 (97 requested) and removed 49 (48 requested) atoms. Cycle 40: After refmac, R = 0.1785 (Rfree = 0.000) for 12849 atoms. Found 11 (97 requested) and removed 52 (48 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.46 Search for helices and strands: 0 residues in 0 chains, 13177 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 13200 seeds are put forward Round 1: 721 peptides, 132 chains. Longest chain 14 peptides. Score 0.373 Round 2: 780 peptides, 119 chains. Longest chain 18 peptides. Score 0.478 Round 3: 800 peptides, 120 chains. Longest chain 20 peptides. Score 0.492 Round 4: 822 peptides, 118 chains. Longest chain 22 peptides. Score 0.518 Round 5: 812 peptides, 121 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 4 Chains 120, Residues 704, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 23836 reflections ( 99.97 % complete ) and 29932 restraints for refining 12962 atoms. 27139 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2137 (Rfree = 0.000) for 12962 atoms. Found 45 (97 requested) and removed 64 (48 requested) atoms. Cycle 42: After refmac, R = 0.2120 (Rfree = 0.000) for 12923 atoms. Found 45 (97 requested) and removed 53 (48 requested) atoms. Cycle 43: After refmac, R = 0.2134 (Rfree = 0.000) for 12902 atoms. Found 64 (97 requested) and removed 71 (48 requested) atoms. Cycle 44: After refmac, R = 0.2102 (Rfree = 0.000) for 12884 atoms. Found 38 (97 requested) and removed 62 (48 requested) atoms. Cycle 45: After refmac, R = 0.1903 (Rfree = 0.000) for 12848 atoms. Found 16 (97 requested) and removed 54 (48 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 13157 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 13173 seeds are put forward Round 1: 675 peptides, 121 chains. Longest chain 15 peptides. Score 0.373 Round 2: 756 peptides, 122 chains. Longest chain 17 peptides. Score 0.446 Round 3: 774 peptides, 120 chains. Longest chain 19 peptides. Score 0.469 Round 4: 757 peptides, 116 chains. Longest chain 17 peptides. Score 0.470 Round 5: 740 peptides, 119 chains. Longest chain 16 peptides. Score 0.443 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 116, Residues 641, Estimated correctness of the model 0.0 % 5 chains (42 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 107 B and 121 B 117 chains (648 residues) following loop building 4 chains (55 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23836 reflections ( 99.97 % complete ) and 29715 restraints for refining 12962 atoms. 27099 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2138 (Rfree = 0.000) for 12962 atoms. Found 0 (97 requested) and removed 48 (48 requested) atoms. Cycle 47: After refmac, R = 0.2023 (Rfree = 0.000) for 12892 atoms. Found 0 (97 requested) and removed 48 (48 requested) atoms. Cycle 48: After refmac, R = 0.1984 (Rfree = 0.000) for 12825 atoms. Found 0 (96 requested) and removed 48 (48 requested) atoms. Cycle 49: After refmac, R = 0.1965 (Rfree = 0.000) for 12772 atoms. Found 0 (96 requested) and removed 48 (48 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:18:06 GMT 2018 Job finished. TimeTaking 152.18 Used memory is bytes: 16699000