null Mon 24 Dec 07:28:27 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 1vkd-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-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/1vkd-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-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 07:28:31 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/1vkd-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-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 1692 and 0 Target number of residues in the AU: 1692 Target solvent content: 0.5928 Checking the provided sequence file Detected sequence length: 338 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 2028 Adjusted target solvent content: 0.51 Input MTZ file: 1vkd-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: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 16224 target number of atoms Had to go as low as 0.65 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: 127.440 3.400 Wilson plot Bfac: 49.74 31768 reflections ( 99.74 % complete ) and 0 restraints for refining 18053 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3149 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2654 (Rfree = 0.000) for 18053 atoms. Found 136 (136 requested) and removed 159 (68 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.00 Search for helices and strands: 0 residues in 0 chains, 18188 seeds are put forward NCS extension: 0 residues added, 18188 seeds are put forward Round 1: 921 peptides, 178 chains. Longest chain 12 peptides. Score 0.336 Round 2: 1100 peptides, 184 chains. Longest chain 19 peptides. Score 0.445 Round 3: 1164 peptides, 179 chains. Longest chain 18 peptides. Score 0.500 Round 4: 1225 peptides, 180 chains. Longest chain 22 peptides. Score 0.534 Round 5: 1224 peptides, 183 chains. Longest chain 18 peptides. Score 0.526 Taking the results from Round 4 Chains 187, Residues 1045, Estimated correctness of the model 5.7 % 17 chains (103 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 31332 restraints for refining 14750 atoms. 27030 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2443 (Rfree = 0.000) for 14750 atoms. Found 103 (111 requested) and removed 122 (55 requested) atoms. Cycle 2: After refmac, R = 0.2304 (Rfree = 0.000) for 14566 atoms. Found 61 (111 requested) and removed 76 (55 requested) atoms. Cycle 3: After refmac, R = 0.2267 (Rfree = 0.000) for 14500 atoms. Found 39 (109 requested) and removed 67 (54 requested) atoms. Cycle 4: After refmac, R = 0.2182 (Rfree = 0.000) for 14415 atoms. Found 36 (109 requested) and removed 66 (54 requested) atoms. Cycle 5: After refmac, R = 0.2137 (Rfree = 0.000) for 14343 atoms. Found 30 (108 requested) and removed 67 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 14605 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 14622 seeds are put forward Round 1: 1099 peptides, 187 chains. Longest chain 17 peptides. Score 0.436 Round 2: 1209 peptides, 169 chains. Longest chain 21 peptides. Score 0.553 Round 3: 1288 peptides, 183 chains. Longest chain 24 peptides. Score 0.563 Round 4: 1251 peptides, 167 chains. Longest chain 24 peptides. Score 0.582 Round 5: 1251 peptides, 166 chains. Longest chain 24 peptides. Score 0.584 Taking the results from Round 5 Chains 173, Residues 1085, Estimated correctness of the model 23.4 % 17 chains (135 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 31734 restraints for refining 14751 atoms. 27117 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2396 (Rfree = 0.000) for 14751 atoms. Found 111 (111 requested) and removed 116 (55 requested) atoms. Cycle 7: After refmac, R = 0.2212 (Rfree = 0.000) for 14670 atoms. Found 37 (111 requested) and removed 71 (55 requested) atoms. Cycle 8: After refmac, R = 0.2140 (Rfree = 0.000) for 14603 atoms. Found 27 (110 requested) and removed 60 (55 requested) atoms. Cycle 9: After refmac, R = 0.2095 (Rfree = 0.000) for 14550 atoms. Found 30 (110 requested) and removed 64 (55 requested) atoms. Cycle 10: After refmac, R = 0.2057 (Rfree = 0.000) for 14499 atoms. Found 22 (109 requested) and removed 59 (54 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.05 Search for helices and strands: 0 residues in 0 chains, 14680 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 14702 seeds are put forward Round 1: 1131 peptides, 177 chains. Longest chain 24 peptides. Score 0.485 Round 2: 1295 peptides, 180 chains. Longest chain 31 peptides. Score 0.574 Round 3: 1266 peptides, 169 chains. Longest chain 28 peptides. Score 0.585 Round 4: 1277 peptides, 164 chains. Longest chain 29 peptides. Score 0.603 Round 5: 1267 peptides, 164 chains. Longest chain 30 peptides. Score 0.598 Taking the results from Round 4 Chains 170, Residues 1113, Estimated correctness of the model 29.7 % 13 chains (130 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 31558 restraints for refining 14748 atoms. 26774 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2351 (Rfree = 0.000) for 14748 atoms. Found 111 (111 requested) and removed 89 (55 requested) atoms. Cycle 12: After refmac, R = 0.2172 (Rfree = 0.000) for 14706 atoms. Found 41 (111 requested) and removed 65 (55 requested) atoms. Cycle 13: After refmac, R = 0.2116 (Rfree = 0.000) for 14659 atoms. Found 28 (110 requested) and removed 63 (55 requested) atoms. Cycle 14: After refmac, R = 0.2087 (Rfree = 0.000) for 14611 atoms. Found 30 (110 requested) and removed 60 (55 requested) atoms. Cycle 15: After refmac, R = 0.2068 (Rfree = 0.000) for 14559 atoms. Found 25 (110 requested) and removed 62 (55 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 3.02 Search for helices and strands: 0 residues in 0 chains, 14714 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 14745 seeds are put forward Round 1: 1133 peptides, 184 chains. Longest chain 30 peptides. Score 0.467 Round 2: 1258 peptides, 172 chains. Longest chain 32 peptides. Score 0.573 Round 3: 1268 peptides, 169 chains. Longest chain 22 peptides. Score 0.586 Round 4: 1238 peptides, 165 chains. Longest chain 24 peptides. Score 0.579 Round 5: 1258 peptides, 164 chains. Longest chain 24 peptides. Score 0.593 Taking the results from Round 5 Chains 166, Residues 1094, Estimated correctness of the model 26.4 % 11 chains (80 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 31960 restraints for refining 14750 atoms. 27486 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2324 (Rfree = 0.000) for 14750 atoms. Found 101 (111 requested) and removed 88 (55 requested) atoms. Cycle 17: After refmac, R = 0.2159 (Rfree = 0.000) for 14711 atoms. Found 53 (111 requested) and removed 68 (55 requested) atoms. Cycle 18: After refmac, R = 0.2092 (Rfree = 0.000) for 14664 atoms. Found 36 (110 requested) and removed 72 (55 requested) atoms. Cycle 19: After refmac, R = 0.2042 (Rfree = 0.000) for 14616 atoms. Found 27 (110 requested) and removed 59 (55 requested) atoms. Cycle 20: After refmac, R = 0.2007 (Rfree = 0.000) for 14578 atoms. Found 21 (110 requested) and removed 56 (55 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 14748 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 14777 seeds are put forward Round 1: 1118 peptides, 182 chains. Longest chain 28 peptides. Score 0.462 Round 2: 1209 peptides, 166 chains. Longest chain 24 peptides. Score 0.561 Round 3: 1224 peptides, 167 chains. Longest chain 24 peptides. Score 0.567 Round 4: 1255 peptides, 164 chains. Longest chain 24 peptides. Score 0.591 Round 5: 1228 peptides, 153 chains. Longest chain 24 peptides. Score 0.603 Taking the results from Round 5 Chains 160, Residues 1075, Estimated correctness of the model 29.7 % 11 chains (129 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 31371 restraints for refining 14751 atoms. 26707 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2267 (Rfree = 0.000) for 14751 atoms. Found 78 (111 requested) and removed 94 (55 requested) atoms. Cycle 22: After refmac, R = 0.2103 (Rfree = 0.000) for 14671 atoms. Found 30 (111 requested) and removed 71 (55 requested) atoms. Cycle 23: After refmac, R = 0.2066 (Rfree = 0.000) for 14601 atoms. Found 36 (110 requested) and removed 68 (55 requested) atoms. Cycle 24: After refmac, R = 0.2017 (Rfree = 0.000) for 14553 atoms. Found 28 (110 requested) and removed 62 (55 requested) atoms. Cycle 25: After refmac, R = 0.2010 (Rfree = 0.000) for 14499 atoms. Found 34 (109 requested) and removed 56 (54 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.05 Search for helices and strands: 0 residues in 0 chains, 14682 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 14707 seeds are put forward Round 1: 1057 peptides, 180 chains. Longest chain 18 peptides. Score 0.427 Round 2: 1139 peptides, 162 chains. Longest chain 20 peptides. Score 0.530 Round 3: 1203 peptides, 163 chains. Longest chain 21 peptides. Score 0.565 Round 4: 1183 peptides, 161 chains. Longest chain 24 peptides. Score 0.559 Round 5: 1221 peptides, 160 chains. Longest chain 23 peptides. Score 0.582 Taking the results from Round 5 Chains 168, Residues 1061, Estimated correctness of the model 22.7 % 12 chains (96 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 31781 restraints for refining 14751 atoms. 27373 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2217 (Rfree = 0.000) for 14751 atoms. Found 85 (111 requested) and removed 83 (55 requested) atoms. Cycle 27: After refmac, R = 0.2049 (Rfree = 0.000) for 14706 atoms. Found 33 (111 requested) and removed 67 (55 requested) atoms. Cycle 28: After refmac, R = 0.2032 (Rfree = 0.000) for 14644 atoms. Found 36 (110 requested) and removed 66 (55 requested) atoms. Cycle 29: After refmac, R = 0.2006 (Rfree = 0.000) for 14598 atoms. Found 44 (110 requested) and removed 66 (55 requested) atoms. Cycle 30: After refmac, R = 0.1988 (Rfree = 0.000) for 14565 atoms. Found 33 (110 requested) and removed 59 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 14754 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 14779 seeds are put forward Round 1: 986 peptides, 178 chains. Longest chain 16 peptides. Score 0.384 Round 2: 1083 peptides, 162 chains. Longest chain 23 peptides. Score 0.496 Round 3: 1133 peptides, 155 chains. Longest chain 26 peptides. Score 0.545 Round 4: 1129 peptides, 159 chains. Longest chain 19 peptides. Score 0.532 Round 5: 1157 peptides, 160 chains. Longest chain 28 peptides. Score 0.546 Taking the results from Round 5 Chains 165, Residues 997, Estimated correctness of the model 10.1 % 13 chains (118 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 31883 restraints for refining 14750 atoms. 27589 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2199 (Rfree = 0.000) for 14750 atoms. Found 90 (111 requested) and removed 75 (55 requested) atoms. Cycle 32: After refmac, R = 0.2073 (Rfree = 0.000) for 14729 atoms. Found 39 (111 requested) and removed 71 (55 requested) atoms. Cycle 33: After refmac, R = 0.2065 (Rfree = 0.000) for 14675 atoms. Found 35 (110 requested) and removed 61 (55 requested) atoms. Cycle 34: After refmac, R = 0.2032 (Rfree = 0.000) for 14635 atoms. Found 32 (110 requested) and removed 61 (55 requested) atoms. Cycle 35: After refmac, R = 0.2000 (Rfree = 0.000) for 14596 atoms. Found 35 (110 requested) and removed 57 (55 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 14757 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 14773 seeds are put forward Round 1: 955 peptides, 167 chains. Longest chain 15 peptides. Score 0.395 Round 2: 1075 peptides, 153 chains. Longest chain 20 peptides. Score 0.516 Round 3: 1062 peptides, 157 chains. Longest chain 20 peptides. Score 0.496 Round 4: 1057 peptides, 146 chains. Longest chain 21 peptides. Score 0.524 Round 5: 1026 peptides, 146 chains. Longest chain 21 peptides. Score 0.505 Taking the results from Round 4 Chains 146, Residues 911, Estimated correctness of the model 1.9 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 33044 restraints for refining 14751 atoms. 29443 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2165 (Rfree = 0.000) for 14751 atoms. Found 81 (111 requested) and removed 70 (55 requested) atoms. Cycle 37: After refmac, R = 0.2034 (Rfree = 0.000) for 14732 atoms. Found 35 (111 requested) and removed 62 (55 requested) atoms. Cycle 38: After refmac, R = 0.2025 (Rfree = 0.000) for 14688 atoms. Found 31 (111 requested) and removed 56 (55 requested) atoms. Cycle 39: After refmac, R = 0.1997 (Rfree = 0.000) for 14655 atoms. Found 26 (110 requested) and removed 56 (55 requested) atoms. Cycle 40: After refmac, R = 0.1942 (Rfree = 0.000) for 14611 atoms. Found 37 (110 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 3.01 Search for helices and strands: 0 residues in 0 chains, 14738 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 14755 seeds are put forward Round 1: 914 peptides, 168 chains. Longest chain 16 peptides. Score 0.362 Round 2: 1020 peptides, 153 chains. Longest chain 20 peptides. Score 0.481 Round 3: 1022 peptides, 159 chains. Longest chain 15 peptides. Score 0.465 Round 4: 1030 peptides, 148 chains. Longest chain 23 peptides. Score 0.501 Round 5: 1011 peptides, 148 chains. Longest chain 20 peptides. Score 0.489 Taking the results from Round 4 Chains 151, Residues 882, Estimated correctness of the model 0.0 % 8 chains (61 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 32985 restraints for refining 14751 atoms. 29365 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2138 (Rfree = 0.000) for 14751 atoms. Found 72 (111 requested) and removed 70 (55 requested) atoms. Cycle 42: After refmac, R = 0.2012 (Rfree = 0.000) for 14722 atoms. Found 24 (111 requested) and removed 60 (55 requested) atoms. Cycle 43: After refmac, R = 0.2015 (Rfree = 0.000) for 14672 atoms. Found 37 (110 requested) and removed 61 (55 requested) atoms. Cycle 44: After refmac, R = 0.2014 (Rfree = 0.000) for 14635 atoms. Found 33 (110 requested) and removed 63 (55 requested) atoms. Cycle 45: After refmac, R = 0.1984 (Rfree = 0.000) for 14589 atoms. Found 25 (110 requested) and removed 60 (55 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 3.01 Search for helices and strands: 0 residues in 0 chains, 14718 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 14740 seeds are put forward Round 1: 910 peptides, 172 chains. Longest chain 14 peptides. Score 0.347 Round 2: 997 peptides, 164 chains. Longest chain 16 peptides. Score 0.434 Round 3: 998 peptides, 164 chains. Longest chain 15 peptides. Score 0.434 Round 4: 1035 peptides, 158 chains. Longest chain 22 peptides. Score 0.476 Round 5: 1032 peptides, 158 chains. Longest chain 18 peptides. Score 0.474 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 159, Residues 877, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 303 B and 311 B 157 chains (877 residues) following loop building 5 chains (37 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 31768 reflections ( 99.74 % complete ) and 33020 restraints for refining 14750 atoms. 29597 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2071 (Rfree = 0.000) for 14750 atoms. Found 0 (111 requested) and removed 55 (55 requested) atoms. Cycle 47: After refmac, R = 0.1994 (Rfree = 0.000) for 14661 atoms. Found 0 (110 requested) and removed 55 (55 requested) atoms. Cycle 48: After refmac, R = 0.2017 (Rfree = 0.000) for 14595 atoms. Found 0 (110 requested) and removed 55 (55 requested) atoms. Cycle 49: After refmac, R = 0.2016 (Rfree = 0.000) for 14518 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:53:46 GMT 2018 Job finished. TimeTaking 145.32 Used memory is bytes: 24550664