null Mon 24 Dec 00:18:13 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 1vkd-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.6-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/1vkd-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.6-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 00:18:18 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/1vkd-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.6-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 1656 and 0 Target number of residues in the AU: 1656 Target solvent content: 0.6015 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-3.6-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: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 16224 target number of atoms Had to go as low as 0.70 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 3.600 Wilson plot Bfac: 53.16 26847 reflections ( 99.71 % complete ) and 0 restraints for refining 17849 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.2909 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2547 (Rfree = 0.000) for 17849 atoms. Found 114 (114 requested) and removed 108 (57 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 18042 seeds are put forward NCS extension: 0 residues added, 18042 seeds are put forward Round 1: 1025 peptides, 178 chains. Longest chain 13 peptides. Score 0.411 Round 2: 1222 peptides, 167 chains. Longest chain 19 peptides. Score 0.566 Round 3: 1325 peptides, 172 chains. Longest chain 22 peptides. Score 0.609 Round 4: 1352 peptides, 161 chains. Longest chain 30 peptides. Score 0.647 Round 5: 1369 peptides, 158 chains. Longest chain 28 peptides. Score 0.661 Taking the results from Round 5 Chains 166, Residues 1211, Estimated correctness of the model 37.0 % 22 chains (230 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 29266 restraints for refining 14705 atoms. 23702 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2289 (Rfree = 0.000) for 14705 atoms. Found 90 (94 requested) and removed 130 (47 requested) atoms. Cycle 2: After refmac, R = 0.2124 (Rfree = 0.000) for 14483 atoms. Found 52 (94 requested) and removed 71 (47 requested) atoms. Cycle 3: After refmac, R = 0.2062 (Rfree = 0.000) for 14390 atoms. Found 39 (92 requested) and removed 71 (46 requested) atoms. Cycle 4: After refmac, R = 0.1993 (Rfree = 0.000) for 14316 atoms. Found 22 (92 requested) and removed 63 (46 requested) atoms. Cycle 5: After refmac, R = 0.1937 (Rfree = 0.000) for 14239 atoms. Found 20 (91 requested) and removed 57 (45 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 14465 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 14491 seeds are put forward Round 1: 1220 peptides, 165 chains. Longest chain 28 peptides. Score 0.570 Round 2: 1311 peptides, 150 chains. Longest chain 28 peptides. Score 0.651 Round 3: 1331 peptides, 147 chains. Longest chain 33 peptides. Score 0.667 Round 4: 1369 peptides, 147 chains. Longest chain 30 peptides. Score 0.684 Round 5: 1392 peptides, 149 chains. Longest chain 39 peptides. Score 0.690 Taking the results from Round 5 Chains 161, Residues 1243, Estimated correctness of the model 46.5 % 15 chains (219 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 29776 restraints for refining 14704 atoms. 24088 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2280 (Rfree = 0.000) for 14704 atoms. Found 73 (94 requested) and removed 103 (47 requested) atoms. Cycle 7: After refmac, R = 0.2114 (Rfree = 0.000) for 14590 atoms. Found 39 (94 requested) and removed 72 (47 requested) atoms. Cycle 8: After refmac, R = 0.2038 (Rfree = 0.000) for 14528 atoms. Found 22 (93 requested) and removed 62 (46 requested) atoms. Cycle 9: After refmac, R = 0.2001 (Rfree = 0.000) for 14467 atoms. Found 19 (92 requested) and removed 55 (46 requested) atoms. Cycle 10: After refmac, R = 0.1968 (Rfree = 0.000) for 14418 atoms. Found 14 (92 requested) and removed 56 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 14638 seeds are put forward NCS extension: 6 residues added (12 deleted due to clashes), 14644 seeds are put forward Round 1: 1216 peptides, 177 chains. Longest chain 27 peptides. Score 0.537 Round 2: 1315 peptides, 156 chains. Longest chain 29 peptides. Score 0.640 Round 3: 1339 peptides, 160 chains. Longest chain 32 peptides. Score 0.643 Round 4: 1357 peptides, 153 chains. Longest chain 33 peptides. Score 0.666 Round 5: 1395 peptides, 150 chains. Longest chain 32 peptides. Score 0.689 Taking the results from Round 5 Chains 164, Residues 1245, Estimated correctness of the model 46.2 % 15 chains (195 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 30045 restraints for refining 14704 atoms. 24490 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2273 (Rfree = 0.000) for 14704 atoms. Found 62 (94 requested) and removed 115 (47 requested) atoms. Cycle 12: After refmac, R = 0.2061 (Rfree = 0.000) for 14585 atoms. Found 23 (93 requested) and removed 68 (46 requested) atoms. Cycle 13: After refmac, R = 0.1994 (Rfree = 0.000) for 14492 atoms. Found 19 (93 requested) and removed 59 (46 requested) atoms. Cycle 14: After refmac, R = 0.1987 (Rfree = 0.000) for 14429 atoms. Found 24 (92 requested) and removed 68 (46 requested) atoms. Cycle 15: After refmac, R = 0.1933 (Rfree = 0.000) for 14366 atoms. Found 22 (92 requested) and removed 56 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 14594 seeds are put forward NCS extension: 20 residues added (9 deleted due to clashes), 14614 seeds are put forward Round 1: 1227 peptides, 179 chains. Longest chain 23 peptides. Score 0.538 Round 2: 1320 peptides, 163 chains. Longest chain 36 peptides. Score 0.627 Round 3: 1347 peptides, 156 chains. Longest chain 39 peptides. Score 0.655 Round 4: 1310 peptides, 162 chains. Longest chain 26 peptides. Score 0.624 Round 5: 1339 peptides, 155 chains. Longest chain 28 peptides. Score 0.654 Taking the results from Round 3 Chains 163, Residues 1191, Estimated correctness of the model 34.9 % 10 chains (117 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 31181 restraints for refining 14707 atoms. 26104 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2169 (Rfree = 0.000) for 14707 atoms. Found 62 (94 requested) and removed 78 (47 requested) atoms. Cycle 17: After refmac, R = 0.2032 (Rfree = 0.000) for 14631 atoms. Found 25 (94 requested) and removed 62 (47 requested) atoms. Cycle 18: After refmac, R = 0.1986 (Rfree = 0.000) for 14559 atoms. Found 28 (93 requested) and removed 62 (46 requested) atoms. Cycle 19: After refmac, R = 0.1925 (Rfree = 0.000) for 14492 atoms. Found 24 (93 requested) and removed 60 (46 requested) atoms. Cycle 20: After refmac, R = 0.1891 (Rfree = 0.000) for 14433 atoms. Found 23 (92 requested) and removed 59 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 14648 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 14662 seeds are put forward Round 1: 1110 peptides, 169 chains. Longest chain 31 peptides. Score 0.494 Round 2: 1186 peptides, 146 chains. Longest chain 31 peptides. Score 0.598 Round 3: 1239 peptides, 155 chains. Longest chain 38 peptides. Score 0.604 Round 4: 1243 peptides, 148 chains. Longest chain 30 peptides. Score 0.622 Round 5: 1264 peptides, 168 chains. Longest chain 27 peptides. Score 0.586 Taking the results from Round 4 Chains 160, Residues 1095, Estimated correctness of the model 23.0 % 11 chains (142 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 31311 restraints for refining 14705 atoms. 26493 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2092 (Rfree = 0.000) for 14705 atoms. Found 67 (94 requested) and removed 86 (47 requested) atoms. Cycle 22: After refmac, R = 0.1951 (Rfree = 0.000) for 14619 atoms. Found 37 (94 requested) and removed 60 (47 requested) atoms. Cycle 23: After refmac, R = 0.1890 (Rfree = 0.000) for 14554 atoms. Found 35 (93 requested) and removed 62 (46 requested) atoms. Cycle 24: After refmac, R = 0.1848 (Rfree = 0.000) for 14494 atoms. Found 39 (93 requested) and removed 54 (46 requested) atoms. Cycle 25: After refmac, R = 0.1801 (Rfree = 0.000) for 14462 atoms. Found 22 (92 requested) and removed 53 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 14653 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 14666 seeds are put forward Round 1: 1081 peptides, 179 chains. Longest chain 18 peptides. Score 0.447 Round 2: 1215 peptides, 178 chains. Longest chain 24 peptides. Score 0.534 Round 3: 1181 peptides, 161 chains. Longest chain 38 peptides. Score 0.557 Round 4: 1212 peptides, 154 chains. Longest chain 22 peptides. Score 0.592 Round 5: 1228 peptides, 158 chains. Longest chain 26 peptides. Score 0.591 Taking the results from Round 4 Chains 159, Residues 1058, Estimated correctness of the model 11.5 % 14 chains (100 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 32208 restraints for refining 14707 atoms. 27813 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2075 (Rfree = 0.000) for 14707 atoms. Found 75 (94 requested) and removed 78 (47 requested) atoms. Cycle 27: After refmac, R = 0.1941 (Rfree = 0.000) for 14643 atoms. Found 47 (94 requested) and removed 64 (47 requested) atoms. Cycle 28: After refmac, R = 0.1879 (Rfree = 0.000) for 14584 atoms. Found 53 (93 requested) and removed 60 (46 requested) atoms. Cycle 29: After refmac, R = 0.1828 (Rfree = 0.000) for 14555 atoms. Found 48 (93 requested) and removed 58 (46 requested) atoms. Cycle 30: After refmac, R = 0.1787 (Rfree = 0.000) for 14515 atoms. Found 33 (93 requested) and removed 65 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 14678 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 14701 seeds are put forward Round 1: 1092 peptides, 185 chains. Longest chain 23 peptides. Score 0.437 Round 2: 1186 peptides, 176 chains. Longest chain 29 peptides. Score 0.522 Round 3: 1222 peptides, 172 chains. Longest chain 25 peptides. Score 0.553 Round 4: 1213 peptides, 169 chains. Longest chain 22 peptides. Score 0.556 Round 5: 1233 peptides, 172 chains. Longest chain 30 peptides. Score 0.559 Taking the results from Round 5 Chains 177, Residues 1061, Estimated correctness of the model 0.0 % 8 chains (86 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 31993 restraints for refining 14706 atoms. 27607 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2029 (Rfree = 0.000) for 14706 atoms. Found 60 (94 requested) and removed 69 (47 requested) atoms. Cycle 32: After refmac, R = 0.1922 (Rfree = 0.000) for 14625 atoms. Found 44 (94 requested) and removed 61 (47 requested) atoms. Cycle 33: After refmac, R = 0.1839 (Rfree = 0.000) for 14567 atoms. Found 44 (93 requested) and removed 66 (46 requested) atoms. Cycle 34: After refmac, R = 0.1768 (Rfree = 0.000) for 14520 atoms. Found 32 (93 requested) and removed 61 (46 requested) atoms. Cycle 35: After refmac, R = 0.1704 (Rfree = 0.000) for 14481 atoms. Found 28 (92 requested) and removed 58 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 14663 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 14675 seeds are put forward Round 1: 1013 peptides, 190 chains. Longest chain 13 peptides. Score 0.366 Round 2: 1147 peptides, 170 chains. Longest chain 28 peptides. Score 0.514 Round 3: 1149 peptides, 167 chains. Longest chain 22 peptides. Score 0.523 Round 4: 1132 peptides, 163 chains. Longest chain 27 peptides. Score 0.523 Round 5: 1118 peptides, 157 chains. Longest chain 26 peptides. Score 0.531 Taking the results from Round 5 Chains 164, Residues 961, Estimated correctness of the model 0.0 % 13 chains (106 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 32406 restraints for refining 14707 atoms. 28347 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1956 (Rfree = 0.000) for 14707 atoms. Found 84 (94 requested) and removed 79 (47 requested) atoms. Cycle 37: After refmac, R = 0.1772 (Rfree = 0.000) for 14670 atoms. Found 40 (94 requested) and removed 60 (47 requested) atoms. Cycle 38: After refmac, R = 0.1747 (Rfree = 0.000) for 14610 atoms. Found 32 (93 requested) and removed 67 (46 requested) atoms. Cycle 39: After refmac, R = 0.1693 (Rfree = 0.000) for 14550 atoms. Found 42 (93 requested) and removed 58 (46 requested) atoms. Cycle 40: After refmac, R = 0.1655 (Rfree = 0.000) for 14516 atoms. Found 30 (93 requested) and removed 56 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 14760 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 14783 seeds are put forward Round 1: 921 peptides, 166 chains. Longest chain 18 peptides. Score 0.374 Round 2: 1062 peptides, 159 chains. Longest chain 34 peptides. Score 0.491 Round 3: 1083 peptides, 155 chains. Longest chain 24 peptides. Score 0.515 Round 4: 1075 peptides, 148 chains. Longest chain 26 peptides. Score 0.529 Round 5: 1072 peptides, 156 chains. Longest chain 26 peptides. Score 0.506 Taking the results from Round 4 Chains 148, Residues 927, Estimated correctness of the model 0.0 % 11 chains (41 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 33366 restraints for refining 14705 atoms. 29720 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1910 (Rfree = 0.000) for 14705 atoms. Found 84 (94 requested) and removed 66 (47 requested) atoms. Cycle 42: After refmac, R = 0.1761 (Rfree = 0.000) for 14682 atoms. Found 41 (94 requested) and removed 60 (47 requested) atoms. Cycle 43: After refmac, R = 0.1728 (Rfree = 0.000) for 14634 atoms. Found 51 (94 requested) and removed 55 (47 requested) atoms. Cycle 44: After refmac, R = 0.1692 (Rfree = 0.000) for 14612 atoms. Found 44 (93 requested) and removed 53 (46 requested) atoms. Cycle 45: After refmac, R = 0.1671 (Rfree = 0.000) for 14584 atoms. Found 45 (93 requested) and removed 53 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 14800 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 14831 seeds are put forward Round 1: 885 peptides, 166 chains. Longest chain 17 peptides. Score 0.347 Round 2: 1005 peptides, 155 chains. Longest chain 26 peptides. Score 0.465 Round 3: 1014 peptides, 158 chains. Longest chain 22 peptides. Score 0.463 Round 4: 1027 peptides, 152 chains. Longest chain 22 peptides. Score 0.488 Round 5: 996 peptides, 149 chains. Longest chain 20 peptides. Score 0.477 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 153, Residues 875, Estimated correctness of the model 0.0 % 6 chains (31 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 153 chains (875 residues) following loop building 6 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26847 reflections ( 99.71 % complete ) and 33510 restraints for refining 14704 atoms. 30057 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1869 (Rfree = 0.000) for 14704 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 47: After refmac, R = 0.1843 (Rfree = 0.000) for 14611 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 48: After refmac, R = 0.1825 (Rfree = 0.000) for 14550 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 49: After refmac, R = 0.1732 (Rfree = 0.000) for 14485 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:02:30 GMT 2018 Job finished. TimeTaking 164.29 Used memory is bytes: 7870912