null Mon 24 Dec 00:34:45 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-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-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-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 00:34:49 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-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-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 1613 and 0 Target number of residues in the AU: 1613 Target solvent content: 0.6118 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 57.67 22890 reflections ( 99.67 % complete ) and 0 restraints for refining 17855 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.2980 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2793 (Rfree = 0.000) for 17855 atoms. Found 98 (98 requested) and removed 83 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 18026 seeds are put forward NCS extension: 0 residues added, 18026 seeds are put forward Round 1: 944 peptides, 180 chains. Longest chain 15 peptides. Score 0.347 Round 2: 1187 peptides, 183 chains. Longest chain 17 peptides. Score 0.504 Round 3: 1231 peptides, 162 chains. Longest chain 31 peptides. Score 0.583 Round 4: 1249 peptides, 163 chains. Longest chain 20 peptides. Score 0.590 Round 5: 1309 peptides, 162 chains. Longest chain 22 peptides. Score 0.624 Taking the results from Round 5 Chains 169, Residues 1147, Estimated correctness of the model 9.7 % 17 chains (103 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 31707 restraints for refining 14674 atoms. 26990 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2286 (Rfree = 0.000) for 14674 atoms. Found 66 (80 requested) and removed 97 (40 requested) atoms. Cycle 2: After refmac, R = 0.2129 (Rfree = 0.000) for 14439 atoms. Found 45 (80 requested) and removed 78 (40 requested) atoms. Cycle 3: After refmac, R = 0.2045 (Rfree = 0.000) for 14338 atoms. Found 27 (79 requested) and removed 64 (39 requested) atoms. Cycle 4: After refmac, R = 0.1986 (Rfree = 0.000) for 14270 atoms. Found 20 (78 requested) and removed 51 (39 requested) atoms. Cycle 5: After refmac, R = 0.1955 (Rfree = 0.000) for 14213 atoms. Found 18 (78 requested) and removed 56 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 14482 seeds are put forward NCS extension: 16 residues added (7 deleted due to clashes), 14498 seeds are put forward Round 1: 1155 peptides, 182 chains. Longest chain 17 peptides. Score 0.486 Round 2: 1248 peptides, 166 chains. Longest chain 20 peptides. Score 0.582 Round 3: 1294 peptides, 162 chains. Longest chain 26 peptides. Score 0.616 Round 4: 1271 peptides, 160 chains. Longest chain 27 peptides. Score 0.609 Round 5: 1272 peptides, 161 chains. Longest chain 29 peptides. Score 0.607 Taking the results from Round 3 Chains 169, Residues 1132, Estimated correctness of the model 6.2 % 12 chains (123 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 31528 restraints for refining 14672 atoms. 26677 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2189 (Rfree = 0.000) for 14672 atoms. Found 59 (80 requested) and removed 99 (40 requested) atoms. Cycle 7: After refmac, R = 0.2073 (Rfree = 0.000) for 14492 atoms. Found 33 (80 requested) and removed 67 (40 requested) atoms. Cycle 8: After refmac, R = 0.2022 (Rfree = 0.000) for 14400 atoms. Found 19 (79 requested) and removed 53 (39 requested) atoms. Cycle 9: After refmac, R = 0.2025 (Rfree = 0.000) for 14336 atoms. Found 21 (79 requested) and removed 66 (39 requested) atoms. Cycle 10: After refmac, R = 0.2018 (Rfree = 0.000) for 14265 atoms. Found 17 (78 requested) and removed 67 (39 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 14473 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 14487 seeds are put forward Round 1: 1147 peptides, 180 chains. Longest chain 16 peptides. Score 0.487 Round 2: 1243 peptides, 167 chains. Longest chain 22 peptides. Score 0.577 Round 3: 1280 peptides, 157 chains. Longest chain 23 peptides. Score 0.620 Round 4: 1298 peptides, 155 chains. Longest chain 26 peptides. Score 0.634 Round 5: 1278 peptides, 158 chains. Longest chain 20 peptides. Score 0.617 Taking the results from Round 4 Chains 161, Residues 1143, Estimated correctness of the model 14.1 % 9 chains (66 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 32309 restraints for refining 14673 atoms. 27684 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2195 (Rfree = 0.000) for 14673 atoms. Found 64 (80 requested) and removed 83 (40 requested) atoms. Cycle 12: After refmac, R = 0.2024 (Rfree = 0.000) for 14549 atoms. Found 34 (80 requested) and removed 66 (40 requested) atoms. Cycle 13: After refmac, R = 0.1943 (Rfree = 0.000) for 14475 atoms. Found 25 (79 requested) and removed 65 (39 requested) atoms. Cycle 14: After refmac, R = 0.1910 (Rfree = 0.000) for 14408 atoms. Found 31 (79 requested) and removed 63 (39 requested) atoms. Cycle 15: After refmac, R = 0.1881 (Rfree = 0.000) for 14358 atoms. Found 24 (79 requested) and removed 67 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 14525 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 14552 seeds are put forward Round 1: 1084 peptides, 183 chains. Longest chain 19 peptides. Score 0.437 Round 2: 1155 peptides, 163 chains. Longest chain 21 peptides. Score 0.537 Round 3: 1211 peptides, 162 chains. Longest chain 33 peptides. Score 0.572 Round 4: 1216 peptides, 163 chains. Longest chain 24 peptides. Score 0.572 Round 5: 1203 peptides, 151 chains. Longest chain 26 peptides. Score 0.595 Taking the results from Round 5 Chains 160, Residues 1052, Estimated correctness of the model 0.0 % 10 chains (92 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 32385 restraints for refining 14674 atoms. 28031 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2114 (Rfree = 0.000) for 14674 atoms. Found 76 (80 requested) and removed 87 (40 requested) atoms. Cycle 17: After refmac, R = 0.1931 (Rfree = 0.000) for 14581 atoms. Found 27 (80 requested) and removed 64 (40 requested) atoms. Cycle 18: After refmac, R = 0.1886 (Rfree = 0.000) for 14506 atoms. Found 29 (79 requested) and removed 66 (39 requested) atoms. Cycle 19: After refmac, R = 0.1856 (Rfree = 0.000) for 14445 atoms. Found 26 (79 requested) and removed 59 (39 requested) atoms. Cycle 20: After refmac, R = 0.1822 (Rfree = 0.000) for 14396 atoms. Found 22 (79 requested) and removed 60 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 14621 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 14633 seeds are put forward Round 1: 999 peptides, 175 chains. Longest chain 15 peptides. Score 0.402 Round 2: 1131 peptides, 164 chains. Longest chain 21 peptides. Score 0.520 Round 3: 1161 peptides, 165 chains. Longest chain 20 peptides. Score 0.536 Round 4: 1199 peptides, 172 chains. Longest chain 21 peptides. Score 0.540 Round 5: 1214 peptides, 164 chains. Longest chain 22 peptides. Score 0.569 Taking the results from Round 5 Chains 172, Residues 1050, Estimated correctness of the model 0.0 % 10 chains (85 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 32611 restraints for refining 14672 atoms. 28292 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2103 (Rfree = 0.000) for 14672 atoms. Found 45 (80 requested) and removed 83 (40 requested) atoms. Cycle 22: After refmac, R = 0.2005 (Rfree = 0.000) for 14556 atoms. Found 53 (80 requested) and removed 64 (40 requested) atoms. Cycle 23: After refmac, R = 0.1884 (Rfree = 0.000) for 14485 atoms. Found 31 (79 requested) and removed 61 (39 requested) atoms. Cycle 24: After refmac, R = 0.1814 (Rfree = 0.000) for 14413 atoms. Found 28 (79 requested) and removed 48 (39 requested) atoms. Cycle 25: After refmac, R = 0.1749 (Rfree = 0.000) for 14363 atoms. Found 24 (79 requested) and removed 50 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 14579 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 14599 seeds are put forward Round 1: 1027 peptides, 189 chains. Longest chain 16 peptides. Score 0.380 Round 2: 1098 peptides, 167 chains. Longest chain 18 peptides. Score 0.492 Round 3: 1171 peptides, 173 chains. Longest chain 17 peptides. Score 0.520 Round 4: 1175 peptides, 167 chains. Longest chain 19 peptides. Score 0.539 Round 5: 1184 peptides, 167 chains. Longest chain 18 peptides. Score 0.544 Taking the results from Round 5 Chains 172, Residues 1017, Estimated correctness of the model 0.0 % 9 chains (88 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 32651 restraints for refining 14675 atoms. 28382 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2073 (Rfree = 0.000) for 14675 atoms. Found 54 (80 requested) and removed 79 (40 requested) atoms. Cycle 27: After refmac, R = 0.1939 (Rfree = 0.000) for 14572 atoms. Found 28 (80 requested) and removed 66 (40 requested) atoms. Cycle 28: After refmac, R = 0.1940 (Rfree = 0.000) for 14492 atoms. Found 37 (79 requested) and removed 60 (39 requested) atoms. Cycle 29: After refmac, R = 0.1872 (Rfree = 0.000) for 14450 atoms. Found 25 (79 requested) and removed 55 (39 requested) atoms. Cycle 30: After refmac, R = 0.1813 (Rfree = 0.000) for 14414 atoms. Found 17 (79 requested) and removed 63 (39 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 14623 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 14638 seeds are put forward Round 1: 987 peptides, 173 chains. Longest chain 14 peptides. Score 0.400 Round 2: 1062 peptides, 161 chains. Longest chain 21 peptides. Score 0.485 Round 3: 1098 peptides, 166 chains. Longest chain 18 peptides. Score 0.494 Round 4: 1075 peptides, 148 chains. Longest chain 22 peptides. Score 0.529 Round 5: 1050 peptides, 151 chains. Longest chain 22 peptides. Score 0.506 Taking the results from Round 4 Chains 154, Residues 927, Estimated correctness of the model 0.0 % 7 chains (61 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33449 restraints for refining 14674 atoms. 29678 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2087 (Rfree = 0.000) for 14674 atoms. Found 55 (80 requested) and removed 81 (40 requested) atoms. Cycle 32: After refmac, R = 0.1998 (Rfree = 0.000) for 14587 atoms. Found 58 (80 requested) and removed 72 (40 requested) atoms. Cycle 33: After refmac, R = 0.1870 (Rfree = 0.000) for 14552 atoms. Found 45 (80 requested) and removed 54 (40 requested) atoms. Cycle 34: After refmac, R = 0.1755 (Rfree = 0.000) for 14524 atoms. Found 16 (79 requested) and removed 58 (39 requested) atoms. Cycle 35: After refmac, R = 0.1718 (Rfree = 0.000) for 14467 atoms. Found 39 (79 requested) and removed 48 (39 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 14690 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 14708 seeds are put forward Round 1: 934 peptides, 165 chains. Longest chain 21 peptides. Score 0.386 Round 2: 1014 peptides, 154 chains. Longest chain 19 peptides. Score 0.474 Round 3: 1051 peptides, 152 chains. Longest chain 23 peptides. Score 0.504 Round 4: 1002 peptides, 149 chains. Longest chain 17 peptides. Score 0.481 Round 5: 1016 peptides, 144 chains. Longest chain 20 peptides. Score 0.504 Taking the results from Round 5 Chains 149, Residues 872, Estimated correctness of the model 0.0 % 7 chains (48 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33900 restraints for refining 14673 atoms. 30403 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2044 (Rfree = 0.000) for 14673 atoms. Found 63 (80 requested) and removed 75 (40 requested) atoms. Cycle 37: After refmac, R = 0.1887 (Rfree = 0.000) for 14608 atoms. Found 24 (80 requested) and removed 60 (40 requested) atoms. Cycle 38: After refmac, R = 0.1823 (Rfree = 0.000) for 14544 atoms. Found 23 (80 requested) and removed 57 (40 requested) atoms. Cycle 39: After refmac, R = 0.1768 (Rfree = 0.000) for 14481 atoms. Found 32 (79 requested) and removed 50 (39 requested) atoms. Cycle 40: After refmac, R = 0.1747 (Rfree = 0.000) for 14443 atoms. Found 32 (79 requested) and removed 46 (39 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 14668 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 14693 seeds are put forward Round 1: 830 peptides, 156 chains. Longest chain 14 peptides. Score 0.338 Round 2: 948 peptides, 153 chains. Longest chain 16 peptides. Score 0.433 Round 3: 951 peptides, 155 chains. Longest chain 20 peptides. Score 0.429 Round 4: 976 peptides, 150 chains. Longest chain 17 peptides. Score 0.461 Round 5: 955 peptides, 143 chains. Longest chain 21 peptides. Score 0.467 Taking the results from Round 5 Chains 147, Residues 812, Estimated correctness of the model 0.0 % 9 chains (67 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33585 restraints for refining 14673 atoms. 30247 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1904 (Rfree = 0.000) for 14673 atoms. Found 49 (80 requested) and removed 70 (40 requested) atoms. Cycle 42: After refmac, R = 0.1817 (Rfree = 0.000) for 14599 atoms. Found 29 (80 requested) and removed 55 (40 requested) atoms. Cycle 43: After refmac, R = 0.1776 (Rfree = 0.000) for 14548 atoms. Found 43 (80 requested) and removed 57 (40 requested) atoms. Cycle 44: After refmac, R = 0.1743 (Rfree = 0.000) for 14519 atoms. Found 31 (79 requested) and removed 53 (39 requested) atoms. Cycle 45: After refmac, R = 0.1773 (Rfree = 0.000) for 14481 atoms. Found 43 (79 requested) and removed 61 (39 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.29 Search for helices and strands: 0 residues in 0 chains, 14684 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 14706 seeds are put forward Round 1: 712 peptides, 144 chains. Longest chain 12 peptides. Score 0.285 Round 2: 798 peptides, 134 chains. Longest chain 16 peptides. Score 0.385 Round 3: 787 peptides, 125 chains. Longest chain 15 peptides. Score 0.406 Round 4: 830 peptides, 126 chains. Longest chain 19 peptides. Score 0.433 Round 5: 832 peptides, 124 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 124, Residues 708, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 124 chains (708 residues) following loop building 2 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22890 reflections ( 99.67 % complete ) and 34688 restraints for refining 14674 atoms. 31901 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1908 (Rfree = 0.000) for 14674 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 47: After refmac, R = 0.1896 (Rfree = 0.000) for 14592 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 48: After refmac, R = 0.1857 (Rfree = 0.000) for 14517 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 49: After refmac, R = 0.1786 (Rfree = 0.000) for 14452 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:53:24 GMT 2018 Job finished. TimeTaking 138.64 Used memory is bytes: 16642744