Tue 25 Dec 19:27:55 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 1vkd-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-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/1vkd-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-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 ============================================================ Tue 25 Dec 19:28:04 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/1vkd-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-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 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-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: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-3.8-parrot-hancs.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 Failed to save intermediate PDB 22890 reflections ( 99.67 % complete ) and 0 restraints for refining 18079 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.2968 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2800 (Rfree = 0.000) for 18079 atoms. Found 99 (99 requested) and removed 97 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 18263 seeds are put forward NCS extension: 0 residues added, 18263 seeds are put forward Round 1: 901 peptides, 176 chains. Longest chain 13 peptides. Score 0.327 Round 2: 1216 peptides, 183 chains. Longest chain 20 peptides. Score 0.521 Round 3: 1252 peptides, 168 chains. Longest chain 22 peptides. Score 0.580 Round 4: 1295 peptides, 172 chains. Longest chain 23 peptides. Score 0.593 Round 5: 1314 peptides, 165 chains. Longest chain 22 peptides. Score 0.619 Taking the results from Round 5 Chains 174, Residues 1149, Estimated correctness of the model 7.5 % 10 chains (76 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 31753 restraints for refining 14671 atoms. 27078 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2242 (Rfree = 0.000) for 14671 atoms. Found 58 (80 requested) and removed 90 (40 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2077 (Rfree = 0.000) for 14459 atoms. Found 38 (80 requested) and removed 84 (40 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2089 (Rfree = 0.000) for 14333 atoms. Found 49 (79 requested) and removed 90 (39 requested) atoms. Cycle 4: After refmac, R = 0.1971 (Rfree = 0.000) for 14250 atoms. Found 35 (78 requested) and removed 71 (39 requested) atoms. Cycle 5: After refmac, R = 0.1941 (Rfree = 0.000) for 14178 atoms. Found 24 (78 requested) and removed 64 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 14443 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 14460 seeds are put forward Round 1: 1153 peptides, 180 chains. Longest chain 15 peptides. Score 0.490 Round 2: 1277 peptides, 160 chains. Longest chain 29 peptides. Score 0.612 Round 3: 1283 peptides, 160 chains. Longest chain 36 peptides. Score 0.615 Round 4: 1298 peptides, 157 chains. Longest chain 35 peptides. Score 0.630 Round 5: 1306 peptides, 153 chains. Longest chain 36 peptides. Score 0.642 Taking the results from Round 5 Chains 163, Residues 1153, Estimated correctness of the model 17.5 % 9 chains (98 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 31629 restraints for refining 14674 atoms. 26822 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2209 (Rfree = 0.000) for 14674 atoms. Found 69 (80 requested) and removed 94 (40 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1998 (Rfree = 0.000) for 14556 atoms. Found 28 (80 requested) and removed 78 (40 requested) atoms. Cycle 8: After refmac, R = 0.1960 (Rfree = 0.000) for 14442 atoms. Found 22 (79 requested) and removed 69 (39 requested) atoms. Cycle 9: After refmac, R = 0.1988 (Rfree = 0.000) for 14352 atoms. Found 75 (79 requested) and removed 83 (39 requested) atoms. Cycle 10: After refmac, R = 0.1902 (Rfree = 0.000) for 14320 atoms. Found 55 (78 requested) and removed 72 (39 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 14590 seeds are put forward NCS extension: 20 residues added (10 deleted due to clashes), 14610 seeds are put forward Round 1: 1131 peptides, 192 chains. Longest chain 20 peptides. Score 0.443 Round 2: 1207 peptides, 176 chains. Longest chain 22 peptides. Score 0.534 Round 3: 1262 peptides, 168 chains. Longest chain 32 peptides. Score 0.585 Round 4: 1259 peptides, 159 chains. Longest chain 28 peptides. Score 0.605 Round 5: 1247 peptides, 162 chains. Longest chain 22 peptides. Score 0.592 Taking the results from Round 4 Chains 170, Residues 1100, Estimated correctness of the model 1.2 % 14 chains (144 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 31642 restraints for refining 14675 atoms. 26873 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2150 (Rfree = 0.000) for 14675 atoms. Found 75 (80 requested) and removed 108 (40 requested) atoms. Cycle 12: After refmac, R = 0.1973 (Rfree = 0.000) for 14508 atoms. Found 42 (80 requested) and removed 57 (40 requested) atoms. Cycle 13: After refmac, R = 0.1939 (Rfree = 0.000) for 14434 atoms. Found 31 (79 requested) and removed 51 (39 requested) atoms. Cycle 14: After refmac, R = 0.1889 (Rfree = 0.000) for 14380 atoms. Found 35 (79 requested) and removed 53 (39 requested) atoms. Cycle 15: After refmac, R = 0.1798 (Rfree = 0.000) for 14335 atoms. Found 28 (78 requested) and removed 54 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 14537 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 14557 seeds are put forward Round 1: 1073 peptides, 187 chains. Longest chain 15 peptides. Score 0.418 Round 2: 1180 peptides, 168 chains. Longest chain 24 peptides. Score 0.539 Round 3: 1181 peptides, 158 chains. Longest chain 29 peptides. Score 0.565 Round 4: 1207 peptides, 160 chains. Longest chain 20 peptides. Score 0.575 Round 5: 1203 peptides, 161 chains. Longest chain 22 peptides. Score 0.570 Taking the results from Round 4 Chains 164, Residues 1047, Estimated correctness of the model 0.0 % 8 chains (63 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 22890 reflections ( 99.67 % complete ) and 32896 restraints for refining 14675 atoms. 28646 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2151 (Rfree = 0.000) for 14675 atoms. Found 66 (80 requested) and removed 79 (40 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2011 (Rfree = 0.000) for 14592 atoms. Found 33 (80 requested) and removed 69 (40 requested) atoms. Cycle 18: After refmac, R = 0.1935 (Rfree = 0.000) for 14514 atoms. Found 26 (80 requested) and removed 73 (40 requested) atoms. Cycle 19: After refmac, R = 0.1871 (Rfree = 0.000) for 14434 atoms. Found 43 (79 requested) and removed 58 (39 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1803 (Rfree = 0.000) for 14391 atoms. Found 22 (79 requested) and removed 51 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 14619 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 14630 seeds are put forward Round 1: 984 peptides, 174 chains. Longest chain 14 peptides. Score 0.395 Round 2: 1106 peptides, 167 chains. Longest chain 17 peptides. Score 0.497 Round 3: 1116 peptides, 162 chains. Longest chain 20 peptides. Score 0.516 Round 4: 1150 peptides, 163 chains. Longest chain 17 peptides. Score 0.534 Round 5: 1147 peptides, 162 chains. Longest chain 23 peptides. Score 0.535 Taking the results from Round 5 Chains 167, Residues 985, Estimated correctness of the model 0.0 % 7 chains (46 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33714 restraints for refining 14675 atoms. 29788 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2099 (Rfree = 0.000) for 14675 atoms. Found 48 (80 requested) and removed 80 (40 requested) atoms. Cycle 22: After refmac, R = 0.1976 (Rfree = 0.000) for 14581 atoms. Found 39 (80 requested) and removed 67 (40 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1857 (Rfree = 0.000) for 14518 atoms. Found 28 (80 requested) and removed 66 (40 requested) atoms. Cycle 24: After refmac, R = 0.1798 (Rfree = 0.000) for 14442 atoms. Found 20 (79 requested) and removed 57 (39 requested) atoms. Cycle 25: After refmac, R = 0.1745 (Rfree = 0.000) for 14381 atoms. Found 26 (79 requested) and removed 53 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 14622 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 14636 seeds are put forward Round 1: 962 peptides, 177 chains. Longest chain 15 peptides. Score 0.369 Round 2: 1044 peptides, 161 chains. Longest chain 22 peptides. Score 0.474 Round 3: 1081 peptides, 160 chains. Longest chain 21 peptides. Score 0.500 Round 4: 1116 peptides, 163 chains. Longest chain 34 peptides. Score 0.514 Round 5: 1133 peptides, 161 chains. Longest chain 24 peptides. Score 0.529 Taking the results from Round 5 Chains 163, Residues 972, Estimated correctness of the model 0.0 % 9 chains (57 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33400 restraints for refining 14674 atoms. 29502 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2095 (Rfree = 0.000) for 14674 atoms. Found 44 (80 requested) and removed 70 (40 requested) atoms. Cycle 27: After refmac, R = 0.2019 (Rfree = 0.000) for 14541 atoms. Found 36 (80 requested) and removed 57 (40 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1920 (Rfree = 0.000) for 14472 atoms. Found 51 (79 requested) and removed 65 (39 requested) atoms. Cycle 29: After refmac, R = 0.1866 (Rfree = 0.000) for 14420 atoms. Found 39 (79 requested) and removed 54 (39 requested) atoms. Cycle 30: After refmac, R = 0.1787 (Rfree = 0.000) for 14376 atoms. Found 30 (79 requested) and removed 54 (39 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 14564 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 14579 seeds are put forward Round 1: 929 peptides, 175 chains. Longest chain 16 peptides. Score 0.351 Round 2: 1004 peptides, 155 chains. Longest chain 24 peptides. Score 0.465 Round 3: 996 peptides, 150 chains. Longest chain 24 peptides. Score 0.474 Round 4: 991 peptides, 145 chains. Longest chain 21 peptides. Score 0.485 Round 5: 1020 peptides, 152 chains. Longest chain 21 peptides. Score 0.484 Taking the results from Round 4 Chains 147, Residues 846, Estimated correctness of the model 0.0 % 7 chains (59 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33600 restraints for refining 14675 atoms. 30172 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1976 (Rfree = 0.000) for 14675 atoms. Found 49 (80 requested) and removed 79 (40 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1881 (Rfree = 0.000) for 14565 atoms. Found 59 (80 requested) and removed 60 (40 requested) atoms. Cycle 33: After refmac, R = 0.1805 (Rfree = 0.000) for 14533 atoms. Found 56 (80 requested) and removed 58 (40 requested) atoms. Cycle 34: After refmac, R = 0.1744 (Rfree = 0.000) for 14502 atoms. Found 47 (79 requested) and removed 59 (39 requested) atoms. Cycle 35: After refmac, R = 0.1732 (Rfree = 0.000) for 14460 atoms. Found 46 (79 requested) and removed 59 (39 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 14681 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 14704 seeds are put forward Round 1: 892 peptides, 173 chains. Longest chain 13 peptides. Score 0.330 Round 2: 978 peptides, 163 chains. Longest chain 22 peptides. Score 0.423 Round 3: 993 peptides, 159 chains. Longest chain 16 peptides. Score 0.446 Round 4: 999 peptides, 146 chains. Longest chain 17 peptides. Score 0.487 Round 5: 1028 peptides, 162 chains. Longest chain 18 peptides. Score 0.460 Taking the results from Round 4 Chains 147, Residues 853, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33484 restraints for refining 14675 atoms. 30071 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1896 (Rfree = 0.000) for 14675 atoms. Found 61 (80 requested) and removed 65 (40 requested) atoms. Cycle 37: After refmac, R = 0.1760 (Rfree = 0.000) for 14609 atoms. Found 33 (80 requested) and removed 67 (40 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1681 (Rfree = 0.000) for 14553 atoms. Found 34 (80 requested) and removed 51 (40 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1652 (Rfree = 0.000) for 14514 atoms. Found 39 (79 requested) and removed 52 (39 requested) atoms. Cycle 40: After refmac, R = 0.1645 (Rfree = 0.000) for 14485 atoms. Found 38 (79 requested) and removed 50 (39 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 14722 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 14736 seeds are put forward Round 1: 844 peptides, 169 chains. Longest chain 14 peptides. Score 0.306 Round 2: 954 peptides, 157 chains. Longest chain 18 peptides. Score 0.425 Round 3: 967 peptides, 150 chains. Longest chain 19 peptides. Score 0.455 Round 4: 945 peptides, 145 chains. Longest chain 19 peptides. Score 0.455 Round 5: 950 peptides, 139 chains. Longest chain 24 peptides. Score 0.476 Taking the results from Round 5 Chains 140, Residues 811, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33863 restraints for refining 14674 atoms. 30666 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1875 (Rfree = 0.000) for 14674 atoms. Found 48 (80 requested) and removed 52 (40 requested) atoms. Cycle 42: After refmac, R = 0.1801 (Rfree = 0.000) for 14607 atoms. Found 39 (80 requested) and removed 50 (40 requested) atoms. Cycle 43: After refmac, R = 0.1744 (Rfree = 0.000) for 14572 atoms. Found 34 (80 requested) and removed 62 (40 requested) atoms. Cycle 44: After refmac, R = 0.1699 (Rfree = 0.000) for 14514 atoms. Found 34 (79 requested) and removed 47 (39 requested) atoms. Cycle 45: After refmac, R = 0.1711 (Rfree = 0.000) for 14481 atoms. Found 45 (79 requested) and removed 48 (39 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 14687 seeds are put forward NCS extension: 48 residues added (1 deleted due to clashes), 14735 seeds are put forward Round 1: 774 peptides, 146 chains. Longest chain 20 peptides. Score 0.327 Round 2: 882 peptides, 138 chains. Longest chain 25 peptides. Score 0.433 Round 3: 921 peptides, 141 chains. Longest chain 23 peptides. Score 0.450 Round 4: 931 peptides, 147 chains. Longest chain 19 peptides. Score 0.439 Round 5: 932 peptides, 142 chains. Longest chain 18 peptides. Score 0.455 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 146, Residues 790, Estimated correctness of the model 0.0 % 8 chains (62 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 146 chains (790 residues) following loop building 8 chains (62 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22890 reflections ( 99.67 % complete ) and 33705 restraints for refining 14673 atoms. 30490 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1934 (Rfree = 0.000) for 14673 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 47: After refmac, R = 0.1849 (Rfree = 0.000) for 14590 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 48: After refmac, R = 0.1793 (Rfree = 0.000) for 14532 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1786 (Rfree = 0.000) for 14475 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 22:32:08 GMT 2018 Job finished. TimeTaking 184.22