null Sun 23 Dec 22:22:42 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 2osd-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2osd-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2osd-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-3.2-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/2osd-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-3.2-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 ============================================================ Sun 23 Dec 22:22:56 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/2osd-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-3.2-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 115 and 0 Target number of residues in the AU: 115 Target solvent content: 0.6639 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 163 Adjusted target solvent content: 0.52 Input MTZ file: 2osd-3.2-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: 96 Cell parameters: 55.786 55.786 118.990 90.000 90.000 90.000 Input sequence file: 2osd-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1304 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 Loops will be built when appropriate and at the last cycle Resolution range: 50.510 3.200 Wilson plot Bfac: 86.81 3429 reflections ( 99.83 % complete ) and 0 restraints for refining 1440 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3557 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3182 (Rfree = 0.000) for 1440 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.39 Search for helices and strands: 0 residues in 0 chains, 1470 seeds are put forward Round 1: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.368 Round 2: 88 peptides, 15 chains. Longest chain 14 peptides. Score 0.429 Round 3: 84 peptides, 13 chains. Longest chain 19 peptides. Score 0.467 Round 4: 91 peptides, 14 chains. Longest chain 14 peptides. Score 0.488 Round 5: 100 peptides, 12 chains. Longest chain 20 peptides. Score 0.614 Taking the results from Round 5 Chains 14, Residues 88, Estimated correctness of the model 44.8 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3429 reflections ( 99.83 % complete ) and 2587 restraints for refining 1190 atoms. 2177 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3051 (Rfree = 0.000) for 1190 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 2: After refmac, R = 0.2822 (Rfree = 0.000) for 1179 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 3: After refmac, R = 0.2853 (Rfree = 0.000) for 1170 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2642 (Rfree = 0.000) for 1159 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2470 (Rfree = 0.000) for 1160 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 1218 seeds are put forward Round 1: 78 peptides, 12 chains. Longest chain 10 peptides. Score 0.454 Round 2: 92 peptides, 10 chains. Longest chain 21 peptides. Score 0.621 Round 3: 104 peptides, 9 chains. Longest chain 35 peptides. Score 0.715 Round 4: 92 peptides, 9 chains. Longest chain 20 peptides. Score 0.650 Round 5: 86 peptides, 11 chains. Longest chain 14 peptides. Score 0.550 Taking the results from Round 3 Chains 9, Residues 95, Estimated correctness of the model 68.3 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 3429 reflections ( 99.83 % complete ) and 2266 restraints for refining 1190 atoms. 1747 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2823 (Rfree = 0.000) for 1190 atoms. Found 8 (10 requested) and removed 14 (5 requested) atoms. Cycle 7: After refmac, R = 0.2958 (Rfree = 0.000) for 1173 atoms. Found 9 (10 requested) and removed 12 (5 requested) atoms. Cycle 8: After refmac, R = 0.2574 (Rfree = 0.000) for 1161 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 9: After refmac, R = 0.2404 (Rfree = 0.000) for 1153 atoms. Found 6 (9 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2204 (Rfree = 0.000) for 1150 atoms. Found 3 (9 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 1195 seeds are put forward Round 1: 84 peptides, 11 chains. Longest chain 14 peptides. Score 0.535 Round 2: 102 peptides, 13 chains. Longest chain 25 peptides. Score 0.598 Round 3: 95 peptides, 10 chains. Longest chain 24 peptides. Score 0.640 Round 4: 96 peptides, 11 chains. Longest chain 20 peptides. Score 0.617 Round 5: 102 peptides, 10 chains. Longest chain 21 peptides. Score 0.680 Taking the results from Round 5 Chains 10, Residues 92, Estimated correctness of the model 60.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3429 reflections ( 99.83 % complete ) and 2576 restraints for refining 1190 atoms. 2218 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2822 (Rfree = 0.000) for 1190 atoms. Found 8 (9 requested) and removed 7 (5 requested) atoms. Cycle 12: After refmac, R = 0.2361 (Rfree = 0.000) for 1183 atoms. Found 7 (9 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.2100 (Rfree = 0.000) for 1177 atoms. Found 3 (9 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.1992 (Rfree = 0.000) for 1174 atoms. Found 3 (9 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2078 (Rfree = 0.000) for 1170 atoms. Found 2 (9 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 1216 seeds are put forward Round 1: 95 peptides, 11 chains. Longest chain 22 peptides. Score 0.611 Round 2: 109 peptides, 10 chains. Longest chain 31 peptides. Score 0.716 Round 3: 107 peptides, 9 chains. Longest chain 31 peptides. Score 0.729 Round 4: 106 peptides, 10 chains. Longest chain 25 peptides. Score 0.701 Round 5: 105 peptides, 10 chains. Longest chain 31 peptides. Score 0.696 Taking the results from Round 3 Chains 10, Residues 98, Estimated correctness of the model 71.1 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3429 reflections ( 99.83 % complete ) and 2184 restraints for refining 1190 atoms. 1675 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2626 (Rfree = 0.000) for 1190 atoms. Found 7 (9 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.2334 (Rfree = 0.000) for 1183 atoms. Found 5 (9 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2239 (Rfree = 0.000) for 1179 atoms. Found 2 (9 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2185 (Rfree = 0.000) for 1170 atoms. Found 2 (8 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2158 (Rfree = 0.000) for 1165 atoms. Found 3 (8 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 1221 seeds are put forward Round 1: 91 peptides, 11 chains. Longest chain 17 peptides. Score 0.585 Round 2: 93 peptides, 11 chains. Longest chain 19 peptides. Score 0.598 Round 3: 102 peptides, 12 chains. Longest chain 16 peptides. Score 0.626 Round 4: 107 peptides, 11 chains. Longest chain 20 peptides. Score 0.681 Round 5: 99 peptides, 11 chains. Longest chain 21 peptides. Score 0.636 Taking the results from Round 4 Chains 11, Residues 96, Estimated correctness of the model 61.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3429 reflections ( 99.83 % complete ) and 2374 restraints for refining 1190 atoms. 1906 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2548 (Rfree = 0.000) for 1190 atoms. Found 8 (8 requested) and removed 6 (5 requested) atoms. Cycle 22: After refmac, R = 0.2270 (Rfree = 0.000) for 1183 atoms. Found 3 (8 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2160 (Rfree = 0.000) for 1176 atoms. Found 5 (8 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2043 (Rfree = 0.000) for 1173 atoms. Found 3 (8 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2029 (Rfree = 0.000) for 1168 atoms. Found 2 (8 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 1213 seeds are put forward Round 1: 87 peptides, 11 chains. Longest chain 19 peptides. Score 0.557 Round 2: 100 peptides, 12 chains. Longest chain 22 peptides. Score 0.614 Round 3: 104 peptides, 11 chains. Longest chain 27 peptides. Score 0.665 Round 4: 101 peptides, 12 chains. Longest chain 21 peptides. Score 0.620 Round 5: 98 peptides, 11 chains. Longest chain 24 peptides. Score 0.630 Taking the results from Round 3 Chains 11, Residues 93, Estimated correctness of the model 57.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3429 reflections ( 99.83 % complete ) and 2616 restraints for refining 1189 atoms. 2255 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2506 (Rfree = 0.000) for 1189 atoms. Found 8 (8 requested) and removed 6 (5 requested) atoms. Cycle 27: After refmac, R = 0.2253 (Rfree = 0.000) for 1182 atoms. Found 3 (8 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2307 (Rfree = 0.000) for 1178 atoms. Found 8 (8 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2207 (Rfree = 0.000) for 1178 atoms. Found 3 (8 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2051 (Rfree = 0.000) for 1173 atoms. Found 1 (8 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 1213 seeds are put forward Round 1: 75 peptides, 11 chains. Longest chain 11 peptides. Score 0.466 Round 2: 88 peptides, 10 chains. Longest chain 21 peptides. Score 0.595 Round 3: 96 peptides, 11 chains. Longest chain 21 peptides. Score 0.617 Round 4: 96 peptides, 10 chains. Longest chain 23 peptides. Score 0.646 Round 5: 94 peptides, 11 chains. Longest chain 20 peptides. Score 0.604 Taking the results from Round 4 Chains 11, Residues 86, Estimated correctness of the model 52.9 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3429 reflections ( 99.83 % complete ) and 2407 restraints for refining 1189 atoms. 1970 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2544 (Rfree = 0.000) for 1189 atoms. Found 8 (8 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2222 (Rfree = 0.000) for 1188 atoms. Found 3 (8 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.2074 (Rfree = 0.000) for 1183 atoms. Found 3 (8 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1985 (Rfree = 0.000) for 1178 atoms. Found 1 (8 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.1976 (Rfree = 0.000) for 1171 atoms. Found 2 (8 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.40 Search for helices and strands: 0 residues in 0 chains, 1205 seeds are put forward Round 1: 83 peptides, 11 chains. Longest chain 17 peptides. Score 0.528 Round 2: 97 peptides, 11 chains. Longest chain 18 peptides. Score 0.623 Round 3: 100 peptides, 11 chains. Longest chain 25 peptides. Score 0.642 Round 4: 99 peptides, 11 chains. Longest chain 28 peptides. Score 0.636 Round 5: 105 peptides, 10 chains. Longest chain 29 peptides. Score 0.696 Taking the results from Round 5 Chains 10, Residues 95, Estimated correctness of the model 64.3 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3429 reflections ( 99.83 % complete ) and 2402 restraints for refining 1190 atoms. 1937 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2767 (Rfree = 0.000) for 1190 atoms. Found 8 (8 requested) and removed 12 (5 requested) atoms. Cycle 37: After refmac, R = 0.3141 (Rfree = 0.000) for 1169 atoms. Found 8 (8 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.2740 (Rfree = 0.000) for 1158 atoms. Found 8 (8 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2766 (Rfree = 0.000) for 1156 atoms. Found 8 (8 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.2520 (Rfree = 0.000) for 1151 atoms. Found 6 (8 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 1212 seeds are put forward Round 1: 82 peptides, 13 chains. Longest chain 14 peptides. Score 0.451 Round 2: 88 peptides, 9 chains. Longest chain 23 peptides. Score 0.625 Round 3: 94 peptides, 8 chains. Longest chain 28 peptides. Score 0.688 Round 4: 93 peptides, 9 chains. Longest chain 23 peptides. Score 0.656 Round 5: 90 peptides, 9 chains. Longest chain 19 peptides. Score 0.638 Taking the results from Round 3 Chains 8, Residues 86, Estimated correctness of the model 62.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3429 reflections ( 99.83 % complete ) and 2498 restraints for refining 1135 atoms. 2162 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2776 (Rfree = 0.000) for 1135 atoms. Found 8 (8 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2593 (Rfree = 0.000) for 1136 atoms. Found 8 (8 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2911 (Rfree = 0.000) for 1134 atoms. Found 8 (8 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2573 (Rfree = 0.000) for 1134 atoms. Found 8 (8 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.2750 (Rfree = 0.000) for 1131 atoms. Found 8 (8 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 1174 seeds are put forward Round 1: 75 peptides, 13 chains. Longest chain 12 peptides. Score 0.392 Round 2: 85 peptides, 12 chains. Longest chain 13 peptides. Score 0.510 Round 3: 91 peptides, 12 chains. Longest chain 15 peptides. Score 0.553 Round 4: 91 peptides, 12 chains. Longest chain 14 peptides. Score 0.553 Round 5: 91 peptides, 13 chains. Longest chain 15 peptides. Score 0.521 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 79, Estimated correctness of the model 27.8 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2osd-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3429 reflections ( 99.83 % complete ) and 2613 restraints for refining 1171 atoms. 2309 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2837 (Rfree = 0.000) for 1171 atoms. Found 0 (8 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2223 (Rfree = 0.000) for 1163 atoms. Found 0 (8 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2140 (Rfree = 0.000) for 1157 atoms. Found 0 (8 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2059 (Rfree = 0.000) for 1152 atoms. Found 0 (8 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:22:46 GMT 2018 Job finished. TimeTaking 60.07 Used memory is bytes: 13653928