Sun 23 Dec 22:22:59 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2osd-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2osd-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-4.0-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 22:23:08 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-4.0-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 104 and 0 Target number of residues in the AU: 104 Target solvent content: 0.6960 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1304 target number of atoms Had to go as low as 0.75 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 4.001 Wilson plot Bfac: 115.04 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1804 reflections ( 99.67 % complete ) and 0 restraints for refining 1435 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3827 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3791 (Rfree = 0.000) for 1435 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.02 3.91 Search for helices and strands: 0 residues in 0 chains, 1457 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 8 peptides. Score 0.251 Round 2: 53 peptides, 11 chains. Longest chain 6 peptides. Score 0.265 Round 3: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.295 Round 4: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.362 Round 5: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.419 Taking the results from Round 5 Chains 10, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1804 reflections ( 99.67 % complete ) and 2889 restraints for refining 1178 atoms. 2679 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3041 (Rfree = 0.000) for 1178 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 2: After refmac, R = 0.2481 (Rfree = 0.000) for 1155 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 3: After refmac, R = 0.2883 (Rfree = 0.000) for 1150 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 4: After refmac, R = 0.2519 (Rfree = 0.000) for 1143 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 5: After refmac, R = 0.2505 (Rfree = 0.000) for 1142 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.05 3.94 Search for helices and strands: 0 residues in 0 chains, 1188 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.312 Round 2: 70 peptides, 12 chains. Longest chain 9 peptides. Score 0.386 Round 3: 64 peptides, 10 chains. Longest chain 10 peptides. Score 0.411 Round 4: 71 peptides, 11 chains. Longest chain 11 peptides. Score 0.433 Round 5: 73 peptides, 11 chains. Longest chain 9 peptides. Score 0.450 Taking the results from Round 5 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1804 reflections ( 99.67 % complete ) and 2817 restraints for refining 1178 atoms. 2580 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2390 (Rfree = 0.000) for 1178 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 7: After refmac, R = 0.2214 (Rfree = 0.000) for 1165 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.2510 (Rfree = 0.000) for 1160 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.2282 (Rfree = 0.000) for 1153 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.2644 (Rfree = 0.000) for 1151 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.02 3.91 Search for helices and strands: 0 residues in 0 chains, 1193 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.292 Round 2: 65 peptides, 10 chains. Longest chain 9 peptides. Score 0.419 Round 3: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.466 Round 4: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.445 Round 5: 68 peptides, 9 chains. Longest chain 12 peptides. Score 0.482 Taking the results from Round 5 Chains 9, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1804 reflections ( 99.67 % complete ) and 2815 restraints for refining 1178 atoms. 2588 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2147 (Rfree = 0.000) for 1178 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. Cycle 12: After refmac, R = 0.2213 (Rfree = 0.000) for 1164 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.2144 (Rfree = 0.000) for 1154 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.2354 (Rfree = 0.000) for 1147 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.2457 (Rfree = 0.000) for 1145 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.03 3.92 Search for helices and strands: 0 residues in 0 chains, 1186 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.251 Round 2: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.395 Round 3: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.395 Round 4: 74 peptides, 14 chains. Longest chain 8 peptides. Score 0.345 Round 5: 76 peptides, 11 chains. Longest chain 12 peptides. Score 0.474 Taking the results from Round 5 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1804 reflections ( 99.67 % complete ) and 2796 restraints for refining 1178 atoms. 2547 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2903 (Rfree = 0.000) for 1178 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 17: After refmac, R = 0.2319 (Rfree = 0.000) for 1159 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.2554 (Rfree = 0.000) for 1145 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.2402 (Rfree = 0.000) for 1136 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2265 (Rfree = 0.000) for 1132 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.04 3.93 Search for helices and strands: 0 residues in 0 chains, 1175 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.242 Round 2: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.306 Round 3: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.354 Round 4: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.401 Round 5: 79 peptides, 12 chains. Longest chain 19 peptides. Score 0.462 Taking the results from Round 5 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1804 reflections ( 99.67 % complete ) and 2585 restraints for refining 1162 atoms. 2329 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2211 (Rfree = 0.000) for 1162 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 22: After refmac, R = 0.2076 (Rfree = 0.000) for 1148 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 23: After refmac, R = 0.2127 (Rfree = 0.000) for 1144 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.1869 (Rfree = 0.000) for 1139 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.1843 (Rfree = 0.000) for 1138 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.03 3.92 Search for helices and strands: 0 residues in 0 chains, 1175 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 6 peptides. Score 0.277 Round 2: 61 peptides, 10 chains. Longest chain 9 peptides. Score 0.384 Round 3: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.371 Round 4: 66 peptides, 10 chains. Longest chain 10 peptides. Score 0.428 Round 5: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.359 Taking the results from Round 4 Chains 10, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1804 reflections ( 99.67 % complete ) and 2706 restraints for refining 1178 atoms. 2492 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2220 (Rfree = 0.000) for 1178 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 27: After refmac, R = 0.2284 (Rfree = 0.000) for 1172 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 28: After refmac, R = 0.1988 (Rfree = 0.000) for 1164 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.2138 (Rfree = 0.000) for 1163 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.1731 (Rfree = 0.000) for 1164 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.10 3.99 Search for helices and strands: 0 residues in 0 chains, 1207 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 5 peptides. Score 0.210 Round 2: 60 peptides, 10 chains. Longest chain 8 peptides. Score 0.375 Round 3: 54 peptides, 9 chains. Longest chain 9 peptides. Score 0.360 Round 4: 65 peptides, 10 chains. Longest chain 9 peptides. Score 0.419 Round 5: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.353 Taking the results from Round 4 Chains 10, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1804 reflections ( 99.67 % complete ) and 2784 restraints for refining 1178 atoms. 2574 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1914 (Rfree = 0.000) for 1178 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. Cycle 32: After refmac, R = 0.1678 (Rfree = 0.000) for 1162 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.1635 (Rfree = 0.000) for 1158 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.2147 (Rfree = 0.000) for 1155 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 35: After refmac, R = 0.2114 (Rfree = 0.000) for 1153 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.08 3.97 Search for helices and strands: 0 residues in 0 chains, 1189 seeds are put forward Round 1: 40 peptides, 8 chains. Longest chain 8 peptides. Score 0.262 Round 2: 55 peptides, 10 chains. Longest chain 12 peptides. Score 0.327 Round 3: 52 peptides, 10 chains. Longest chain 10 peptides. Score 0.298 Round 4: 51 peptides, 9 chains. Longest chain 14 peptides. Score 0.331 Round 5: 60 peptides, 9 chains. Longest chain 17 peptides. Score 0.415 Taking the results from Round 5 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1804 reflections ( 99.67 % complete ) and 2793 restraints for refining 1178 atoms. 2598 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2402 (Rfree = 0.000) for 1178 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 37: After refmac, R = 0.2191 (Rfree = 0.000) for 1171 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 38: After refmac, R = 0.2356 (Rfree = 0.000) for 1159 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.2240 (Rfree = 0.000) for 1159 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2072 (Rfree = 0.000) for 1147 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.05 3.94 Search for helices and strands: 0 residues in 0 chains, 1184 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 8 peptides. Score 0.224 Round 2: 55 peptides, 11 chains. Longest chain 9 peptides. Score 0.285 Round 3: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.325 Round 4: 62 peptides, 11 chains. Longest chain 11 peptides. Score 0.353 Round 5: 62 peptides, 12 chains. Longest chain 12 peptides. Score 0.312 Taking the results from Round 4 Chains 11, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1804 reflections ( 99.67 % complete ) and 2634 restraints for refining 1123 atoms. 2441 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1928 (Rfree = 0.000) for 1123 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 42: After refmac, R = 0.2462 (Rfree = 0.000) for 1117 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 43: After refmac, R = 0.1947 (Rfree = 0.000) for 1115 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.2327 (Rfree = 0.000) for 1113 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2277 (Rfree = 0.000) for 1109 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.08 3.97 Search for helices and strands: 0 residues in 0 chains, 1149 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 9 peptides. Score 0.259 Round 2: 40 peptides, 8 chains. Longest chain 8 peptides. Score 0.262 Round 3: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.290 Round 4: 40 peptides, 7 chains. Longest chain 10 peptides. Score 0.309 Round 5: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.301 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2osd-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1804 reflections ( 99.67 % complete ) and 2709 restraints for refining 1130 atoms. 2584 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2579 (Rfree = 0.000) for 1130 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2459 (Rfree = 0.000) for 1111 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2522 (Rfree = 0.000) for 1102 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2531 (Rfree = 0.000) for 1096 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... TimeTaking 25.9