Sun 23 Dec 22:22:58 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 2o7t-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-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/2o7t-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-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 22:23:07 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/2o7t-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-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 116 and 0 Target number of residues in the AU: 116 Target solvent content: 0.6804 Checking the provided sequence file Detected sequence length: 199 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 199 Adjusted target solvent content: 0.45 Input MTZ file: 2o7t-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: 154 Cell parameters: 51.232 51.232 129.642 90.000 90.000 120.000 Input sequence file: 2o7t-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1592 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 Loops will be built when appropriate and at the last cycle Resolution range: 26.172 4.001 Wilson plot Bfac: 99.68 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1872 reflections ( 99.52 % complete ) and 0 restraints for refining 1757 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3758 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3715 (Rfree = 0.000) for 1757 atoms. Found 8 (8 requested) and removed 26 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 4.09 Search for helices and strands: 0 residues in 0 chains, 1776 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.253 Round 2: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.330 Round 3: 60 peptides, 9 chains. Longest chain 10 peptides. Score 0.404 Round 4: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.350 Round 5: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.385 Taking the results from Round 3 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1872 reflections ( 99.52 % complete ) and 3620 restraints for refining 1437 atoms. 3425 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3404 (Rfree = 0.000) for 1437 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.3429 (Rfree = 0.000) for 1401 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.3418 (Rfree = 0.000) for 1370 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 4: After refmac, R = 0.3319 (Rfree = 0.000) for 1348 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2857 (Rfree = 0.000) for 1338 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.79 4.05 Search for helices and strands: 0 residues in 0 chains, 1388 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 6 peptides. Score 0.266 Round 2: 79 peptides, 14 chains. Longest chain 12 peptides. Score 0.379 Round 3: 85 peptides, 15 chains. Longest chain 8 peptides. Score 0.393 Round 4: 78 peptides, 13 chains. Longest chain 12 peptides. Score 0.407 Round 5: 86 peptides, 15 chains. Longest chain 9 peptides. Score 0.402 Taking the results from Round 4 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1872 reflections ( 99.52 % complete ) and 2814 restraints for refining 1243 atoms. 2567 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3129 (Rfree = 0.000) for 1243 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 7: After refmac, R = 0.3038 (Rfree = 0.000) for 1220 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2827 (Rfree = 0.000) for 1206 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 9: After refmac, R = 0.2927 (Rfree = 0.000) for 1195 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 10: After refmac, R = 0.2926 (Rfree = 0.000) for 1182 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.80 4.06 Search for helices and strands: 0 residues in 0 chains, 1237 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.263 Round 2: 68 peptides, 12 chains. Longest chain 12 peptides. Score 0.359 Round 3: 66 peptides, 10 chains. Longest chain 19 peptides. Score 0.417 Round 4: 66 peptides, 10 chains. Longest chain 17 peptides. Score 0.417 Round 5: 73 peptides, 9 chains. Longest chain 19 peptides. Score 0.507 Taking the results from Round 5 Chains 9, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1872 reflections ( 99.52 % complete ) and 2533 restraints for refining 1169 atoms. 2286 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3313 (Rfree = 0.000) for 1169 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 12: After refmac, R = 0.2973 (Rfree = 0.000) for 1152 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 13: After refmac, R = 0.3079 (Rfree = 0.000) for 1141 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 14: After refmac, R = 0.3063 (Rfree = 0.000) for 1129 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 15: After refmac, R = 0.3006 (Rfree = 0.000) for 1123 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 4.11 Search for helices and strands: 0 residues in 0 chains, 1188 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 8 peptides. Score 0.270 Round 2: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.376 Round 3: 79 peptides, 13 chains. Longest chain 10 peptides. Score 0.415 Round 4: 85 peptides, 14 chains. Longest chain 8 peptides. Score 0.428 Round 5: 81 peptides, 12 chains. Longest chain 13 peptides. Score 0.465 Taking the results from Round 5 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1872 reflections ( 99.52 % complete ) and 2886 restraints for refining 1275 atoms. 2622 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3064 (Rfree = 0.000) for 1275 atoms. Found 6 (6 requested) and removed 22 (3 requested) atoms. Cycle 17: After refmac, R = 0.2915 (Rfree = 0.000) for 1247 atoms. Found 5 (5 requested) and removed 21 (2 requested) atoms. Cycle 18: After refmac, R = 0.2929 (Rfree = 0.000) for 1223 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 19: After refmac, R = 0.2969 (Rfree = 0.000) for 1211 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 20: After refmac, R = 0.2879 (Rfree = 0.000) for 1208 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 4.03 Search for helices and strands: 0 residues in 0 chains, 1272 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.310 Round 2: 75 peptides, 13 chains. Longest chain 8 peptides. Score 0.382 Round 3: 78 peptides, 13 chains. Longest chain 9 peptides. Score 0.407 Round 4: 71 peptides, 11 chains. Longest chain 10 peptides. Score 0.421 Round 5: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.405 Taking the results from Round 4 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1872 reflections ( 99.52 % complete ) and 2801 restraints for refining 1237 atoms. 2572 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3123 (Rfree = 0.000) for 1237 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. Cycle 22: After refmac, R = 0.2516 (Rfree = 0.000) for 1217 atoms. Found 5 (5 requested) and removed 62 (2 requested) atoms. Cycle 23: After refmac, R = 0.2922 (Rfree = 0.000) for 1154 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. Cycle 24: After refmac, R = 0.2947 (Rfree = 0.000) for 1138 atoms. Found 5 (5 requested) and removed 18 (2 requested) atoms. Cycle 25: After refmac, R = 0.2849 (Rfree = 0.000) for 1121 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 4.11 Search for helices and strands: 0 residues in 0 chains, 1164 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.283 Round 2: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.317 Round 3: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.423 Round 4: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.415 Round 5: 71 peptides, 14 chains. Longest chain 7 peptides. Score 0.310 Taking the results from Round 3 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1872 reflections ( 99.52 % complete ) and 2524 restraints for refining 1145 atoms. 2269 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3214 (Rfree = 0.000) for 1145 atoms. Found 5 (5 requested) and removed 46 (2 requested) atoms. Cycle 27: After refmac, R = 0.2804 (Rfree = 0.000) for 1100 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.3125 (Rfree = 0.000) for 1098 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 29: After refmac, R = 0.2899 (Rfree = 0.000) for 1092 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 30: After refmac, R = 0.2887 (Rfree = 0.000) for 1082 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.86 4.13 Search for helices and strands: 0 residues in 0 chains, 1159 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 5 peptides. Score 0.198 Round 2: 69 peptides, 13 chains. Longest chain 6 peptides. Score 0.330 Round 3: 72 peptides, 13 chains. Longest chain 8 peptides. Score 0.356 Round 4: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.363 Round 5: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.307 Taking the results from Round 4 Chains 14, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1872 reflections ( 99.52 % complete ) and 2576 restraints for refining 1183 atoms. 2338 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3083 (Rfree = 0.000) for 1183 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 32: After refmac, R = 0.2742 (Rfree = 0.000) for 1174 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 33: After refmac, R = 0.3065 (Rfree = 0.000) for 1164 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. Cycle 34: After refmac, R = 0.2748 (Rfree = 0.000) for 1148 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 35: After refmac, R = 0.2971 (Rfree = 0.000) for 1136 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.86 4.13 Search for helices and strands: 0 residues in 0 chains, 1206 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 6 peptides. Score 0.247 Round 2: 78 peptides, 12 chains. Longest chain 12 peptides. Score 0.442 Round 3: 83 peptides, 13 chains. Longest chain 13 peptides. Score 0.447 Round 4: 78 peptides, 12 chains. Longest chain 13 peptides. Score 0.442 Round 5: 77 peptides, 11 chains. Longest chain 15 peptides. Score 0.469 Taking the results from Round 5 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1872 reflections ( 99.52 % complete ) and 2666 restraints for refining 1233 atoms. 2413 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3268 (Rfree = 0.000) for 1233 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 37: After refmac, R = 0.3012 (Rfree = 0.000) for 1221 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 38: After refmac, R = 0.2389 (Rfree = 0.000) for 1210 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.2384 (Rfree = 0.000) for 1206 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.2342 (Rfree = 0.000) for 1202 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.88 4.15 Search for helices and strands: 0 residues in 0 chains, 1249 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.242 Round 2: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.292 Round 3: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.289 Round 4: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.366 Round 5: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 5 Chains 10, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1872 reflections ( 99.52 % complete ) and 2583 restraints for refining 1145 atoms. 2393 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3151 (Rfree = 0.000) for 1145 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 42: After refmac, R = 0.3017 (Rfree = 0.000) for 1139 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 43: After refmac, R = 0.2940 (Rfree = 0.000) for 1131 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2955 (Rfree = 0.000) for 1125 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.2966 (Rfree = 0.000) for 1120 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.86 4.13 Search for helices and strands: 0 residues in 0 chains, 1177 seeds are put forward Round 1: 45 peptides, 9 chains. Longest chain 10 peptides. Score 0.265 Round 2: 55 peptides, 10 chains. Longest chain 10 peptides. Score 0.320 Round 3: 59 peptides, 12 chains. Longest chain 10 peptides. Score 0.277 Round 4: 65 peptides, 11 chains. Longest chain 16 peptides. Score 0.371 Round 5: 58 peptides, 10 chains. Longest chain 12 peptides. Score 0.348 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 54, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 2o7t-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1872 reflections ( 99.52 % complete ) and 2358 restraints for refining 1167 atoms. 2090 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3021 (Rfree = 0.000) for 1167 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2921 (Rfree = 0.000) for 1156 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2876 (Rfree = 0.000) for 1145 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.3143 (Rfree = 0.000) for 1143 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... TimeTaking 26.22