null Sun 23 Dec 22:23:14 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-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/2o7t-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-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 ============================================================ Sun 23 Dec 22:23:22 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-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 121 and 0 Target number of residues in the AU: 121 Target solvent content: 0.6667 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-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: 154 Cell parameters: 51.232 51.232 129.642 90.000 90.000 120.000 Input sequence file: 2o7t-3.8-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 3.802 Wilson plot Bfac: 89.81 2171 reflections ( 99.59 % complete ) and 0 restraints for refining 1767 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3822 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3682 (Rfree = 0.000) for 1767 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.93 Search for helices and strands: 0 residues in 0 chains, 1809 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 8 peptides. Score 0.232 Round 2: 57 peptides, 12 chains. Longest chain 8 peptides. Score 0.258 Round 3: 71 peptides, 16 chains. Longest chain 7 peptides. Score 0.234 Round 4: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.255 Round 5: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.305 Taking the results from Round 5 Chains 12, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2171 reflections ( 99.59 % complete ) and 3750 restraints for refining 1438 atoms. 3562 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3463 (Rfree = 0.000) for 1438 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.3405 (Rfree = 0.000) for 1408 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 3: After refmac, R = 0.3319 (Rfree = 0.000) for 1389 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 4: After refmac, R = 0.3414 (Rfree = 0.000) for 1368 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 5: After refmac, R = 0.3323 (Rfree = 0.000) for 1353 atoms. Found 4 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.89 Search for helices and strands: 0 residues in 0 chains, 1406 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 6 peptides. Score 0.219 Round 2: 67 peptides, 15 chains. Longest chain 7 peptides. Score 0.235 Round 3: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.289 Round 4: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.373 Round 5: 77 peptides, 14 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 4 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2171 reflections ( 99.59 % complete ) and 2813 restraints for refining 1229 atoms. 2582 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2883 (Rfree = 0.000) for 1229 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 7: After refmac, R = 0.3078 (Rfree = 0.000) for 1206 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.3189 (Rfree = 0.000) for 1192 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.3162 (Rfree = 0.000) for 1182 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.2986 (Rfree = 0.000) for 1179 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 1254 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.229 Round 2: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.371 Round 3: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.402 Round 4: 86 peptides, 13 chains. Longest chain 14 peptides. Score 0.470 Round 5: 87 peptides, 14 chains. Longest chain 10 peptides. Score 0.444 Taking the results from Round 4 Chains 13, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2171 reflections ( 99.59 % complete ) and 2728 restraints for refining 1210 atoms. 2449 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3230 (Rfree = 0.000) for 1210 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 12: After refmac, R = 0.2970 (Rfree = 0.000) for 1191 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 13: After refmac, R = 0.3053 (Rfree = 0.000) for 1180 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 14: After refmac, R = 0.2784 (Rfree = 0.000) for 1169 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.3089 (Rfree = 0.000) for 1168 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 3.91 Search for helices and strands: 0 residues in 0 chains, 1237 seeds are put forward Round 1: 76 peptides, 15 chains. Longest chain 10 peptides. Score 0.317 Round 2: 91 peptides, 16 chains. Longest chain 14 peptides. Score 0.407 Round 3: 85 peptides, 14 chains. Longest chain 14 peptides. Score 0.428 Round 4: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.420 Round 5: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.385 Taking the results from Round 3 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2171 reflections ( 99.59 % complete ) and 2699 restraints for refining 1224 atoms. 2429 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3445 (Rfree = 0.000) for 1224 atoms. Found 5 (6 requested) and removed 63 (3 requested) atoms. Cycle 17: After refmac, R = 0.3691 (Rfree = 0.000) for 1157 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 18: After refmac, R = 0.3129 (Rfree = 0.000) for 1145 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.3315 (Rfree = 0.000) for 1142 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 20: After refmac, R = 0.2802 (Rfree = 0.000) for 1133 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.97 Search for helices and strands: 0 residues in 0 chains, 1219 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 9 peptides. Score 0.254 Round 2: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.352 Round 3: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.428 Round 4: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.399 Round 5: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 3 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2171 reflections ( 99.59 % complete ) and 2547 restraints for refining 1164 atoms. 2277 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3136 (Rfree = 0.000) for 1164 atoms. Found 6 (6 requested) and removed 35 (3 requested) atoms. Cycle 22: After refmac, R = 0.2956 (Rfree = 0.000) for 1126 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2740 (Rfree = 0.000) for 1125 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.2813 (Rfree = 0.000) for 1121 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.3049 (Rfree = 0.000) for 1119 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.91 Search for helices and strands: 0 residues in 0 chains, 1179 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 10 peptides. Score 0.247 Round 2: 79 peptides, 15 chains. Longest chain 11 peptides. Score 0.343 Round 3: 67 peptides, 13 chains. Longest chain 11 peptides. Score 0.312 Round 4: 79 peptides, 15 chains. Longest chain 11 peptides. Score 0.343 Round 5: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.385 Taking the results from Round 5 Chains 12, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2171 reflections ( 99.59 % complete ) and 2782 restraints for refining 1206 atoms. 2558 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2945 (Rfree = 0.000) for 1206 atoms. Found 6 (6 requested) and removed 65 (3 requested) atoms. Cycle 27: After refmac, R = 0.3107 (Rfree = 0.000) for 1143 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 28: After refmac, R = 0.3093 (Rfree = 0.000) for 1130 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2968 (Rfree = 0.000) for 1124 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. Cycle 30: After refmac, R = 0.3081 (Rfree = 0.000) for 1115 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 1163 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.266 Round 2: 69 peptides, 13 chains. Longest chain 7 peptides. Score 0.330 Round 3: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.312 Round 4: 64 peptides, 12 chains. Longest chain 7 peptides. Score 0.324 Round 5: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.305 Taking the results from Round 2 Chains 13, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2171 reflections ( 99.59 % complete ) and 2478 restraints for refining 1127 atoms. 2267 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3015 (Rfree = 0.000) for 1127 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 32: After refmac, R = 0.3049 (Rfree = 0.000) for 1119 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 33: After refmac, R = 0.2888 (Rfree = 0.000) for 1108 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 34: After refmac, R = 0.2843 (Rfree = 0.000) for 1102 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 35: After refmac, R = 0.2693 (Rfree = 0.000) for 1093 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.86 Search for helices and strands: 0 residues in 0 chains, 1138 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 5 peptides. Score 0.209 Round 2: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.287 Round 3: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.268 Round 4: 53 peptides, 11 chains. Longest chain 8 peptides. Score 0.260 Round 5: 53 peptides, 10 chains. Longest chain 11 peptides. Score 0.302 Taking the results from Round 5 Chains 10, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2171 reflections ( 99.59 % complete ) and 2707 restraints for refining 1171 atoms. 2545 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3213 (Rfree = 0.000) for 1171 atoms. Found 6 (6 requested) and removed 42 (3 requested) atoms. Cycle 37: After refmac, R = 0.3123 (Rfree = 0.000) for 1127 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 38: After refmac, R = 0.2805 (Rfree = 0.000) for 1113 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.3215 (Rfree = 0.000) for 1110 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 40: After refmac, R = 0.2983 (Rfree = 0.000) for 1102 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.96 Search for helices and strands: 0 residues in 0 chains, 1143 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.200 Round 2: 45 peptides, 9 chains. Longest chain 6 peptides. Score 0.265 Round 3: 48 peptides, 10 chains. Longest chain 8 peptides. Score 0.253 Round 4: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.292 Round 5: 46 peptides, 8 chains. Longest chain 9 peptides. Score 0.319 Taking the results from Round 5 Chains 8, Residues 38, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2171 reflections ( 99.59 % complete ) and 2327 restraints for refining 1068 atoms. 2162 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2998 (Rfree = 0.000) for 1068 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 42: After refmac, R = 0.3227 (Rfree = 0.000) for 1054 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 43: After refmac, R = 0.2787 (Rfree = 0.000) for 1048 atoms. Found 5 (5 requested) and removed 26 (2 requested) atoms. Cycle 44: After refmac, R = 0.2808 (Rfree = 0.000) for 1026 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.2890 (Rfree = 0.000) for 1025 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.96 Search for helices and strands: 0 residues in 0 chains, 1099 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 6 peptides. Score 0.199 Round 2: 56 peptides, 11 chains. Longest chain 9 peptides. Score 0.289 Round 3: 48 peptides, 10 chains. Longest chain 8 peptides. Score 0.253 Round 4: 43 peptides, 9 chains. Longest chain 6 peptides. Score 0.245 Round 5: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.263 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 45, 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 2o7t-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2171 reflections ( 99.59 % complete ) and 2245 restraints for refining 1032 atoms. 2076 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2923 (Rfree = 0.000) for 1032 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3005 (Rfree = 0.000) for 1028 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.3019 (Rfree = 0.000) for 1023 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2638 (Rfree = 0.000) for 1018 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:59 GMT 2018 Job finished. TimeTaking 25.74 Used memory is bytes: 21811008