null Sun 23 Dec 22:22:49 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 2oh3-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-3.8-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/2oh3-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-3.8-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 22:22:58 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/2oh3-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-3.8-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 137 and 0 Target number of residues in the AU: 137 Target solvent content: 0.6591 Checking the provided sequence file Detected sequence length: 167 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 167 Adjusted target solvent content: 0.58 Input MTZ file: 2oh3-3.8-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: 23 Cell parameters: 64.360 75.280 89.790 90.000 90.000 90.000 Input sequence file: 2oh3-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1336 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: 57.688 3.803 Wilson plot Bfac: 82.80 2252 reflections ( 97.57 % complete ) and 0 restraints for refining 1473 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3367 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3179 (Rfree = 0.000) for 1473 atoms. Found 8 (8 requested) and removed 76 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.17 Search for helices and strands: 0 residues in 0 chains, 1433 seeds are put forward Round 1: 67 peptides, 12 chains. Longest chain 9 peptides. Score 0.338 Round 2: 82 peptides, 12 chains. Longest chain 12 peptides. Score 0.452 Round 3: 100 peptides, 11 chains. Longest chain 31 peptides. Score 0.596 Round 4: 105 peptides, 13 chains. Longest chain 28 peptides. Score 0.572 Round 5: 94 peptides, 11 chains. Longest chain 27 peptides. Score 0.561 Taking the results from Round 3 Chains 12, Residues 89, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2252 reflections ( 97.57 % complete ) and 2699 restraints for refining 1207 atoms. 2319 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2692 (Rfree = 0.000) for 1207 atoms. Found 6 (6 requested) and removed 32 (3 requested) atoms. Cycle 2: After refmac, R = 0.2793 (Rfree = 0.000) for 1166 atoms. Found 6 (6 requested) and removed 31 (3 requested) atoms. Cycle 3: After refmac, R = 0.2526 (Rfree = 0.000) for 1135 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 4: After refmac, R = 0.2422 (Rfree = 0.000) for 1115 atoms. Found 2 (6 requested) and removed 14 (3 requested) atoms. Cycle 5: After refmac, R = 0.2335 (Rfree = 0.000) for 1101 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.23 Search for helices and strands: 0 residues in 0 chains, 1168 seeds are put forward Round 1: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.333 Round 2: 81 peptides, 12 chains. Longest chain 12 peptides. Score 0.445 Round 3: 83 peptides, 11 chains. Longest chain 14 peptides. Score 0.490 Round 4: 82 peptides, 12 chains. Longest chain 14 peptides. Score 0.452 Round 5: 79 peptides, 9 chains. Longest chain 14 peptides. Score 0.525 Taking the results from Round 5 Chains 10, Residues 70, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2252 reflections ( 97.57 % complete ) and 2695 restraints for refining 1195 atoms. 2384 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3066 (Rfree = 0.000) for 1195 atoms. Found 6 (6 requested) and removed 24 (3 requested) atoms. Cycle 7: After refmac, R = 0.2618 (Rfree = 0.000) for 1168 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 8: After refmac, R = 0.2467 (Rfree = 0.000) for 1143 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 9: After refmac, R = 0.2732 (Rfree = 0.000) for 1130 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 10: After refmac, R = 0.2635 (Rfree = 0.000) for 1117 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.22 Search for helices and strands: 0 residues in 0 chains, 1178 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 8 peptides. Score 0.278 Round 2: 88 peptides, 15 chains. Longest chain 10 peptides. Score 0.400 Round 3: 92 peptides, 17 chains. Longest chain 9 peptides. Score 0.366 Round 4: 78 peptides, 13 chains. Longest chain 16 peptides. Score 0.390 Round 5: 98 peptides, 18 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 2 Chains 15, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2252 reflections ( 97.57 % complete ) and 2545 restraints for refining 1163 atoms. 2268 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2631 (Rfree = 0.000) for 1163 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 12: After refmac, R = 0.2503 (Rfree = 0.000) for 1141 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 13: After refmac, R = 0.2834 (Rfree = 0.000) for 1128 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 14: After refmac, R = 0.2778 (Rfree = 0.000) for 1115 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 15: After refmac, R = 0.3219 (Rfree = 0.000) for 1102 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.10 Search for helices and strands: 0 residues in 0 chains, 1150 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 9 peptides. Score 0.285 Round 2: 90 peptides, 17 chains. Longest chain 7 peptides. Score 0.350 Round 3: 99 peptides, 17 chains. Longest chain 9 peptides. Score 0.417 Round 4: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.383 Round 5: 89 peptides, 16 chains. Longest chain 8 peptides. Score 0.375 Taking the results from Round 3 Chains 17, Residues 82, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2252 reflections ( 97.57 % complete ) and 2500 restraints for refining 1166 atoms. 2168 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2744 (Rfree = 0.000) for 1166 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 17: After refmac, R = 0.2531 (Rfree = 0.000) for 1149 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 18: After refmac, R = 0.2593 (Rfree = 0.000) for 1139 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.2522 (Rfree = 0.000) for 1135 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 20: After refmac, R = 0.2545 (Rfree = 0.000) for 1133 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.12 Search for helices and strands: 0 residues in 0 chains, 1177 seeds are put forward Round 1: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.325 Round 2: 83 peptides, 15 chains. Longest chain 15 peptides. Score 0.362 Round 3: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.357 Round 4: 72 peptides, 13 chains. Longest chain 8 peptides. Score 0.343 Round 5: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 5 Chains 13, Residues 62, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2252 reflections ( 97.57 % complete ) and 2676 restraints for refining 1207 atoms. 2408 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2704 (Rfree = 0.000) for 1207 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 22: After refmac, R = 0.2527 (Rfree = 0.000) for 1192 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 23: After refmac, R = 0.2538 (Rfree = 0.000) for 1179 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.2405 (Rfree = 0.000) for 1172 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. Cycle 25: After refmac, R = 0.2344 (Rfree = 0.000) for 1165 atoms. Found 3 (6 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.01 Search for helices and strands: 0 residues in 0 chains, 1206 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 12 peptides. Score 0.317 Round 2: 77 peptides, 13 chains. Longest chain 14 peptides. Score 0.383 Round 3: 81 peptides, 14 chains. Longest chain 13 peptides. Score 0.380 Round 4: 73 peptides, 13 chains. Longest chain 12 peptides. Score 0.351 Round 5: 73 peptides, 11 chains. Longest chain 11 peptides. Score 0.419 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 ------------------------------------------------------ 2252 reflections ( 97.57 % complete ) and 2732 restraints for refining 1208 atoms. 2495 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2608 (Rfree = 0.000) for 1208 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 27: After refmac, R = 0.2448 (Rfree = 0.000) for 1193 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 28: After refmac, R = 0.2478 (Rfree = 0.000) for 1185 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 29: After refmac, R = 0.2446 (Rfree = 0.000) for 1171 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 30: After refmac, R = 0.2347 (Rfree = 0.000) for 1169 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.10 Search for helices and strands: 0 residues in 0 chains, 1208 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 6 peptides. Score 0.238 Round 2: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.337 Round 3: 80 peptides, 16 chains. Longest chain 9 peptides. Score 0.305 Round 4: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.405 Round 5: 75 peptides, 15 chains. Longest chain 6 peptides. Score 0.298 Taking the results from Round 4 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2252 reflections ( 97.57 % complete ) and 2706 restraints for refining 1208 atoms. 2451 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2747 (Rfree = 0.000) for 1208 atoms. Found 5 (6 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.2472 (Rfree = 0.000) for 1197 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.2497 (Rfree = 0.000) for 1198 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.2458 (Rfree = 0.000) for 1194 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2400 (Rfree = 0.000) for 1194 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.10 Search for helices and strands: 0 residues in 0 chains, 1213 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 7 peptides. Score 0.288 Round 2: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.300 Round 3: 74 peptides, 14 chains. Longest chain 8 peptides. Score 0.325 Round 4: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.319 Round 5: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 5 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2252 reflections ( 97.57 % complete ) and 2832 restraints for refining 1208 atoms. 2627 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2894 (Rfree = 0.000) for 1208 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 37: After refmac, R = 0.2878 (Rfree = 0.000) for 1203 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 38: After refmac, R = 0.2485 (Rfree = 0.000) for 1195 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.2449 (Rfree = 0.000) for 1194 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 40: After refmac, R = 0.3283 (Rfree = 0.000) for 1194 atoms. Found 6 (6 requested) and removed 26 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 2.97 Search for helices and strands: 0 residues in 0 chains, 1206 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 8 peptides. Score 0.234 Round 2: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.290 Round 3: 58 peptides, 12 chains. Longest chain 8 peptides. Score 0.261 Round 4: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.349 Round 5: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.307 Taking the results from Round 4 Chains 11, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2252 reflections ( 97.57 % complete ) and 2747 restraints for refining 1207 atoms. 2546 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3173 (Rfree = 0.000) for 1207 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 42: After refmac, R = 0.3184 (Rfree = 0.000) for 1193 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 43: After refmac, R = 0.2944 (Rfree = 0.000) for 1185 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 44: After refmac, R = 0.3157 (Rfree = 0.000) for 1181 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.2718 (Rfree = 0.000) for 1180 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 2.72 Search for helices and strands: 0 residues in 0 chains, 1199 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 8 peptides. Score 0.217 Round 2: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.305 Round 3: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.277 Round 4: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.313 Round 5: 68 peptides, 11 chains. Longest chain 10 peptides. Score 0.381 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 57, 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 2oh3-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2252 reflections ( 97.57 % complete ) and 2555 restraints for refining 1176 atoms. 2338 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2664 (Rfree = 0.000) for 1176 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3041 (Rfree = 0.000) for 1166 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3044 (Rfree = 0.000) for 1162 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3164 (Rfree = 0.000) for 1158 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:07 GMT 2018 Job finished. TimeTaking 25.3 Used memory is bytes: 17755336