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 2oh3-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-3.6-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/2oh3-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-3.6-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/2oh3-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-3.6-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 142 and 0 Target number of residues in the AU: 142 Target solvent content: 0.6467 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: 2oh3-3.6-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: 2oh3-3.6-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 3.600 Wilson plot Bfac: 76.00 2653 reflections ( 97.75 % complete ) and 0 restraints for refining 1482 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3343 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3381 (Rfree = 0.000) for 1482 atoms. Found 9 (9 requested) and removed 72 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 2.80 Search for helices and strands: 0 residues in 0 chains, 1450 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 7 peptides. Score 0.221 Round 2: 88 peptides, 16 chains. Longest chain 9 peptides. Score 0.368 Round 3: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.434 Round 4: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.434 Round 5: 101 peptides, 14 chains. Longest chain 14 peptides. Score 0.520 Taking the results from Round 5 Chains 14, Residues 87, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2653 reflections ( 97.75 % complete ) and 2764 restraints for refining 1210 atoms. 2386 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2671 (Rfree = 0.000) for 1210 atoms. Found 7 (7 requested) and removed 25 (3 requested) atoms. Cycle 2: After refmac, R = 0.2662 (Rfree = 0.000) for 1177 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 3: After refmac, R = 0.2628 (Rfree = 0.000) for 1162 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 4: After refmac, R = 0.2635 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 5: After refmac, R = 0.2760 (Rfree = 0.000) for 1138 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.72 Search for helices and strands: 0 residues in 0 chains, 1199 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.275 Round 2: 94 peptides, 14 chains. Longest chain 12 peptides. Score 0.474 Round 3: 95 peptides, 13 chains. Longest chain 14 peptides. Score 0.510 Round 4: 101 peptides, 16 chains. Longest chain 12 peptides. Score 0.462 Round 5: 102 peptides, 13 chains. Longest chain 18 peptides. Score 0.554 Taking the results from Round 5 Chains 15, Residues 89, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2653 reflections ( 97.75 % complete ) and 2580 restraints for refining 1209 atoms. 2201 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3059 (Rfree = 0.000) for 1209 atoms. Found 7 (7 requested) and removed 45 (3 requested) atoms. Cycle 7: After refmac, R = 0.2992 (Rfree = 0.000) for 1164 atoms. Found 7 (7 requested) and removed 34 (3 requested) atoms. Cycle 8: After refmac, R = 0.2800 (Rfree = 0.000) for 1131 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 9: After refmac, R = 0.2720 (Rfree = 0.000) for 1122 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 10: After refmac, R = 0.2826 (Rfree = 0.000) for 1114 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 1180 seeds are put forward Round 1: 82 peptides, 15 chains. Longest chain 12 peptides. Score 0.354 Round 2: 87 peptides, 13 chains. Longest chain 13 peptides. Score 0.456 Round 3: 98 peptides, 15 chains. Longest chain 15 peptides. Score 0.471 Round 4: 91 peptides, 13 chains. Longest chain 15 peptides. Score 0.483 Round 5: 108 peptides, 17 chains. Longest chain 13 peptides. Score 0.479 Taking the results from Round 4 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2653 reflections ( 97.75 % complete ) and 2652 restraints for refining 1182 atoms. 2353 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2961 (Rfree = 0.000) for 1182 atoms. Found 7 (7 requested) and removed 48 (3 requested) atoms. Cycle 12: After refmac, R = 0.2770 (Rfree = 0.000) for 1139 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 13: After refmac, R = 0.2624 (Rfree = 0.000) for 1129 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 14: After refmac, R = 0.2420 (Rfree = 0.000) for 1121 atoms. Found 3 (7 requested) and removed 9 (3 requested) atoms. Cycle 15: After refmac, R = 0.2457 (Rfree = 0.000) for 1114 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 2.86 Search for helices and strands: 0 residues in 0 chains, 1131 seeds are put forward Round 1: 70 peptides, 12 chains. Longest chain 14 peptides. Score 0.362 Round 2: 75 peptides, 11 chains. Longest chain 15 peptides. Score 0.434 Round 3: 79 peptides, 12 chains. Longest chain 15 peptides. Score 0.430 Round 4: 78 peptides, 12 chains. Longest chain 16 peptides. Score 0.423 Round 5: 74 peptides, 12 chains. Longest chain 17 peptides. Score 0.393 Taking the results from Round 2 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2653 reflections ( 97.75 % complete ) and 2532 restraints for refining 1146 atoms. 2287 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2787 (Rfree = 0.000) for 1146 atoms. Found 7 (7 requested) and removed 20 (3 requested) atoms. Cycle 17: After refmac, R = 0.3523 (Rfree = 0.000) for 1128 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 18: After refmac, R = 0.2958 (Rfree = 0.000) for 1112 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 19: After refmac, R = 0.2663 (Rfree = 0.000) for 1103 atoms. Found 5 (7 requested) and removed 12 (3 requested) atoms. Cycle 20: After refmac, R = 0.2836 (Rfree = 0.000) for 1092 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.88 2.59 Search for helices and strands: 0 residues in 0 chains, 1133 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 10 peptides. Score 0.298 Round 2: 93 peptides, 19 chains. Longest chain 12 peptides. Score 0.308 Round 3: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.315 Round 4: 84 peptides, 16 chains. Longest chain 10 peptides. Score 0.337 Round 5: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 5 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2653 reflections ( 97.75 % complete ) and 2564 restraints for refining 1211 atoms. 2242 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2869 (Rfree = 0.000) for 1211 atoms. Found 4 (7 requested) and removed 23 (3 requested) atoms. Cycle 22: After refmac, R = 0.2817 (Rfree = 0.000) for 1180 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 23: After refmac, R = 0.3174 (Rfree = 0.000) for 1169 atoms. Found 7 (7 requested) and removed 18 (3 requested) atoms. Cycle 24: After refmac, R = 0.3242 (Rfree = 0.000) for 1155 atoms. Found 7 (7 requested) and removed 21 (3 requested) atoms. Cycle 25: After refmac, R = 0.2980 (Rfree = 0.000) for 1133 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.60 2.34 Search for helices and strands: 0 residues in 0 chains, 1169 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 11 peptides. Score 0.254 Round 2: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.383 Round 3: 86 peptides, 17 chains. Longest chain 11 peptides. Score 0.319 Round 4: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.335 Round 5: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 5 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2653 reflections ( 97.75 % complete ) and 2570 restraints for refining 1211 atoms. 2266 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3096 (Rfree = 0.000) for 1211 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 27: After refmac, R = 0.3060 (Rfree = 0.000) for 1195 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 28: After refmac, R = 0.3113 (Rfree = 0.000) for 1182 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 29: After refmac, R = 0.3052 (Rfree = 0.000) for 1173 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 30: After refmac, R = 0.3059 (Rfree = 0.000) for 1167 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.55 2.29 Search for helices and strands: 0 residues in 0 chains, 1225 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 7 peptides. Score 0.230 Round 2: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.308 Round 3: 80 peptides, 16 chains. Longest chain 11 peptides. Score 0.305 Round 4: 84 peptides, 17 chains. Longest chain 7 peptides. Score 0.303 Round 5: 79 peptides, 14 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 5 Chains 14, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2653 reflections ( 97.75 % complete ) and 2715 restraints for refining 1211 atoms. 2469 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3573 (Rfree = 0.000) for 1211 atoms. Found 7 (7 requested) and removed 18 (3 requested) atoms. Cycle 32: After refmac, R = 0.3167 (Rfree = 0.000) for 1192 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.3154 (Rfree = 0.000) for 1181 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2975 (Rfree = 0.000) for 1182 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2861 (Rfree = 0.000) for 1181 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 2.82 Search for helices and strands: 0 residues in 0 chains, 1211 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.228 Round 2: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.259 Round 3: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.336 Round 4: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.285 Round 5: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.321 Taking the results from Round 3 Chains 10, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2653 reflections ( 97.75 % complete ) and 2524 restraints for refining 1131 atoms. 2342 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2937 (Rfree = 0.000) for 1131 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 37: After refmac, R = 0.2926 (Rfree = 0.000) for 1128 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.3071 (Rfree = 0.000) for 1127 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 39: After refmac, R = 0.2640 (Rfree = 0.000) for 1126 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.2646 (Rfree = 0.000) for 1125 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 2.78 Search for helices and strands: 0 residues in 0 chains, 1147 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.269 Round 2: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.348 Round 3: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.349 Round 4: 69 peptides, 11 chains. Longest chain 12 peptides. Score 0.389 Round 5: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.354 Taking the results from Round 4 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2653 reflections ( 97.75 % complete ) and 2539 restraints for refining 1162 atoms. 2318 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2756 (Rfree = 0.000) for 1162 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 42: After refmac, R = 0.2515 (Rfree = 0.000) for 1157 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 43: After refmac, R = 0.2633 (Rfree = 0.000) for 1155 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.2538 (Rfree = 0.000) for 1153 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 45: After refmac, R = 0.2401 (Rfree = 0.000) for 1148 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 2.89 Search for helices and strands: 0 residues in 0 chains, 1168 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 6 peptides. Score 0.221 Round 2: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.275 Round 3: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.308 Round 4: 75 peptides, 14 chains. Longest chain 7 peptides. Score 0.333 Round 5: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 61, 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. 2653 reflections ( 97.75 % complete ) and 2741 restraints for refining 1211 atoms. 2511 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2590 (Rfree = 0.000) for 1211 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2531 (Rfree = 0.000) for 1207 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2637 (Rfree = 0.000) for 1202 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2489 (Rfree = 0.000) for 1197 atoms. TimeTaking 57.15