null Sun 23 Dec 22:22:56 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2osd-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2osd-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-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/2osd-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-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 22:23:05 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-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 110 and 0 Target number of residues in the AU: 110 Target solvent content: 0.6785 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-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: 96 Cell parameters: 55.786 55.786 118.990 90.000 90.000 90.000 Input sequence file: 2osd-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1304 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: 50.510 3.600 Wilson plot Bfac: 99.42 2445 reflections ( 99.76 % complete ) and 0 restraints for refining 1452 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3651 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3156 (Rfree = 0.000) for 1452 atoms. Found 9 (9 requested) and removed 74 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 1406 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 10 peptides. Score 0.321 Round 2: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.418 Round 3: 83 peptides, 11 chains. Longest chain 17 peptides. Score 0.528 Round 4: 86 peptides, 10 chains. Longest chain 15 peptides. Score 0.582 Round 5: 84 peptides, 12 chains. Longest chain 16 peptides. Score 0.502 Taking the results from Round 4 Chains 10, Residues 76, Estimated correctness of the model 7.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2445 reflections ( 99.76 % complete ) and 2756 restraints for refining 1170 atoms. 2462 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3032 (Rfree = 0.000) for 1170 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 2: After refmac, R = 0.2847 (Rfree = 0.000) for 1152 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2735 (Rfree = 0.000) for 1136 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.2586 (Rfree = 0.000) for 1122 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.2489 (Rfree = 0.000) for 1113 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 1156 seeds are put forward Round 1: 60 peptides, 9 chains. Longest chain 15 peptides. Score 0.415 Round 2: 80 peptides, 12 chains. Longest chain 15 peptides. Score 0.471 Round 3: 84 peptides, 12 chains. Longest chain 12 peptides. Score 0.502 Round 4: 82 peptides, 12 chains. Longest chain 13 peptides. Score 0.486 Round 5: 81 peptides, 9 chains. Longest chain 13 peptides. Score 0.579 Taking the results from Round 5 Chains 9, Residues 72, Estimated correctness of the model 6.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2445 reflections ( 99.76 % complete ) and 2429 restraints for refining 1094 atoms. 2150 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2506 (Rfree = 0.000) for 1094 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 7: After refmac, R = 0.2494 (Rfree = 0.000) for 1084 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.2340 (Rfree = 0.000) for 1082 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.2537 (Rfree = 0.000) for 1082 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2407 (Rfree = 0.000) for 1082 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 1137 seeds are put forward Round 1: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.371 Round 2: 75 peptides, 12 chains. Longest chain 10 peptides. Score 0.429 Round 3: 81 peptides, 13 chains. Longest chain 11 peptides. Score 0.443 Round 4: 73 peptides, 11 chains. Longest chain 15 peptides. Score 0.450 Round 5: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 4 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2445 reflections ( 99.76 % complete ) and 2464 restraints for refining 1101 atoms. 2227 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2965 (Rfree = 0.000) for 1101 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 12: After refmac, R = 0.2565 (Rfree = 0.000) for 1089 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 13: After refmac, R = 0.2695 (Rfree = 0.000) for 1084 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.3137 (Rfree = 0.000) for 1081 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2366 (Rfree = 0.000) for 1078 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 1126 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 11 peptides. Score 0.285 Round 2: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.338 Round 3: 69 peptides, 12 chains. Longest chain 8 peptides. Score 0.377 Round 4: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.401 Round 5: 72 peptides, 11 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 5 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2445 reflections ( 99.76 % complete ) and 2676 restraints for refining 1163 atoms. 2443 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2648 (Rfree = 0.000) for 1163 atoms. Found 5 (7 requested) and removed 10 (3 requested) atoms. Cycle 17: After refmac, R = 0.2626 (Rfree = 0.000) for 1143 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 18: After refmac, R = 0.2690 (Rfree = 0.000) for 1133 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2524 (Rfree = 0.000) for 1127 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2443 (Rfree = 0.000) for 1122 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1183 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.298 Round 2: 66 peptides, 11 chains. Longest chain 12 peptides. Score 0.389 Round 3: 69 peptides, 9 chains. Longest chain 22 peptides. Score 0.490 Round 4: 61 peptides, 10 chains. Longest chain 12 peptides. Score 0.384 Round 5: 69 peptides, 9 chains. Longest chain 17 peptides. Score 0.490 Taking the results from Round 5 Chains 9, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2445 reflections ( 99.76 % complete ) and 2552 restraints for refining 1135 atoms. 2321 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2580 (Rfree = 0.000) for 1135 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 22: After refmac, R = 0.2620 (Rfree = 0.000) for 1120 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2401 (Rfree = 0.000) for 1116 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.2460 (Rfree = 0.000) for 1117 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1986 (Rfree = 0.000) for 1117 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 1160 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 11 peptides. Score 0.356 Round 2: 78 peptides, 13 chains. Longest chain 13 peptides. Score 0.418 Round 3: 75 peptides, 12 chains. Longest chain 14 peptides. Score 0.429 Round 4: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.412 Round 5: 70 peptides, 12 chains. Longest chain 13 peptides. Score 0.386 Taking the results from Round 3 Chains 12, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2445 reflections ( 99.76 % complete ) and 2568 restraints for refining 1125 atoms. 2328 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2437 (Rfree = 0.000) for 1125 atoms. Found 5 (7 requested) and removed 25 (3 requested) atoms. Cycle 27: After refmac, R = 0.2496 (Rfree = 0.000) for 1099 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.2265 (Rfree = 0.000) for 1098 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.2400 (Rfree = 0.000) for 1097 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.2280 (Rfree = 0.000) for 1099 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 1147 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.273 Round 2: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.353 Round 3: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.371 Round 4: 72 peptides, 11 chains. Longest chain 11 peptides. Score 0.441 Round 5: 65 peptides, 10 chains. Longest chain 11 peptides. Score 0.419 Taking the results from Round 4 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2445 reflections ( 99.76 % complete ) and 2591 restraints for refining 1111 atoms. 2358 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2466 (Rfree = 0.000) for 1111 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 32: After refmac, R = 0.2579 (Rfree = 0.000) for 1102 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.2315 (Rfree = 0.000) for 1099 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2336 (Rfree = 0.000) for 1099 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2342 (Rfree = 0.000) for 1100 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 1144 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 8 peptides. Score 0.242 Round 2: 59 peptides, 11 chains. Longest chain 11 peptides. Score 0.324 Round 3: 66 peptides, 12 chains. Longest chain 11 peptides. Score 0.350 Round 4: 65 peptides, 12 chains. Longest chain 11 peptides. Score 0.340 Round 5: 62 peptides, 10 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 5 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2445 reflections ( 99.76 % complete ) and 2788 restraints for refining 1176 atoms. 2590 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2621 (Rfree = 0.000) for 1176 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2576 (Rfree = 0.000) for 1162 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.2464 (Rfree = 0.000) for 1156 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 39: After refmac, R = 0.2666 (Rfree = 0.000) for 1149 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 40: After refmac, R = 0.2288 (Rfree = 0.000) for 1145 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 1190 seeds are put forward Round 1: 41 peptides, 10 chains. Longest chain 5 peptides. Score 0.178 Round 2: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.233 Round 3: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.265 Round 4: 52 peptides, 10 chains. Longest chain 10 peptides. Score 0.298 Round 5: 59 peptides, 11 chains. Longest chain 11 peptides. Score 0.324 Taking the results from Round 5 Chains 11, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2445 reflections ( 99.76 % complete ) and 2600 restraints for refining 1110 atoms. 2419 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2453 (Rfree = 0.000) for 1110 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.2351 (Rfree = 0.000) for 1108 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.2321 (Rfree = 0.000) for 1108 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.1873 (Rfree = 0.000) for 1108 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.1824 (Rfree = 0.000) for 1106 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 1140 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.202 Round 2: 51 peptides, 11 chains. Longest chain 6 peptides. Score 0.244 Round 3: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.285 Round 4: 59 peptides, 9 chains. Longest chain 12 peptides. Score 0.406 Round 5: 57 peptides, 10 chains. Longest chain 13 peptides. Score 0.346 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 50, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2445 reflections ( 99.76 % complete ) and 2722 restraints for refining 1163 atoms. 2531 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2142 (Rfree = 0.000) for 1163 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2325 (Rfree = 0.000) for 1157 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2277 (Rfree = 0.000) for 1150 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2086 (Rfree = 0.000) for 1142 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:17 GMT 2018 Job finished. TimeTaking 25.35 Used memory is bytes: 20948856