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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2osd-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2osd-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-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/2osd-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-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 22:23:06 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-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 107 and 0 Target number of residues in the AU: 107 Target solvent content: 0.6872 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-3.8-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: 96 Cell parameters: 55.786 55.786 118.990 90.000 90.000 90.000 Input sequence file: 2osd-3.8-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 3.800 Wilson plot Bfac: 107.59 2097 reflections ( 99.71 % complete ) and 0 restraints for refining 1454 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3720 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3346 (Rfree = 0.000) for 1454 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.93 3.83 Search for helices and strands: 0 residues in 0 chains, 1469 seeds are put forward Round 1: 61 peptides, 11 chains. Longest chain 11 peptides. Score 0.343 Round 2: 77 peptides, 11 chains. Longest chain 13 peptides. Score 0.482 Round 3: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.453 Round 4: 75 peptides, 11 chains. Longest chain 17 peptides. Score 0.466 Round 5: 77 peptides, 10 chains. Longest chain 13 peptides. Score 0.517 Taking the results from Round 5 Chains 10, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.71 % complete ) and 2856 restraints for refining 1179 atoms. 2598 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2779 (Rfree = 0.000) for 1179 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 2: After refmac, R = 0.2516 (Rfree = 0.000) for 1163 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.2444 (Rfree = 0.000) for 1152 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.2403 (Rfree = 0.000) for 1147 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2427 (Rfree = 0.000) for 1141 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.99 3.89 Search for helices and strands: 0 residues in 0 chains, 1169 seeds are put forward Round 1: 66 peptides, 10 chains. Longest chain 10 peptides. Score 0.428 Round 2: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.416 Round 3: 74 peptides, 10 chains. Longest chain 14 peptides. Score 0.494 Round 4: 72 peptides, 7 chains. Longest chain 23 peptides. Score 0.583 Round 5: 72 peptides, 11 chains. Longest chain 12 peptides. Score 0.441 Taking the results from Round 4 Chains 7, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.71 % complete ) and 2862 restraints for refining 1174 atoms. 2609 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2672 (Rfree = 0.000) for 1174 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 7: After refmac, R = 0.2490 (Rfree = 0.000) for 1166 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 8: After refmac, R = 0.2445 (Rfree = 0.000) for 1161 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.2393 (Rfree = 0.000) for 1157 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2340 (Rfree = 0.000) for 1152 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.94 3.84 Search for helices and strands: 0 residues in 0 chains, 1177 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 7 peptides. Score 0.305 Round 2: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.371 Round 3: 72 peptides, 10 chains. Longest chain 12 peptides. Score 0.478 Round 4: 71 peptides, 10 chains. Longest chain 10 peptides. Score 0.470 Round 5: 73 peptides, 11 chains. Longest chain 12 peptides. Score 0.450 Taking the results from Round 3 Chains 10, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.71 % complete ) and 2791 restraints for refining 1179 atoms. 2553 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2561 (Rfree = 0.000) for 1179 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.2511 (Rfree = 0.000) for 1162 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2464 (Rfree = 0.000) for 1156 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.2089 (Rfree = 0.000) for 1151 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.1951 (Rfree = 0.000) for 1146 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.91 3.81 Search for helices and strands: 0 residues in 0 chains, 1172 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.283 Round 2: 71 peptides, 12 chains. Longest chain 13 peptides. Score 0.395 Round 3: 78 peptides, 11 chains. Longest chain 12 peptides. Score 0.490 Round 4: 81 peptides, 12 chains. Longest chain 12 peptides. Score 0.478 Round 5: 79 peptides, 12 chains. Longest chain 12 peptides. Score 0.462 Taking the results from Round 3 Chains 11, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.71 % complete ) and 2721 restraints for refining 1149 atoms. 2464 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2312 (Rfree = 0.000) for 1149 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 17: After refmac, R = 0.2199 (Rfree = 0.000) for 1143 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2212 (Rfree = 0.000) for 1142 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2152 (Rfree = 0.000) for 1142 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1922 (Rfree = 0.000) for 1138 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.89 3.79 Search for helices and strands: 0 residues in 0 chains, 1166 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.277 Round 2: 63 peptides, 8 chains. Longest chain 17 peptides. Score 0.479 Round 3: 52 peptides, 8 chains. Longest chain 16 peptides. Score 0.383 Round 4: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.369 Round 5: 58 peptides, 8 chains. Longest chain 12 peptides. Score 0.437 Taking the results from Round 2 Chains 8, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.71 % complete ) and 2821 restraints for refining 1178 atoms. 2609 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2545 (Rfree = 0.000) for 1178 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 22: After refmac, R = 0.2394 (Rfree = 0.000) for 1174 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2561 (Rfree = 0.000) for 1170 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.1964 (Rfree = 0.000) for 1164 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1935 (Rfree = 0.000) for 1159 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.98 3.88 Search for helices and strands: 0 residues in 0 chains, 1211 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 9 peptides. Score 0.233 Round 2: 58 peptides, 9 chains. Longest chain 11 peptides. Score 0.397 Round 3: 60 peptides, 10 chains. Longest chain 12 peptides. Score 0.375 Round 4: 54 peptides, 9 chains. Longest chain 10 peptides. Score 0.360 Round 5: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.315 Taking the results from Round 2 Chains 9, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.71 % complete ) and 2836 restraints for refining 1179 atoms. 2649 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2363 (Rfree = 0.000) for 1179 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 27: After refmac, R = 0.2539 (Rfree = 0.000) for 1180 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.2496 (Rfree = 0.000) for 1177 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2446 (Rfree = 0.000) for 1166 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2464 (Rfree = 0.000) for 1160 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.89 3.79 Search for helices and strands: 0 residues in 0 chains, 1192 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.213 Round 2: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.277 Round 3: 52 peptides, 9 chains. Longest chain 11 peptides. Score 0.341 Round 4: 53 peptides, 9 chains. Longest chain 10 peptides. Score 0.350 Round 5: 58 peptides, 9 chains. Longest chain 11 peptides. Score 0.397 Taking the results from Round 5 Chains 9, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.71 % complete ) and 2750 restraints for refining 1156 atoms. 2563 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2573 (Rfree = 0.000) for 1156 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.2500 (Rfree = 0.000) for 1150 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2651 (Rfree = 0.000) for 1144 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. Cycle 34: After refmac, R = 0.2613 (Rfree = 0.000) for 1128 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 35: After refmac, R = 0.2439 (Rfree = 0.000) for 1122 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.90 3.80 Search for helices and strands: 0 residues in 0 chains, 1162 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 5 peptides. Score 0.213 Round 2: 52 peptides, 9 chains. Longest chain 11 peptides. Score 0.341 Round 3: 54 peptides, 9 chains. Longest chain 9 peptides. Score 0.360 Round 4: 58 peptides, 10 chains. Longest chain 11 peptides. Score 0.356 Round 5: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 3 Chains 9, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.71 % complete ) and 2418 restraints for refining 1094 atoms. 2247 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2567 (Rfree = 0.000) for 1094 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 37: After refmac, R = 0.2678 (Rfree = 0.000) for 1085 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.2619 (Rfree = 0.000) for 1070 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 39: After refmac, R = 0.2990 (Rfree = 0.000) for 1069 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 40: After refmac, R = 0.2328 (Rfree = 0.000) for 1059 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.93 3.83 Search for helices and strands: 0 residues in 0 chains, 1111 seeds are put forward Round 1: 38 peptides, 9 chains. Longest chain 6 peptides. Score 0.191 Round 2: 52 peptides, 9 chains. Longest chain 9 peptides. Score 0.341 Round 3: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.298 Round 4: 57 peptides, 11 chains. Longest chain 7 peptides. Score 0.305 Round 5: 60 peptides, 10 chains. Longest chain 9 peptides. Score 0.375 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 ------------------------------------------------------ 2097 reflections ( 99.71 % complete ) and 2229 restraints for refining 1038 atoms. 2039 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2188 (Rfree = 0.000) for 1038 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 42: After refmac, R = 0.2292 (Rfree = 0.000) for 1036 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.3048 (Rfree = 0.000) for 1030 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 44: After refmac, R = 0.2497 (Rfree = 0.000) for 1025 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.2897 (Rfree = 0.000) for 1016 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.90 3.80 Search for helices and strands: 0 residues in 0 chains, 1055 seeds are put forward Round 1: 32 peptides, 6 chains. Longest chain 9 peptides. Score 0.270 Round 2: 36 peptides, 6 chains. Longest chain 10 peptides. Score 0.315 Round 3: 35 peptides, 6 chains. Longest chain 7 peptides. Score 0.304 Round 4: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.288 Round 5: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.254 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 30, 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. 2097 reflections ( 99.71 % complete ) and 2253 restraints for refining 1002 atoms. 2139 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2702 (Rfree = 0.000) for 1002 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2299 (Rfree = 0.000) for 989 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2258 (Rfree = 0.000) for 983 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2759 (Rfree = 0.000) for 978 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:30 GMT 2018 Job finished. TimeTaking 25.57 Used memory is bytes: 20771992