null Sun 23 Dec 22:23:01 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 2fzt-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-3.4-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/2fzt-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-3.4-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 22:23:11 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/2fzt-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-3.4-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 124 and 0 Target number of residues in the AU: 124 Target solvent content: 0.6137 Checking the provided sequence file Detected sequence length: 79 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 158 Adjusted target solvent content: 0.51 Input MTZ file: 2fzt-3.4-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: 4 Cell parameters: 49.630 27.430 65.380 90.000 102.600 90.000 Input sequence file: 2fzt-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1264 target number of atoms Had to go as low as 0.75 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 63.805 3.401 Wilson plot Bfac: 57.91 2509 reflections ( 99.52 % complete ) and 0 restraints for refining 1405 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3636 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3415 (Rfree = 0.000) for 1405 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 1453 seeds are put forward NCS extension: 0 residues added, 1453 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 7 peptides. Score 0.232 Round 2: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.324 Round 3: 79 peptides, 13 chains. Longest chain 17 peptides. Score 0.438 Round 4: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.429 Round 5: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.435 Taking the results from Round 3 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2601 restraints for refining 1149 atoms. 2350 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2906 (Rfree = 0.000) for 1149 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 2: After refmac, R = 0.2839 (Rfree = 0.000) for 1131 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 3: After refmac, R = 0.2433 (Rfree = 0.000) for 1128 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2674 (Rfree = 0.000) for 1125 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2444 (Rfree = 0.000) for 1126 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 1214 seeds are put forward NCS extension: 0 residues added, 1214 seeds are put forward Round 1: 63 peptides, 11 chains. Longest chain 7 peptides. Score 0.371 Round 2: 69 peptides, 10 chains. Longest chain 13 peptides. Score 0.466 Round 3: 71 peptides, 10 chains. Longest chain 13 peptides. Score 0.483 Round 4: 83 peptides, 11 chains. Longest chain 13 peptides. Score 0.543 Round 5: 77 peptides, 10 chains. Longest chain 15 peptides. Score 0.532 Taking the results from Round 4 Chains 11, Residues 72, Estimated correctness of the model 8.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2627 restraints for refining 1148 atoms. 2350 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2992 (Rfree = 0.000) for 1148 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 7: After refmac, R = 0.2777 (Rfree = 0.000) for 1140 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2582 (Rfree = 0.000) for 1138 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2559 (Rfree = 0.000) for 1129 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2455 (Rfree = 0.000) for 1128 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 1182 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1196 seeds are put forward Round 1: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.361 Round 2: 72 peptides, 9 chains. Longest chain 12 peptides. Score 0.528 Round 3: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.444 Round 4: 80 peptides, 12 chains. Longest chain 12 peptides. Score 0.484 Round 5: 88 peptides, 12 chains. Longest chain 12 peptides. Score 0.547 Taking the results from Round 5 Chains 12, Residues 76, Estimated correctness of the model 10.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2476 restraints for refining 1128 atoms. 2184 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2816 (Rfree = 0.000) for 1128 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 12: After refmac, R = 0.2441 (Rfree = 0.000) for 1121 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.2230 (Rfree = 0.000) for 1117 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2298 (Rfree = 0.000) for 1112 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2007 (Rfree = 0.000) for 1107 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 1178 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 1183 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.314 Round 2: 80 peptides, 13 chains. Longest chain 12 peptides. Score 0.447 Round 3: 84 peptides, 11 chains. Longest chain 15 peptides. Score 0.551 Round 4: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.483 Round 5: 80 peptides, 13 chains. Longest chain 15 peptides. Score 0.447 Taking the results from Round 3 Chains 11, Residues 73, Estimated correctness of the model 11.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2526 restraints for refining 1149 atoms. 2245 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2878 (Rfree = 0.000) for 1149 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 17: After refmac, R = 0.2385 (Rfree = 0.000) for 1142 atoms. Found 5 (8 requested) and removed 8 (4 requested) atoms. Cycle 18: After refmac, R = 0.2259 (Rfree = 0.000) for 1134 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2154 (Rfree = 0.000) for 1134 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2152 (Rfree = 0.000) for 1132 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 1191 seeds are put forward NCS extension: 0 residues added, 1191 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 5 peptides. Score 0.260 Round 2: 78 peptides, 15 chains. Longest chain 7 peptides. Score 0.351 Round 3: 78 peptides, 11 chains. Longest chain 13 peptides. Score 0.504 Round 4: 82 peptides, 11 chains. Longest chain 17 peptides. Score 0.536 Round 5: 84 peptides, 11 chains. Longest chain 17 peptides. Score 0.551 Taking the results from Round 5 Chains 11, Residues 73, Estimated correctness of the model 11.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2528 restraints for refining 1149 atoms. 2247 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2992 (Rfree = 0.000) for 1149 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2383 (Rfree = 0.000) for 1146 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2706 (Rfree = 0.000) for 1141 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2178 (Rfree = 0.000) for 1141 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2532 (Rfree = 0.000) for 1140 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 1205 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1225 seeds are put forward Round 1: 56 peptides, 13 chains. Longest chain 6 peptides. Score 0.211 Round 2: 72 peptides, 15 chains. Longest chain 6 peptides. Score 0.293 Round 3: 82 peptides, 16 chains. Longest chain 7 peptides. Score 0.349 Round 4: 82 peptides, 13 chains. Longest chain 13 peptides. Score 0.464 Round 5: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.381 Taking the results from Round 4 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2540 restraints for refining 1149 atoms. 2277 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2792 (Rfree = 0.000) for 1149 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 27: After refmac, R = 0.2535 (Rfree = 0.000) for 1146 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2320 (Rfree = 0.000) for 1144 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.2165 (Rfree = 0.000) for 1140 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2071 (Rfree = 0.000) for 1135 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 1189 seeds are put forward NCS extension: 0 residues added, 1189 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.346 Round 2: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.360 Round 3: 72 peptides, 13 chains. Longest chain 12 peptides. Score 0.374 Round 4: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.370 Round 5: 75 peptides, 12 chains. Longest chain 11 peptides. Score 0.441 Taking the results from Round 5 Chains 12, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2618 restraints for refining 1149 atoms. 2378 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2545 (Rfree = 0.000) for 1149 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2404 (Rfree = 0.000) for 1146 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2273 (Rfree = 0.000) for 1147 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.2173 (Rfree = 0.000) for 1144 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.1975 (Rfree = 0.000) for 1141 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 1207 seeds are put forward NCS extension: 10 residues added (1 deleted due to clashes), 1217 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 8 peptides. Score 0.256 Round 2: 61 peptides, 11 chains. Longest chain 11 peptides. Score 0.351 Round 3: 62 peptides, 10 chains. Longest chain 13 peptides. Score 0.403 Round 4: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.399 Round 5: 60 peptides, 10 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 3 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2610 restraints for refining 1149 atoms. 2412 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2661 (Rfree = 0.000) for 1149 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 37: After refmac, R = 0.2218 (Rfree = 0.000) for 1143 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.2242 (Rfree = 0.000) for 1139 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2076 (Rfree = 0.000) for 1140 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1939 (Rfree = 0.000) for 1136 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 1204 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 1214 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.277 Round 2: 60 peptides, 10 chains. Longest chain 14 peptides. Score 0.384 Round 3: 66 peptides, 12 chains. Longest chain 7 peptides. Score 0.358 Round 4: 61 peptides, 12 chains. Longest chain 8 peptides. Score 0.308 Round 5: 57 peptides, 11 chains. Longest chain 14 peptides. Score 0.311 Taking the results from Round 2 Chains 10, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2569 restraints for refining 1149 atoms. 2379 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2283 (Rfree = 0.000) for 1149 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 42: After refmac, R = 0.2135 (Rfree = 0.000) for 1150 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2161 (Rfree = 0.000) for 1139 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2165 (Rfree = 0.000) for 1140 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2183 (Rfree = 0.000) for 1138 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.09 Search for helices and strands: 0 residues in 0 chains, 1190 seeds are put forward NCS extension: 0 residues added, 1190 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.222 Round 2: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.277 Round 3: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.284 Round 4: 60 peptides, 10 chains. Longest chain 8 peptides. Score 0.384 Round 5: 68 peptides, 13 chains. Longest chain 7 peptides. Score 0.336 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, 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 2fzt-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2509 reflections ( 99.52 % complete ) and 2621 restraints for refining 1149 atoms. 2431 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2712 (Rfree = 0.000) for 1149 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2281 (Rfree = 0.000) for 1135 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2372 (Rfree = 0.000) for 1128 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2040 (Rfree = 0.000) for 1120 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:01 GMT 2018 Job finished. TimeTaking 24.99 Used memory is bytes: 20338752