null Mon 24 Dec 01:02:18 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fzt-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fzt-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fzt-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-3.4-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:02:23 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-3.4-parrot-mrncs/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-mrncs.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-mrncs.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 1393 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3613 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3368 (Rfree = 0.000) for 1393 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 1457 seeds are put forward NCS extension: 0 residues added, 1457 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.191 Round 2: 67 peptides, 13 chains. Longest chain 9 peptides. Score 0.326 Round 3: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.411 Round 4: 81 peptides, 14 chains. Longest chain 12 peptides. Score 0.418 Round 5: 77 peptides, 13 chains. Longest chain 13 peptides. Score 0.420 Taking the results from Round 5 Chains 13, Residues 64, 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 1118 atoms. 2297 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3268 (Rfree = 0.000) for 1118 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 2: After refmac, R = 0.3168 (Rfree = 0.000) for 1092 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.2738 (Rfree = 0.000) for 1083 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 4: After refmac, R = 0.3056 (Rfree = 0.000) for 1075 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2811 (Rfree = 0.000) for 1073 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.10 Search for helices and strands: 0 residues in 0 chains, 1147 seeds are put forward NCS extension: 0 residues added, 1147 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.245 Round 2: 70 peptides, 11 chains. Longest chain 10 peptides. Score 0.435 Round 3: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.393 Round 4: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.423 Round 5: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.467 Taking the results from Round 5 Chains 12, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2443 restraints for refining 1111 atoms. 2191 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2756 (Rfree = 0.000) for 1111 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 7: After refmac, R = 0.2702 (Rfree = 0.000) for 1102 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2688 (Rfree = 0.000) for 1097 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2497 (Rfree = 0.000) for 1089 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2332 (Rfree = 0.000) for 1086 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 1132 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 1144 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 7 peptides. Score 0.267 Round 2: 73 peptides, 12 chains. Longest chain 9 peptides. Score 0.423 Round 3: 82 peptides, 13 chains. Longest chain 9 peptides. Score 0.464 Round 4: 80 peptides, 13 chains. Longest chain 12 peptides. Score 0.447 Round 5: 84 peptides, 13 chains. Longest chain 11 peptides. Score 0.481 Taking the results from Round 5 Chains 13, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2395 restraints for refining 1102 atoms. 2124 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3133 (Rfree = 0.000) for 1102 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 12: After refmac, R = 0.2754 (Rfree = 0.000) for 1083 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2474 (Rfree = 0.000) for 1076 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2426 (Rfree = 0.000) for 1074 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2402 (Rfree = 0.000) for 1075 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 1138 seeds are put forward NCS extension: 9 residues added (2 deleted due to clashes), 1147 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 7 peptides. Score 0.334 Round 2: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.302 Round 3: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.351 Round 4: 77 peptides, 13 chains. Longest chain 13 peptides. Score 0.420 Round 5: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.469 Taking the results from Round 5 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2475 restraints for refining 1133 atoms. 2197 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2876 (Rfree = 0.000) for 1133 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 17: After refmac, R = 0.2516 (Rfree = 0.000) for 1119 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.2340 (Rfree = 0.000) for 1111 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.2338 (Rfree = 0.000) for 1106 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.2289 (Rfree = 0.000) for 1099 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 1164 seeds are put forward NCS extension: 0 residues added, 1164 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 10 peptides. Score 0.311 Round 2: 78 peptides, 13 chains. Longest chain 14 peptides. Score 0.429 Round 3: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.360 Round 4: 74 peptides, 15 chains. Longest chain 7 peptides. Score 0.312 Round 5: 75 peptides, 13 chains. Longest chain 11 peptides. Score 0.402 Taking the results from Round 2 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2500 restraints for refining 1109 atoms. 2253 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2662 (Rfree = 0.000) for 1109 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 22: After refmac, R = 0.2515 (Rfree = 0.000) for 1108 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2430 (Rfree = 0.000) for 1103 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2457 (Rfree = 0.000) for 1100 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2296 (Rfree = 0.000) for 1094 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 1159 seeds are put forward NCS extension: 0 residues added, 1159 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.221 Round 2: 75 peptides, 12 chains. Longest chain 12 peptides. Score 0.441 Round 3: 75 peptides, 14 chains. Longest chain 11 peptides. Score 0.362 Round 4: 81 peptides, 13 chains. Longest chain 11 peptides. Score 0.455 Round 5: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.444 Taking the results from Round 4 Chains 13, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2552 restraints for refining 1130 atoms. 2293 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2630 (Rfree = 0.000) for 1130 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 27: After refmac, R = 0.2378 (Rfree = 0.000) for 1125 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2354 (Rfree = 0.000) for 1122 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.2317 (Rfree = 0.000) for 1117 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2298 (Rfree = 0.000) for 1113 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 1164 seeds are put forward NCS extension: 0 residues added, 1164 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 6 peptides. Score 0.256 Round 2: 70 peptides, 13 chains. Longest chain 7 peptides. Score 0.355 Round 3: 74 peptides, 11 chains. Longest chain 11 peptides. Score 0.470 Round 4: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.432 Round 5: 81 peptides, 12 chains. Longest chain 12 peptides. Score 0.492 Taking the results from Round 5 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2602 restraints for refining 1149 atoms. 2338 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2538 (Rfree = 0.000) for 1149 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 32: After refmac, R = 0.2328 (Rfree = 0.000) for 1150 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2241 (Rfree = 0.000) for 1147 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2142 (Rfree = 0.000) for 1144 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2127 (Rfree = 0.000) for 1139 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 1197 seeds are put forward NCS extension: 0 residues added, 1197 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 8 peptides. Score 0.283 Round 2: 83 peptides, 15 chains. Longest chain 11 peptides. Score 0.397 Round 3: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.334 Round 4: 82 peptides, 15 chains. Longest chain 8 peptides. Score 0.388 Round 5: 75 peptides, 11 chains. Longest chain 12 peptides. Score 0.479 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2649 restraints for refining 1149 atoms. 2404 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2443 (Rfree = 0.000) for 1149 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.2299 (Rfree = 0.000) for 1143 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2118 (Rfree = 0.000) for 1134 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2142 (Rfree = 0.000) for 1130 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.1986 (Rfree = 0.000) for 1128 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 3.07 Search for helices and strands: 0 residues in 0 chains, 1173 seeds are put forward NCS extension: 0 residues added, 1173 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 9 peptides. Score 0.277 Round 2: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.396 Round 3: 70 peptides, 12 chains. Longest chain 12 peptides. Score 0.396 Round 4: 70 peptides, 12 chains. Longest chain 12 peptides. Score 0.396 Round 5: 70 peptides, 11 chains. Longest chain 12 peptides. Score 0.435 Taking the results from Round 5 Chains 11, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2509 reflections ( 99.52 % complete ) and 2650 restraints for refining 1149 atoms. 2425 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2550 (Rfree = 0.000) for 1149 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2265 (Rfree = 0.000) for 1141 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2385 (Rfree = 0.000) for 1140 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.2238 (Rfree = 0.000) for 1136 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2121 (Rfree = 0.000) for 1135 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 1205 seeds are put forward NCS extension: 0 residues added, 1205 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 12 peptides. Score 0.306 Round 2: 67 peptides, 11 chains. Longest chain 12 peptides. Score 0.408 Round 3: 71 peptides, 13 chains. Longest chain 12 peptides. Score 0.365 Round 4: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.343 Round 5: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.361 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 56, 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 2589 restraints for refining 1149 atoms. 2376 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2525 (Rfree = 0.000) for 1149 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2479 (Rfree = 0.000) for 1140 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2413 (Rfree = 0.000) for 1133 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2351 (Rfree = 0.000) for 1127 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:24:45 GMT 2018 Job finished. TimeTaking 22.46 Used memory is bytes: 18825400