null Sun 23 Dec 22:22:59 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-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/2fzt-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-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 22:23:08 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-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 120 and 0 Target number of residues in the AU: 120 Target solvent content: 0.6262 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-3.8-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: 4 Cell parameters: 49.630 27.430 65.380 90.000 102.600 90.000 Input sequence file: 2fzt-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1264 target number of atoms Had to go as low as 0.80 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 3.801 Wilson plot Bfac: 64.21 1812 reflections ( 99.34 % complete ) and 0 restraints for refining 1407 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3739 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3403 (Rfree = 0.000) for 1407 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 1447 seeds are put forward NCS extension: 0 residues added, 1447 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.240 Round 2: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.306 Round 3: 75 peptides, 14 chains. Longest chain 11 peptides. Score 0.362 Round 4: 75 peptides, 11 chains. Longest chain 18 peptides. Score 0.479 Round 5: 75 peptides, 11 chains. Longest chain 18 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 ------------------------------------------------------ 1812 reflections ( 99.34 % complete ) and 2680 restraints for refining 1143 atoms. 2435 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2893 (Rfree = 0.000) for 1143 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.2610 (Rfree = 0.000) for 1115 atoms. Found 2 (6 requested) and removed 9 (3 requested) atoms. Cycle 3: After refmac, R = 0.2367 (Rfree = 0.000) for 1096 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2227 (Rfree = 0.000) for 1092 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.2150 (Rfree = 0.000) for 1082 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 1124 seeds are put forward NCS extension: 0 residues added, 1124 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.331 Round 2: 75 peptides, 12 chains. Longest chain 10 peptides. Score 0.441 Round 3: 75 peptides, 12 chains. Longest chain 13 peptides. Score 0.441 Round 4: 79 peptides, 12 chains. Longest chain 13 peptides. Score 0.475 Round 5: 81 peptides, 12 chains. Longest chain 15 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 ------------------------------------------------------ 1812 reflections ( 99.34 % complete ) and 2394 restraints for refining 1084 atoms. 2130 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3137 (Rfree = 0.000) for 1084 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 7: After refmac, R = 0.2677 (Rfree = 0.000) for 1076 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.2440 (Rfree = 0.000) for 1075 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 9: After refmac, R = 0.2451 (Rfree = 0.000) for 1067 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.2324 (Rfree = 0.000) for 1064 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 1126 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 1154 seeds are put forward Round 1: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.374 Round 2: 69 peptides, 10 chains. Longest chain 15 peptides. Score 0.466 Round 3: 73 peptides, 10 chains. Longest chain 16 peptides. Score 0.500 Round 4: 73 peptides, 8 chains. Longest chain 20 peptides. Score 0.572 Round 5: 74 peptides, 9 chains. Longest chain 21 peptides. Score 0.544 Taking the results from Round 4 Chains 8, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1812 reflections ( 99.34 % complete ) and 2457 restraints for refining 1099 atoms. 2205 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2621 (Rfree = 0.000) for 1099 atoms. Found 3 (6 requested) and removed 12 (3 requested) atoms. Cycle 12: After refmac, R = 0.2307 (Rfree = 0.000) for 1086 atoms. Found 3 (5 requested) and removed 6 (2 requested) atoms. Cycle 13: After refmac, R = 0.2278 (Rfree = 0.000) for 1080 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2328 (Rfree = 0.000) for 1076 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.2248 (Rfree = 0.000) for 1076 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 1128 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 1162 seeds are put forward Round 1: 66 peptides, 11 chains. Longest chain 17 peptides. Score 0.399 Round 2: 69 peptides, 10 chains. Longest chain 24 peptides. Score 0.466 Round 3: 73 peptides, 11 chains. Longest chain 20 peptides. Score 0.462 Round 4: 74 peptides, 9 chains. Longest chain 23 peptides. Score 0.544 Round 5: 79 peptides, 8 chains. Longest chain 28 peptides. Score 0.614 Taking the results from Round 5 Chains 8, Residues 71, Estimated correctness of the model 5.2 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 1812 reflections ( 99.34 % complete ) and 2064 restraints for refining 1143 atoms. 1669 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2558 (Rfree = 0.000) for 1143 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. Cycle 17: After refmac, R = 0.2553 (Rfree = 0.000) for 1126 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.2465 (Rfree = 0.000) for 1117 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.2680 (Rfree = 0.000) for 1108 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2282 (Rfree = 0.000) for 1099 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 1143 seeds are put forward NCS extension: 0 residues added, 1143 seeds are put forward Round 1: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.371 Round 2: 74 peptides, 10 chains. Longest chain 19 peptides. Score 0.508 Round 3: 69 peptides, 10 chains. Longest chain 17 peptides. Score 0.466 Round 4: 75 peptides, 10 chains. Longest chain 17 peptides. Score 0.516 Round 5: 70 peptides, 11 chains. Longest chain 14 peptides. Score 0.435 Taking the results from Round 4 Chains 10, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1812 reflections ( 99.34 % complete ) and 2498 restraints for refining 1115 atoms. 2248 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2445 (Rfree = 0.000) for 1115 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 22: After refmac, R = 0.2029 (Rfree = 0.000) for 1105 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.1948 (Rfree = 0.000) for 1101 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.1945 (Rfree = 0.000) for 1097 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1915 (Rfree = 0.000) for 1091 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 1152 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 1180 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 8 peptides. Score 0.262 Round 2: 75 peptides, 14 chains. Longest chain 11 peptides. Score 0.362 Round 3: 68 peptides, 11 chains. Longest chain 16 peptides. Score 0.417 Round 4: 74 peptides, 12 chains. Longest chain 17 peptides. Score 0.432 Round 5: 68 peptides, 11 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 4 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1812 reflections ( 99.34 % complete ) and 2536 restraints for refining 1143 atoms. 2300 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2194 (Rfree = 0.000) for 1143 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.2155 (Rfree = 0.000) for 1136 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.2028 (Rfree = 0.000) for 1132 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.1870 (Rfree = 0.000) for 1130 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.1733 (Rfree = 0.000) for 1127 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 1170 seeds are put forward NCS extension: 0 residues added, 1170 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 9 peptides. Score 0.267 Round 2: 69 peptides, 11 chains. Longest chain 16 peptides. Score 0.427 Round 3: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.355 Round 4: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.405 Round 5: 78 peptides, 11 chains. Longest chain 16 peptides. Score 0.504 Taking the results from Round 5 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 1812 reflections ( 99.34 % complete ) and 2380 restraints for refining 1142 atoms. 2066 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2573 (Rfree = 0.000) for 1142 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 32: After refmac, R = 0.2017 (Rfree = 0.000) for 1134 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.2003 (Rfree = 0.000) for 1130 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.1853 (Rfree = 0.000) for 1127 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1816 (Rfree = 0.000) for 1124 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 1179 seeds are put forward NCS extension: 0 residues added, 1179 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 8 peptides. Score 0.308 Round 2: 59 peptides, 11 chains. Longest chain 11 peptides. Score 0.331 Round 3: 66 peptides, 11 chains. Longest chain 13 peptides. Score 0.399 Round 4: 62 peptides, 9 chains. Longest chain 15 peptides. Score 0.444 Round 5: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.390 Taking the results from Round 4 Chains 9, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1812 reflections ( 99.34 % complete ) and 2639 restraints for refining 1143 atoms. 2436 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2474 (Rfree = 0.000) for 1143 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.2078 (Rfree = 0.000) for 1146 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.2282 (Rfree = 0.000) for 1139 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.2634 (Rfree = 0.000) for 1126 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.1737 (Rfree = 0.000) for 1121 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 1180 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1201 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.238 Round 2: 51 peptides, 10 chains. Longest chain 10 peptides. Score 0.293 Round 3: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.358 Round 4: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.324 Round 5: 53 peptides, 8 chains. Longest chain 10 peptides. Score 0.402 Taking the results from Round 5 Chains 8, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1812 reflections ( 99.34 % complete ) and 2596 restraints for refining 1141 atoms. 2424 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2199 (Rfree = 0.000) for 1141 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 42: After refmac, R = 0.1866 (Rfree = 0.000) for 1137 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.1700 (Rfree = 0.000) for 1134 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1728 (Rfree = 0.000) for 1133 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.1654 (Rfree = 0.000) for 1129 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 1187 seeds are put forward NCS extension: 0 residues added, 1187 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 10 peptides. Score 0.285 Round 2: 51 peptides, 8 chains. Longest chain 12 peptides. Score 0.382 Round 3: 55 peptides, 6 chains. Longest chain 15 peptides. Score 0.504 Round 4: 54 peptides, 6 chains. Longest chain 16 peptides. Score 0.495 Round 5: 52 peptides, 8 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 49, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 2fzt-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1812 reflections ( 99.34 % complete ) and 2368 restraints for refining 1143 atoms. 2112 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2140 (Rfree = 0.000) for 1143 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1828 (Rfree = 0.000) for 1133 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1641 (Rfree = 0.000) for 1123 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1724 (Rfree = 0.000) for 1117 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:46:32 GMT 2018 Job finished. TimeTaking 23.55 Used memory is bytes: 20221000