Sun 23 Dec 22:22:46 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-4.0-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 22:22:56 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-4.0-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 114 and 0 Target number of residues in the AU: 114 Target solvent content: 0.6449 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-4.0-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-4.0-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 4.000 Wilson plot Bfac: 74.39 1566 reflections ( 99.24 % complete ) and 0 restraints for refining 1400 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3891 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3797 (Rfree = 0.000) for 1400 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 1434 seeds are put forward NCS extension: 0 residues added, 1434 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.240 Round 2: 58 peptides, 10 chains. Longest chain 8 peptides. Score 0.364 Round 3: 52 peptides, 8 chains. Longest chain 13 peptides. Score 0.392 Round 4: 59 peptides, 7 chains. Longest chain 14 peptides. Score 0.498 Round 5: 54 peptides, 8 chains. Longest chain 17 peptides. Score 0.411 Taking the results from Round 4 Chains 7, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1566 reflections ( 99.24 % complete ) and 2817 restraints for refining 1142 atoms. 2616 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2695 (Rfree = 0.000) for 1142 atoms. Found 3 (5 requested) and removed 12 (2 requested) atoms. Cycle 2: After refmac, R = 0.2575 (Rfree = 0.000) for 1118 atoms. Found 1 (5 requested) and removed 12 (2 requested) atoms. Cycle 3: After refmac, R = 0.2451 (Rfree = 0.000) for 1104 atoms. Found 2 (5 requested) and removed 10 (2 requested) atoms. Cycle 4: After refmac, R = 0.2604 (Rfree = 0.000) for 1094 atoms. Found 3 (5 requested) and removed 8 (2 requested) atoms. Cycle 5: After refmac, R = 0.2365 (Rfree = 0.000) for 1086 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.44 Search for helices and strands: 0 residues in 0 chains, 1153 seeds are put forward NCS extension: 4 residues added (1 deleted due to clashes), 1157 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.318 Round 2: 55 peptides, 9 chains. Longest chain 10 peptides. Score 0.378 Round 3: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.361 Round 4: 64 peptides, 10 chains. Longest chain 16 peptides. Score 0.421 Round 5: 61 peptides, 9 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 5 Chains 9, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1566 reflections ( 99.24 % complete ) and 2749 restraints for refining 1142 atoms. 2550 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2661 (Rfree = 0.000) for 1142 atoms. Found 2 (5 requested) and removed 15 (2 requested) atoms. Cycle 7: After refmac, R = 0.1945 (Rfree = 0.000) for 1115 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.1928 (Rfree = 0.000) for 1111 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.1854 (Rfree = 0.000) for 1105 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.1758 (Rfree = 0.000) for 1103 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.57 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: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.308 Round 2: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.393 Round 3: 76 peptides, 12 chains. Longest chain 12 peptides. Score 0.450 Round 4: 81 peptides, 12 chains. Longest chain 13 peptides. Score 0.492 Round 5: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.408 Taking the results from Round 4 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1566 reflections ( 99.24 % complete ) and 2506 restraints for refining 1141 atoms. 2242 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2508 (Rfree = 0.000) for 1141 atoms. Found 3 (5 requested) and removed 13 (2 requested) atoms. Cycle 12: After refmac, R = 0.2116 (Rfree = 0.000) for 1126 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 13: After refmac, R = 0.2190 (Rfree = 0.000) for 1118 atoms. Found 2 (5 requested) and removed 8 (2 requested) atoms. Cycle 14: After refmac, R = 0.1986 (Rfree = 0.000) for 1111 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.1966 (Rfree = 0.000) for 1111 atoms. Found 0 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 1167 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1173 seeds are put forward Round 1: 68 peptides, 13 chains. Longest chain 9 peptides. Score 0.336 Round 2: 63 peptides, 10 chains. Longest chain 9 peptides. Score 0.412 Round 3: 79 peptides, 12 chains. Longest chain 9 peptides. Score 0.475 Round 4: 72 peptides, 11 chains. Longest chain 9 peptides. Score 0.453 Round 5: 71 peptides, 11 chains. Longest chain 9 peptides. Score 0.444 Taking the results from Round 3 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1566 reflections ( 99.24 % complete ) and 2622 restraints for refining 1141 atoms. 2366 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2399 (Rfree = 0.000) for 1141 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. Cycle 17: After refmac, R = 0.2027 (Rfree = 0.000) for 1125 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 18: After refmac, R = 0.1976 (Rfree = 0.000) for 1118 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.1806 (Rfree = 0.000) for 1114 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.1875 (Rfree = 0.000) for 1110 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 1167 seeds are put forward NCS extension: 0 residues added, 1167 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 7 peptides. Score 0.331 Round 2: 68 peptides, 10 chains. Longest chain 12 peptides. Score 0.457 Round 3: 71 peptides, 11 chains. Longest chain 13 peptides. Score 0.444 Round 4: 74 peptides, 12 chains. Longest chain 10 peptides. Score 0.432 Round 5: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.393 Taking the results from Round 2 Chains 10, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1566 reflections ( 99.24 % complete ) and 2587 restraints for refining 1142 atoms. 2365 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2211 (Rfree = 0.000) for 1142 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 22: After refmac, R = 0.1855 (Rfree = 0.000) for 1140 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 23: After refmac, R = 0.1923 (Rfree = 0.000) for 1136 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.1837 (Rfree = 0.000) for 1131 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.1716 (Rfree = 0.000) for 1129 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.62 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: 56 peptides, 11 chains. Longest chain 9 peptides. Score 0.300 Round 2: 53 peptides, 9 chains. Longest chain 8 peptides. Score 0.358 Round 3: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.403 Round 4: 63 peptides, 12 chains. Longest chain 8 peptides. Score 0.328 Round 5: 64 peptides, 9 chains. Longest chain 14 peptides. Score 0.461 Taking the results from Round 5 Chains 9, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1566 reflections ( 99.24 % complete ) and 2590 restraints for refining 1142 atoms. 2379 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2624 (Rfree = 0.000) for 1142 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 27: After refmac, R = 0.2163 (Rfree = 0.000) for 1121 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.2108 (Rfree = 0.000) for 1109 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.2002 (Rfree = 0.000) for 1104 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2095 (Rfree = 0.000) for 1099 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 1162 seeds are put forward NCS extension: 0 residues added, 1162 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 7 peptides. Score 0.226 Round 2: 49 peptides, 9 chains. Longest chain 8 peptides. Score 0.317 Round 3: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.351 Round 4: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.311 Round 5: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 5 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1566 reflections ( 99.24 % complete ) and 2352 restraints for refining 1058 atoms. 2143 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2813 (Rfree = 0.000) for 1058 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 32: After refmac, R = 0.2088 (Rfree = 0.000) for 1045 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.2184 (Rfree = 0.000) for 1043 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.1990 (Rfree = 0.000) for 1039 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.1938 (Rfree = 0.000) for 1037 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 1092 seeds are put forward NCS extension: 0 residues added, 1092 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.247 Round 2: 63 peptides, 13 chains. Longest chain 6 peptides. Score 0.286 Round 3: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.399 Round 4: 66 peptides, 11 chains. Longest chain 8 peptides. Score 0.399 Round 5: 68 peptides, 10 chains. Longest chain 9 peptides. Score 0.457 Taking the results from Round 5 Chains 10, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1566 reflections ( 99.24 % complete ) and 2298 restraints for refining 1048 atoms. 2076 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2597 (Rfree = 0.000) for 1048 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 37: After refmac, R = 0.2435 (Rfree = 0.000) for 1045 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.2122 (Rfree = 0.000) for 1043 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 39: After refmac, R = 0.2328 (Rfree = 0.000) for 1038 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2111 (Rfree = 0.000) for 1036 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 1086 seeds are put forward NCS extension: 0 residues added, 1086 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 7 peptides. Score 0.225 Round 2: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.310 Round 3: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.296 Round 4: 52 peptides, 9 chains. Longest chain 11 peptides. Score 0.348 Round 5: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.282 Taking the results from Round 4 Chains 9, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1566 reflections ( 99.24 % complete ) and 2434 restraints for refining 1067 atoms. 2271 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2296 (Rfree = 0.000) for 1067 atoms. Found 3 (5 requested) and removed 11 (2 requested) atoms. Cycle 42: After refmac, R = 0.1957 (Rfree = 0.000) for 1054 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 43: After refmac, R = 0.2174 (Rfree = 0.000) for 1050 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2041 (Rfree = 0.000) for 1051 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.1790 (Rfree = 0.000) for 1049 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 1105 seeds are put forward NCS extension: 0 residues added, 1105 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.247 Round 2: 52 peptides, 11 chains. Longest chain 6 peptides. Score 0.258 Round 3: 45 peptides, 8 chains. Longest chain 13 peptides. Score 0.321 Round 4: 52 peptides, 11 chains. Longest chain 6 peptides. Score 0.258 Round 5: 49 peptides, 9 chains. Longest chain 13 peptides. Score 0.317 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 37, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1566 reflections ( 99.24 % complete ) and 2454 restraints for refining 1061 atoms. 2314 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2345 (Rfree = 0.000) for 1061 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1872 (Rfree = 0.000) for 1058 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2114 (Rfree = 0.000) for 1053 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2034 (Rfree = 0.000) for 1050 atoms. TimeTaking 23.35