Sun 23 Dec 22:23:10 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 1zko-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zko-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zko-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-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/1zko-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-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 22:23:19 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/1zko-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-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 165 and 0 Target number of residues in the AU: 165 Target solvent content: 0.6342 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-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: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2176 target number of atoms Had to go as low as 0.60 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: 47.500 4.001 Wilson plot Bfac: 68.38 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2121 reflections ( 93.19 % complete ) and 0 restraints for refining 2395 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3639 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3505 (Rfree = 0.000) for 2395 atoms. Found 5 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 4.04 Search for helices and strands: 0 residues in 0 chains, 2403 seeds are put forward NCS extension: 0 residues added, 2403 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 5 peptides. Score 0.199 Round 2: 34 peptides, 8 chains. Longest chain 6 peptides. Score 0.188 Round 3: 36 peptides, 8 chains. Longest chain 7 peptides. Score 0.209 Round 4: 47 peptides, 11 chains. Longest chain 7 peptides. Score 0.195 Round 5: 48 peptides, 11 chains. Longest chain 7 peptides. Score 0.204 Taking the results from Round 3 Chains 8, Residues 28, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 4944 restraints for refining 1956 atoms. 4840 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3200 (Rfree = 0.000) for 1956 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 2: After refmac, R = 0.2821 (Rfree = 0.000) for 1948 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2503 (Rfree = 0.000) for 1939 atoms. Found 4 (9 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2708 (Rfree = 0.000) for 1930 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.3284 (Rfree = 0.000) for 1928 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 4.14 Search for helices and strands: 0 residues in 0 chains, 1960 seeds are put forward NCS extension: 0 residues added, 1960 seeds are put forward Round 1: 26 peptides, 6 chains. Longest chain 6 peptides. Score 0.191 Round 2: 27 peptides, 6 chains. Longest chain 6 peptides. Score 0.203 Round 3: 41 peptides, 8 chains. Longest chain 8 peptides. Score 0.256 Round 4: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.241 Round 5: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.224 Taking the results from Round 3 Chains 8, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2964 restraints for refining 1351 atoms. 2840 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3283 (Rfree = 0.000) for 1351 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.3387 (Rfree = 0.000) for 1342 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.2985 (Rfree = 0.000) for 1335 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.3156 (Rfree = 0.000) for 1330 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.3685 (Rfree = 0.000) for 1328 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 1356 seeds are put forward NCS extension: 0 residues added, 1356 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 5 peptides. Score 0.236 Round 2: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.315 Round 3: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.353 Round 4: 90 peptides, 15 chains. Longest chain 17 peptides. Score 0.394 Round 5: 89 peptides, 15 chains. Longest chain 10 peptides. Score 0.388 Taking the results from Round 4 Chains 15, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2493 restraints for refining 1262 atoms. 2208 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3735 (Rfree = 0.000) for 1262 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 12: After refmac, R = 0.3661 (Rfree = 0.000) for 1243 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 13: After refmac, R = 0.3574 (Rfree = 0.000) for 1224 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 14: After refmac, R = 0.3656 (Rfree = 0.000) for 1213 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 15: After refmac, R = 0.3462 (Rfree = 0.000) for 1204 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 4.09 Search for helices and strands: 0 residues in 0 chains, 1226 seeds are put forward NCS extension: 0 residues added, 1226 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 8 peptides. Score 0.254 Round 2: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.341 Round 3: 78 peptides, 13 chains. Longest chain 8 peptides. Score 0.372 Round 4: 79 peptides, 12 chains. Longest chain 14 peptides. Score 0.410 Round 5: 83 peptides, 13 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 4 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2634 restraints for refining 1255 atoms. 2378 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3877 (Rfree = 0.000) for 1255 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 17: After refmac, R = 0.3845 (Rfree = 0.000) for 1237 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 18: After refmac, R = 0.3960 (Rfree = 0.000) for 1229 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 19: After refmac, R = 0.3716 (Rfree = 0.000) for 1219 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 20: After refmac, R = 0.3774 (Rfree = 0.000) for 1208 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 4.11 Search for helices and strands: 0 residues in 0 chains, 1239 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1254 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.270 Round 2: 75 peptides, 12 chains. Longest chain 10 peptides. Score 0.382 Round 3: 66 peptides, 12 chains. Longest chain 9 peptides. Score 0.317 Round 4: 77 peptides, 12 chains. Longest chain 12 peptides. Score 0.396 Round 5: 69 peptides, 10 chains. Longest chain 10 peptides. Score 0.403 Taking the results from Round 5 Chains 10, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2616 restraints for refining 1218 atoms. 2390 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3942 (Rfree = 0.000) for 1218 atoms. Found 5 (5 requested) and removed 74 (2 requested) atoms. Cycle 22: After refmac, R = 0.3915 (Rfree = 0.000) for 1136 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 23: After refmac, R = 0.3868 (Rfree = 0.000) for 1128 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 24: After refmac, R = 0.3854 (Rfree = 0.000) for 1117 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 25: After refmac, R = 0.3937 (Rfree = 0.000) for 1106 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 4.17 Search for helices and strands: 0 residues in 0 chains, 1129 seeds are put forward NCS extension: 0 residues added, 1129 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.266 Round 2: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.303 Round 3: 78 peptides, 15 chains. Longest chain 10 peptides. Score 0.310 Round 4: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.323 Round 5: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.315 Taking the results from Round 4 Chains 16, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2458 restraints for refining 1178 atoms. 2202 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.4082 (Rfree = 0.000) for 1178 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 27: After refmac, R = 0.3994 (Rfree = 0.000) for 1163 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 28: After refmac, R = 0.3921 (Rfree = 0.000) for 1149 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 29: After refmac, R = 0.3946 (Rfree = 0.000) for 1135 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 30: After refmac, R = 0.3937 (Rfree = 0.000) for 1125 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 4.10 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 8 peptides. Score 0.229 Round 2: 71 peptides, 14 chains. Longest chain 11 peptides. Score 0.289 Round 3: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.297 Round 4: 76 peptides, 12 chains. Longest chain 13 peptides. Score 0.389 Round 5: 72 peptides, 12 chains. Longest chain 9 peptides. Score 0.361 Taking the results from Round 4 Chains 12, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2519 restraints for refining 1169 atoms. 2275 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.4357 (Rfree = 0.000) for 1169 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 32: After refmac, R = 0.4055 (Rfree = 0.000) for 1157 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 33: After refmac, R = 0.4212 (Rfree = 0.000) for 1143 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 34: After refmac, R = 0.3887 (Rfree = 0.000) for 1126 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 35: After refmac, R = 0.4155 (Rfree = 0.000) for 1121 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 4.11 Search for helices and strands: 0 residues in 0 chains, 1141 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1159 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 5 peptides. Score 0.194 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.268 Round 3: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.310 Round 4: 71 peptides, 13 chains. Longest chain 8 peptides. Score 0.322 Round 5: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.297 Taking the results from Round 4 Chains 13, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2333 restraints for refining 1104 atoms. 2114 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.4380 (Rfree = 0.000) for 1104 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 37: After refmac, R = 0.4107 (Rfree = 0.000) for 1081 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 38: After refmac, R = 0.4249 (Rfree = 0.000) for 1067 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 39: After refmac, R = 0.4046 (Rfree = 0.000) for 1058 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 40: After refmac, R = 0.4080 (Rfree = 0.000) for 1054 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 4.09 Search for helices and strands: 0 residues in 0 chains, 1071 seeds are put forward NCS extension: 0 residues added, 1071 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.286 Round 2: 70 peptides, 12 chains. Longest chain 14 peptides. Score 0.347 Round 3: 70 peptides, 12 chains. Longest chain 8 peptides. Score 0.347 Round 4: 72 peptides, 13 chains. Longest chain 8 peptides. Score 0.329 Round 5: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 5 Chains 13, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2404 restraints for refining 1155 atoms. 2165 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.4815 (Rfree = 0.000) for 1155 atoms. Found 5 (5 requested) and removed 25 (2 requested) atoms. Cycle 42: After refmac, R = 0.4459 (Rfree = 0.000) for 1121 atoms. Found 5 (5 requested) and removed 18 (2 requested) atoms. Cycle 43: After refmac, R = 0.4443 (Rfree = 0.000) for 1097 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 44: After refmac, R = 0.3925 (Rfree = 0.000) for 1078 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.4281 (Rfree = 0.000) for 1071 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 4.02 Search for helices and strands: 0 residues in 0 chains, 1090 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1093 seeds are put forward Round 1: 49 peptides, 12 chains. Longest chain 5 peptides. Score 0.176 Round 2: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.244 Round 3: 68 peptides, 13 chains. Longest chain 7 peptides. Score 0.299 Round 4: 69 peptides, 13 chains. Longest chain 11 peptides. Score 0.307 Round 5: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.276 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, 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 1zko-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2121 reflections ( 93.19 % complete ) and 2308 restraints for refining 1110 atoms. 2097 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3557 (Rfree = 0.000) for 1110 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3392 (Rfree = 0.000) for 1090 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.3456 (Rfree = 0.000) for 1079 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.3676 (Rfree = 0.000) for 1071 atoms. TimeTaking 25.6