Sun 23 Dec 22:23:05 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 1o6a-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-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/1o6a-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-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 22:23:15 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/1o6a-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6607 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.52 Input MTZ file: 1o6a-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: 92 Cell parameters: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.70 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: 41.713 4.003 Wilson plot Bfac: 84.46 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2090 reflections ( 99.81 % complete ) and 0 restraints for refining 1704 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.4374 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4336 (Rfree = 0.000) for 1704 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1724 seeds are put forward NCS extension: 0 residues added, 1724 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 7 peptides. Score 0.241 Round 2: 80 peptides, 14 chains. Longest chain 11 peptides. Score 0.374 Round 3: 83 peptides, 13 chains. Longest chain 14 peptides. Score 0.429 Round 4: 81 peptides, 12 chains. Longest chain 12 peptides. Score 0.447 Round 5: 82 peptides, 12 chains. Longest chain 11 peptides. Score 0.454 Taking the results from Round 5 Chains 12, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2090 reflections ( 99.81 % complete ) and 3375 restraints for refining 1386 atoms. 3107 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3787 (Rfree = 0.000) for 1386 atoms. Found 5 (6 requested) and removed 24 (3 requested) atoms. Cycle 2: After refmac, R = 0.3535 (Rfree = 0.000) for 1339 atoms. Found 4 (6 requested) and removed 15 (3 requested) atoms. Cycle 3: After refmac, R = 0.3074 (Rfree = 0.000) for 1309 atoms. Found 2 (6 requested) and removed 11 (3 requested) atoms. Cycle 4: After refmac, R = 0.3431 (Rfree = 0.000) for 1282 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 5: After refmac, R = 0.3385 (Rfree = 0.000) for 1257 atoms. Found 5 (6 requested) and removed 15 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 1288 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 1298 seeds are put forward Round 1: 68 peptides, 16 chains. Longest chain 7 peptides. Score 0.203 Round 2: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.332 Round 3: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.384 Round 4: 93 peptides, 15 chains. Longest chain 13 peptides. Score 0.438 Round 5: 85 peptides, 14 chains. Longest chain 16 peptides. Score 0.412 Taking the results from Round 4 Chains 15, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2090 reflections ( 99.81 % complete ) and 2780 restraints for refining 1224 atoms. 2483 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3572 (Rfree = 0.000) for 1224 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 7: After refmac, R = 0.3448 (Rfree = 0.000) for 1202 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 8: After refmac, R = 0.3045 (Rfree = 0.000) for 1183 atoms. Found 4 (5 requested) and removed 8 (2 requested) atoms. Cycle 9: After refmac, R = 0.3266 (Rfree = 0.000) for 1171 atoms. Found 4 (5 requested) and removed 7 (2 requested) atoms. Cycle 10: After refmac, R = 0.3173 (Rfree = 0.000) for 1160 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 1201 seeds are put forward NCS extension: 0 residues added, 1201 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 10 peptides. Score 0.286 Round 2: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.379 Round 3: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.371 Round 4: 86 peptides, 15 chains. Longest chain 17 peptides. Score 0.387 Round 5: 82 peptides, 13 chains. Longest chain 10 peptides. Score 0.422 Taking the results from Round 5 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2090 reflections ( 99.81 % complete ) and 2820 restraints for refining 1222 atoms. 2557 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3550 (Rfree = 0.000) for 1222 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. Cycle 12: After refmac, R = 0.3547 (Rfree = 0.000) for 1206 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 13: After refmac, R = 0.3237 (Rfree = 0.000) for 1186 atoms. Found 3 (5 requested) and removed 20 (2 requested) atoms. Cycle 14: After refmac, R = 0.3559 (Rfree = 0.000) for 1160 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 15: After refmac, R = 0.3228 (Rfree = 0.000) for 1152 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 1196 seeds are put forward NCS extension: 0 residues added, 1196 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 11 peptides. Score 0.276 Round 2: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.407 Round 3: 86 peptides, 12 chains. Longest chain 20 peptides. Score 0.482 Round 4: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.350 Round 5: 83 peptides, 14 chains. Longest chain 13 peptides. Score 0.397 Taking the results from Round 3 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2090 reflections ( 99.81 % complete ) and 2630 restraints for refining 1197 atoms. 2346 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3470 (Rfree = 0.000) for 1197 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 17: After refmac, R = 0.3330 (Rfree = 0.000) for 1172 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 18: After refmac, R = 0.3251 (Rfree = 0.000) for 1155 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 19: After refmac, R = 0.3274 (Rfree = 0.000) for 1144 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 20: After refmac, R = 0.3444 (Rfree = 0.000) for 1134 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 1161 seeds are put forward NCS extension: 0 residues added, 1161 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.316 Round 2: 86 peptides, 14 chains. Longest chain 13 peptides. Score 0.419 Round 3: 86 peptides, 15 chains. Longest chain 13 peptides. Score 0.387 Round 4: 73 peptides, 11 chains. Longest chain 14 peptides. Score 0.421 Round 5: 71 peptides, 13 chains. Longest chain 13 peptides. Score 0.336 Taking the results from Round 4 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2090 reflections ( 99.81 % complete ) and 2954 restraints for refining 1248 atoms. 2717 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3858 (Rfree = 0.000) for 1248 atoms. Found 5 (5 requested) and removed 20 (2 requested) atoms. Cycle 22: After refmac, R = 0.3486 (Rfree = 0.000) for 1220 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 23: After refmac, R = 0.3326 (Rfree = 0.000) for 1203 atoms. Found 3 (5 requested) and removed 13 (2 requested) atoms. Cycle 24: After refmac, R = 0.3267 (Rfree = 0.000) for 1190 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 25: After refmac, R = 0.3483 (Rfree = 0.000) for 1182 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.60 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: 57 peptides, 11 chains. Longest chain 10 peptides. Score 0.291 Round 2: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.350 Round 3: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.417 Round 4: 68 peptides, 8 chains. Longest chain 23 peptides. Score 0.485 Round 5: 68 peptides, 9 chains. Longest chain 13 peptides. Score 0.451 Taking the results from Round 4 Chains 8, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2090 reflections ( 99.81 % complete ) and 2738 restraints for refining 1201 atoms. 2506 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3251 (Rfree = 0.000) for 1201 atoms. Found 5 (5 requested) and removed 20 (2 requested) atoms. Cycle 27: After refmac, R = 0.3134 (Rfree = 0.000) for 1176 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 28: After refmac, R = 0.3219 (Rfree = 0.000) for 1167 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 29: After refmac, R = 0.3152 (Rfree = 0.000) for 1155 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 30: After refmac, R = 0.3104 (Rfree = 0.000) for 1149 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 1185 seeds are put forward NCS extension: 0 residues added, 1185 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.264 Round 2: 70 peptides, 10 chains. Longest chain 21 peptides. Score 0.432 Round 3: 75 peptides, 12 chains. Longest chain 11 peptides. Score 0.402 Round 4: 71 peptides, 10 chains. Longest chain 26 peptides. Score 0.440 Round 5: 70 peptides, 11 chains. Longest chain 11 peptides. Score 0.398 Taking the results from Round 4 Chains 10, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2090 reflections ( 99.81 % complete ) and 2660 restraints for refining 1171 atoms. 2426 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3385 (Rfree = 0.000) for 1171 atoms. Found 5 (5 requested) and removed 20 (2 requested) atoms. Cycle 32: After refmac, R = 0.3277 (Rfree = 0.000) for 1146 atoms. Found 5 (5 requested) and removed 18 (2 requested) atoms. Cycle 33: After refmac, R = 0.3149 (Rfree = 0.000) for 1128 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 34: After refmac, R = 0.3070 (Rfree = 0.000) for 1116 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 35: After refmac, R = 0.3365 (Rfree = 0.000) for 1107 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 1158 seeds are put forward NCS extension: 0 residues added, 1158 seeds are put forward Round 1: 39 peptides, 9 chains. Longest chain 5 peptides. Score 0.200 Round 2: 63 peptides, 11 chains. Longest chain 14 peptides. Score 0.342 Round 3: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.311 Round 4: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.329 Round 5: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.320 Taking the results from Round 2 Chains 11, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2090 reflections ( 99.81 % complete ) and 2438 restraints for refining 1108 atoms. 2241 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3624 (Rfree = 0.000) for 1108 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 37: After refmac, R = 0.3284 (Rfree = 0.000) for 1097 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 38: After refmac, R = 0.3144 (Rfree = 0.000) for 1091 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.3054 (Rfree = 0.000) for 1092 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.3315 (Rfree = 0.000) for 1090 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 1138 seeds are put forward NCS extension: 0 residues added, 1138 seeds are put forward Round 1: 48 peptides, 11 chains. Longest chain 6 peptides. Score 0.207 Round 2: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.308 Round 3: 51 peptides, 10 chains. Longest chain 6 peptides. Score 0.276 Round 4: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.282 Round 5: 52 peptides, 11 chains. Longest chain 6 peptides. Score 0.245 Taking the results from Round 2 Chains 11, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2090 reflections ( 99.81 % complete ) and 2471 restraints for refining 1109 atoms. 2290 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3549 (Rfree = 0.000) for 1109 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 42: After refmac, R = 0.3187 (Rfree = 0.000) for 1100 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 43: After refmac, R = 0.3204 (Rfree = 0.000) for 1091 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 44: After refmac, R = 0.3181 (Rfree = 0.000) for 1085 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.3354 (Rfree = 0.000) for 1085 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 1135 seeds are put forward NCS extension: 0 residues added, 1135 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.208 Round 2: 45 peptides, 9 chains. Longest chain 6 peptides. Score 0.260 Round 3: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.266 Round 4: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.250 Round 5: 52 peptides, 10 chains. Longest chain 7 peptides. Score 0.285 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 42, 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 1o6a-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2090 reflections ( 99.81 % complete ) and 2512 restraints for refining 1122 atoms. 2354 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3421 (Rfree = 0.000) for 1122 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3596 (Rfree = 0.000) for 1113 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.3190 (Rfree = 0.000) for 1105 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.3518 (Rfree = 0.000) for 1099 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... TimeTaking 25.7