Sun 23 Dec 22:23:08 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 2fg9-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-4.0-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/2fg9-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-4.0-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 22:23:18 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/2fg9-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-4.0-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 121 and 0 Target number of residues in the AU: 121 Target solvent content: 0.6734 Checking the provided sequence file Detected sequence length: 178 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 178 Adjusted target solvent content: 0.52 Input MTZ file: 2fg9-4.0-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: 211 Cell parameters: 134.000 134.000 134.000 90.000 90.000 90.000 Input sequence file: 2fg9-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1424 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 Loops will be built when appropriate and at the last cycle Resolution range: 94.752 4.000 Wilson plot Bfac: 93.37 1907 reflections ( 99.37 % complete ) and 0 restraints for refining 1571 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3495 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2721 (Rfree = 0.000) for 1571 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 1588 seeds are put forward Round 1: 66 peptides, 9 chains. Longest chain 17 peptides. Score 0.450 Round 2: 89 peptides, 12 chains. Longest chain 18 peptides. Score 0.520 Round 3: 96 peptides, 13 chains. Longest chain 18 peptides. Score 0.537 Round 4: 95 peptides, 11 chains. Longest chain 18 peptides. Score 0.589 Round 5: 102 peptides, 10 chains. Longest chain 19 peptides. Score 0.656 Taking the results from Round 5 Chains 10, Residues 92, Estimated correctness of the model 9.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1907 reflections ( 99.37 % complete ) and 2926 restraints for refining 1286 atoms. 2568 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3024 (Rfree = 0.000) for 1286 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.2965 (Rfree = 0.000) for 1272 atoms. Found 3 (6 requested) and removed 19 (3 requested) atoms. Cycle 3: After refmac, R = 0.2768 (Rfree = 0.000) for 1252 atoms. Found 0 (5 requested) and removed 9 (2 requested) atoms. Cycle 4: After refmac, R = 0.2688 (Rfree = 0.000) for 1236 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.2712 (Rfree = 0.000) for 1225 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 1280 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 11 peptides. Score 0.372 Round 2: 90 peptides, 15 chains. Longest chain 11 peptides. Score 0.430 Round 3: 95 peptides, 14 chains. Longest chain 13 peptides. Score 0.499 Round 4: 94 peptides, 14 chains. Longest chain 13 peptides. Score 0.492 Round 5: 84 peptides, 12 chains. Longest chain 11 peptides. Score 0.484 Taking the results from Round 3 Chains 14, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1907 reflections ( 99.37 % complete ) and 2955 restraints for refining 1280 atoms. 2645 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2935 (Rfree = 0.000) for 1280 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 7: After refmac, R = 0.2853 (Rfree = 0.000) for 1274 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2701 (Rfree = 0.000) for 1268 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 9: After refmac, R = 0.2525 (Rfree = 0.000) for 1264 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. Cycle 10: After refmac, R = 0.2491 (Rfree = 0.000) for 1257 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.90 3.80 Search for helices and strands: 0 residues in 0 chains, 1293 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.346 Round 2: 103 peptides, 16 chains. Longest chain 11 peptides. Score 0.494 Round 3: 95 peptides, 13 chains. Longest chain 14 peptides. Score 0.530 Round 4: 96 peptides, 12 chains. Longest chain 20 peptides. Score 0.566 Round 5: 106 peptides, 12 chains. Longest chain 27 peptides. Score 0.627 Taking the results from Round 5 Chains 12, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1907 reflections ( 99.37 % complete ) and 2920 restraints for refining 1286 atoms. 2556 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2839 (Rfree = 0.000) for 1286 atoms. Found 2 (6 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2558 (Rfree = 0.000) for 1263 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 13: After refmac, R = 0.2481 (Rfree = 0.000) for 1261 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2461 (Rfree = 0.000) for 1260 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2436 (Rfree = 0.000) for 1257 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.95 3.85 Search for helices and strands: 0 residues in 0 chains, 1292 seeds are put forward Round 1: 69 peptides, 12 chains. Longest chain 13 peptides. Score 0.365 Round 2: 72 peptides, 13 chains. Longest chain 10 peptides. Score 0.354 Round 3: 87 peptides, 13 chains. Longest chain 18 peptides. Score 0.473 Round 4: 83 peptides, 12 chains. Longest chain 18 peptides. Score 0.477 Round 5: 96 peptides, 9 chains. Longest chain 20 peptides. Score 0.650 Taking the results from Round 5 Chains 9, Residues 87, Estimated correctness of the model 7.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1907 reflections ( 99.37 % complete ) and 2926 restraints for refining 1286 atoms. 2587 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2827 (Rfree = 0.000) for 1286 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.2471 (Rfree = 0.000) for 1271 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2374 (Rfree = 0.000) for 1262 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2331 (Rfree = 0.000) for 1258 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.2403 (Rfree = 0.000) for 1254 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.92 3.82 Search for helices and strands: 0 residues in 0 chains, 1302 seeds are put forward Round 1: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.334 Round 2: 71 peptides, 10 chains. Longest chain 14 peptides. Score 0.454 Round 3: 71 peptides, 11 chains. Longest chain 14 peptides. Score 0.418 Round 4: 76 peptides, 11 chains. Longest chain 14 peptides. Score 0.458 Round 5: 76 peptides, 12 chains. Longest chain 11 peptides. Score 0.423 Taking the results from Round 4 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1907 reflections ( 99.37 % complete ) and 3097 restraints for refining 1286 atoms. 2848 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2875 (Rfree = 0.000) for 1286 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 22: After refmac, R = 0.2456 (Rfree = 0.000) for 1281 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2385 (Rfree = 0.000) for 1277 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.2371 (Rfree = 0.000) for 1271 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2325 (Rfree = 0.000) for 1265 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 1300 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.319 Round 2: 65 peptides, 11 chains. Longest chain 11 peptides. Score 0.368 Round 3: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.407 Round 4: 72 peptides, 11 chains. Longest chain 11 peptides. Score 0.426 Round 5: 81 peptides, 12 chains. Longest chain 12 peptides. Score 0.462 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 ------------------------------------------------------ 1907 reflections ( 99.37 % complete ) and 3127 restraints for refining 1286 atoms. 2863 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2797 (Rfree = 0.000) for 1286 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. Cycle 27: After refmac, R = 0.2444 (Rfree = 0.000) for 1275 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2328 (Rfree = 0.000) for 1273 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2371 (Rfree = 0.000) for 1265 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2313 (Rfree = 0.000) for 1261 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 1298 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.288 Round 2: 69 peptides, 11 chains. Longest chain 13 peptides. Score 0.402 Round 3: 73 peptides, 10 chains. Longest chain 13 peptides. Score 0.469 Round 4: 59 peptides, 8 chains. Longest chain 12 peptides. Score 0.431 Round 5: 70 peptides, 10 chains. Longest chain 11 peptides. Score 0.446 Taking the results from Round 3 Chains 10, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1907 reflections ( 99.37 % complete ) and 3146 restraints for refining 1286 atoms. 2904 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2333 (Rfree = 0.000) for 1286 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 32: After refmac, R = 0.2316 (Rfree = 0.000) for 1275 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2232 (Rfree = 0.000) for 1272 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.2184 (Rfree = 0.000) for 1270 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2152 (Rfree = 0.000) for 1265 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 1288 seeds are put forward Round 1: 68 peptides, 13 chains. Longest chain 9 peptides. Score 0.319 Round 2: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.328 Round 3: 68 peptides, 10 chains. Longest chain 15 peptides. Score 0.430 Round 4: 73 peptides, 11 chains. Longest chain 10 peptides. Score 0.434 Round 5: 69 peptides, 10 chains. Longest chain 11 peptides. Score 0.438 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 ------------------------------------------------------ 1907 reflections ( 99.37 % complete ) and 3160 restraints for refining 1286 atoms. 2934 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2301 (Rfree = 0.000) for 1286 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.2198 (Rfree = 0.000) for 1278 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.2121 (Rfree = 0.000) for 1271 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2038 (Rfree = 0.000) for 1269 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.2008 (Rfree = 0.000) for 1268 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 1297 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 11 peptides. Score 0.311 Round 2: 60 peptides, 11 chains. Longest chain 11 peptides. Score 0.325 Round 3: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.316 Round 4: 60 peptides, 10 chains. Longest chain 9 peptides. Score 0.363 Round 5: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.351 Taking the results from Round 4 Chains 10, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1907 reflections ( 99.37 % complete ) and 3177 restraints for refining 1285 atoms. 2987 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2374 (Rfree = 0.000) for 1285 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.2175 (Rfree = 0.000) for 1281 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2207 (Rfree = 0.000) for 1273 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.2270 (Rfree = 0.000) for 1266 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.1995 (Rfree = 0.000) for 1264 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 1302 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.208 Round 2: 57 peptides, 12 chains. Longest chain 7 peptides. Score 0.257 Round 3: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.281 Round 4: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.316 Round 5: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 51, 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 2fg9-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1907 reflections ( 99.37 % complete ) and 3195 restraints for refining 1286 atoms. 3002 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2623 (Rfree = 0.000) for 1286 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2206 (Rfree = 0.000) for 1280 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2079 (Rfree = 0.000) for 1274 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1869 (Rfree = 0.000) for 1269 atoms. TimeTaking 45.37