Sun 23 Dec 22:22:56 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 2o7t-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-3.6-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/2o7t-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-3.6-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 22:23:05 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/2o7t-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-3.6-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 124 and 0 Target number of residues in the AU: 124 Target solvent content: 0.6584 Checking the provided sequence file Detected sequence length: 199 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 199 Adjusted target solvent content: 0.45 Input MTZ file: 2o7t-3.6-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: 154 Cell parameters: 51.232 51.232 129.642 90.000 90.000 120.000 Input sequence file: 2o7t-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1592 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 Loops will be built when appropriate and at the last cycle Resolution range: 26.172 3.601 Wilson plot Bfac: 81.95 2537 reflections ( 99.65 % complete ) and 0 restraints for refining 1769 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3727 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3562 (Rfree = 0.000) for 1769 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 8 peptides. Score 0.250 Round 2: 79 peptides, 18 chains. Longest chain 6 peptides. Score 0.232 Round 3: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.365 Round 4: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.371 Round 5: 100 peptides, 16 chains. Longest chain 13 peptides. Score 0.476 Taking the results from Round 5 Chains 16, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2537 reflections ( 99.65 % complete ) and 3455 restraints for refining 1440 atoms. 3135 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3332 (Rfree = 0.000) for 1440 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 2: After refmac, R = 0.2916 (Rfree = 0.000) for 1399 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.2830 (Rfree = 0.000) for 1381 atoms. Found 5 (8 requested) and removed 13 (4 requested) atoms. Cycle 4: After refmac, R = 0.2993 (Rfree = 0.000) for 1358 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 5: After refmac, R = 0.2945 (Rfree = 0.000) for 1342 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 1413 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.292 Round 2: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.405 Round 3: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.370 Round 4: 90 peptides, 14 chains. Longest chain 13 peptides. Score 0.467 Round 5: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.446 Taking the results from Round 4 Chains 14, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2537 reflections ( 99.65 % complete ) and 3054 restraints for refining 1301 atoms. 2764 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2879 (Rfree = 0.000) for 1301 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 7: After refmac, R = 0.2828 (Rfree = 0.000) for 1285 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 8: After refmac, R = 0.2720 (Rfree = 0.000) for 1277 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.2595 (Rfree = 0.000) for 1271 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2476 (Rfree = 0.000) for 1265 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 1336 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 8 peptides. Score 0.279 Round 2: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.393 Round 3: 82 peptides, 14 chains. Longest chain 14 peptides. Score 0.404 Round 4: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.365 Round 5: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.345 Taking the results from Round 3 Chains 14, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2537 reflections ( 99.65 % complete ) and 3003 restraints for refining 1285 atoms. 2745 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2979 (Rfree = 0.000) for 1285 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.2963 (Rfree = 0.000) for 1275 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.3285 (Rfree = 0.000) for 1257 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2866 (Rfree = 0.000) for 1248 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.2929 (Rfree = 0.000) for 1242 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 1314 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 7 peptides. Score 0.229 Round 2: 61 peptides, 13 chains. Longest chain 8 peptides. Score 0.257 Round 3: 68 peptides, 13 chains. Longest chain 8 peptides. Score 0.321 Round 4: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.345 Round 5: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.371 Taking the results from Round 5 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2537 reflections ( 99.65 % complete ) and 2872 restraints for refining 1264 atoms. 2630 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2975 (Rfree = 0.000) for 1264 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 17: After refmac, R = 0.3191 (Rfree = 0.000) for 1250 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 18: After refmac, R = 0.3081 (Rfree = 0.000) for 1245 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 19: After refmac, R = 0.3034 (Rfree = 0.000) for 1235 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.3122 (Rfree = 0.000) for 1233 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 1312 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 8 peptides. Score 0.247 Round 2: 75 peptides, 15 chains. Longest chain 9 peptides. Score 0.308 Round 3: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.354 Round 4: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.428 Round 5: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.289 Taking the results from Round 4 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2537 reflections ( 99.65 % complete ) and 2753 restraints for refining 1282 atoms. 2483 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3125 (Rfree = 0.000) for 1282 atoms. Found 7 (8 requested) and removed 12 (4 requested) atoms. Cycle 22: After refmac, R = 0.3051 (Rfree = 0.000) for 1270 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.2780 (Rfree = 0.000) for 1263 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2944 (Rfree = 0.000) for 1261 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2769 (Rfree = 0.000) for 1259 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.72 Search for helices and strands: 0 residues in 0 chains, 1319 seeds are put forward Round 1: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.336 Round 2: 71 peptides, 13 chains. Longest chain 9 peptides. Score 0.348 Round 3: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.365 Round 4: 81 peptides, 13 chains. Longest chain 13 peptides. Score 0.431 Round 5: 75 peptides, 12 chains. Longest chain 9 peptides. Score 0.418 Taking the results from Round 4 Chains 13, Residues 68, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2537 reflections ( 99.65 % complete ) and 2723 restraints for refining 1323 atoms. 2413 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2864 (Rfree = 0.000) for 1323 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. Cycle 27: After refmac, R = 0.2599 (Rfree = 0.000) for 1313 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.2398 (Rfree = 0.000) for 1304 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.2297 (Rfree = 0.000) for 1296 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2250 (Rfree = 0.000) for 1292 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 1338 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 9 peptides. Score 0.312 Round 2: 78 peptides, 15 chains. Longest chain 10 peptides. Score 0.335 Round 3: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.379 Round 4: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.352 Round 5: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 3 Chains 14, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2537 reflections ( 99.65 % complete ) and 2968 restraints for refining 1302 atoms. 2722 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2970 (Rfree = 0.000) for 1302 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 32: After refmac, R = 0.2882 (Rfree = 0.000) for 1294 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 33: After refmac, R = 0.2954 (Rfree = 0.000) for 1292 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.2902 (Rfree = 0.000) for 1289 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.2792 (Rfree = 0.000) for 1289 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 1355 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 6 peptides. Score 0.250 Round 2: 64 peptides, 12 chains. Longest chain 10 peptides. Score 0.324 Round 3: 67 peptides, 12 chains. Longest chain 9 peptides. Score 0.350 Round 4: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.353 Round 5: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.380 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 ------------------------------------------------------ 2537 reflections ( 99.65 % complete ) and 2883 restraints for refining 1296 atoms. 2674 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2733 (Rfree = 0.000) for 1296 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2817 (Rfree = 0.000) for 1294 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 38: After refmac, R = 0.2726 (Rfree = 0.000) for 1288 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 39: After refmac, R = 0.2615 (Rfree = 0.000) for 1280 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.2629 (Rfree = 0.000) for 1276 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 1321 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 8 peptides. Score 0.276 Round 2: 55 peptides, 10 chains. Longest chain 8 peptides. Score 0.320 Round 3: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.305 Round 4: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.295 Round 5: 53 peptides, 9 chains. Longest chain 8 peptides. Score 0.343 Taking the results from Round 5 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2537 reflections ( 99.65 % complete ) and 2738 restraints for refining 1242 atoms. 2571 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2737 (Rfree = 0.000) for 1242 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 42: After refmac, R = 0.2768 (Rfree = 0.000) for 1233 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 43: After refmac, R = 0.2855 (Rfree = 0.000) for 1230 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2806 (Rfree = 0.000) for 1227 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.2926 (Rfree = 0.000) for 1227 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.61 Search for helices and strands: 0 residues in 0 chains, 1276 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.212 Round 2: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.282 Round 3: 51 peptides, 9 chains. Longest chain 9 peptides. Score 0.324 Round 4: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.327 Round 5: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.311 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 49, 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 2o7t-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2537 reflections ( 99.65 % complete ) and 2515 restraints for refining 1194 atoms. 2330 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3077 (Rfree = 0.000) for 1194 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3334 (Rfree = 0.000) for 1185 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2805 (Rfree = 0.000) for 1181 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2791 (Rfree = 0.000) for 1177 atoms. TimeTaking 26.93