Sun 23 Dec 22:22:43 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 1vjf-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-3.4-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/1vjf-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-3.4-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 22:22:53 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/1vjf-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-3.4-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 132 and 0 Target number of residues in the AU: 132 Target solvent content: 0.5458 Checking the provided sequence file Detected sequence length: 180 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 180 Adjusted target solvent content: 0.38 Input MTZ file: 1vjf-3.4-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: 96 Cell parameters: 50.903 50.903 121.411 90.000 90.000 90.000 Input sequence file: 1vjf-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1440 target number of atoms Had to go as low as 0.55 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: 46.944 3.402 Wilson plot Bfac: 34.04 2474 reflections ( 99.76 % complete ) and 0 restraints for refining 1599 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3092 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2826 (Rfree = 0.000) for 1599 atoms. Found 8 (12 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.78 3.27 Search for helices and strands: 0 residues in 0 chains, 1617 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 10 peptides. Score 0.284 Round 2: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.397 Round 3: 92 peptides, 14 chains. Longest chain 11 peptides. Score 0.536 Round 4: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.506 Round 5: 112 peptides, 15 chains. Longest chain 14 peptides. Score 0.652 Taking the results from Round 5 Chains 15, Residues 97, Estimated correctness of the model 44.6 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.76 % complete ) and 2818 restraints for refining 1309 atoms. 2408 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3207 (Rfree = 0.000) for 1309 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 2: After refmac, R = 0.2887 (Rfree = 0.000) for 1285 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2300 (Rfree = 0.000) for 1273 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2364 (Rfree = 0.000) for 1266 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.2430 (Rfree = 0.000) for 1256 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.78 3.27 Search for helices and strands: 0 residues in 0 chains, 1300 seeds are put forward Round 1: 91 peptides, 14 chains. Longest chain 10 peptides. Score 0.528 Round 2: 97 peptides, 14 chains. Longest chain 19 peptides. Score 0.577 Round 3: 89 peptides, 12 chains. Longest chain 19 peptides. Score 0.583 Round 4: 96 peptides, 12 chains. Longest chain 19 peptides. Score 0.634 Round 5: 100 peptides, 14 chains. Longest chain 16 peptides. Score 0.599 Taking the results from Round 4 Chains 12, Residues 84, Estimated correctness of the model 39.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.76 % complete ) and 2763 restraints for refining 1227 atoms. 2439 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2819 (Rfree = 0.000) for 1227 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2428 (Rfree = 0.000) for 1218 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2089 (Rfree = 0.000) for 1216 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2095 (Rfree = 0.000) for 1215 atoms. Found 8 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.1987 (Rfree = 0.000) for 1219 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.86 3.37 Search for helices and strands: 0 residues in 0 chains, 1261 seeds are put forward Round 1: 98 peptides, 14 chains. Longest chain 14 peptides. Score 0.584 Round 2: 110 peptides, 14 chains. Longest chain 22 peptides. Score 0.668 Round 3: 112 peptides, 14 chains. Longest chain 22 peptides. Score 0.680 Round 4: 108 peptides, 13 chains. Longest chain 22 peptides. Score 0.683 Round 5: 105 peptides, 12 chains. Longest chain 22 peptides. Score 0.693 Taking the results from Round 5 Chains 14, Residues 93, Estimated correctness of the model 56.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.76 % complete ) and 2618 restraints for refining 1239 atoms. 2212 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2342 (Rfree = 0.000) for 1239 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.2107 (Rfree = 0.000) for 1235 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.2251 (Rfree = 0.000) for 1236 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2027 (Rfree = 0.000) for 1232 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2001 (Rfree = 0.000) for 1226 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.91 3.43 Search for helices and strands: 0 residues in 0 chains, 1259 seeds are put forward Round 1: 94 peptides, 16 chains. Longest chain 16 peptides. Score 0.479 Round 2: 97 peptides, 13 chains. Longest chain 19 peptides. Score 0.610 Round 3: 105 peptides, 14 chains. Longest chain 16 peptides. Score 0.635 Round 4: 100 peptides, 14 chains. Longest chain 11 peptides. Score 0.599 Round 5: 103 peptides, 16 chains. Longest chain 14 peptides. Score 0.555 Taking the results from Round 3 Chains 14, Residues 91, Estimated correctness of the model 39.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.76 % complete ) and 2716 restraints for refining 1245 atoms. 2366 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2692 (Rfree = 0.000) for 1245 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 17: After refmac, R = 0.2581 (Rfree = 0.000) for 1239 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 18: After refmac, R = 0.2544 (Rfree = 0.000) for 1230 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2335 (Rfree = 0.000) for 1229 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2067 (Rfree = 0.000) for 1227 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.93 3.45 Search for helices and strands: 0 residues in 0 chains, 1272 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.395 Round 2: 95 peptides, 12 chains. Longest chain 12 peptides. Score 0.627 Round 3: 97 peptides, 11 chains. Longest chain 13 peptides. Score 0.671 Round 4: 92 peptides, 13 chains. Longest chain 12 peptides. Score 0.572 Round 5: 88 peptides, 10 chains. Longest chain 15 peptides. Score 0.642 Taking the results from Round 3 Chains 11, Residues 86, Estimated correctness of the model 50.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.76 % complete ) and 2763 restraints for refining 1234 atoms. 2430 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2672 (Rfree = 0.000) for 1234 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 22: After refmac, R = 0.2125 (Rfree = 0.000) for 1229 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.2322 (Rfree = 0.000) for 1224 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.1818 (Rfree = 0.000) for 1221 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.1686 (Rfree = 0.000) for 1220 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.90 3.41 Search for helices and strands: 0 residues in 0 chains, 1245 seeds are put forward Round 1: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.488 Round 2: 98 peptides, 15 chains. Longest chain 11 peptides. Score 0.550 Round 3: 103 peptides, 15 chains. Longest chain 13 peptides. Score 0.589 Round 4: 96 peptides, 15 chains. Longest chain 8 peptides. Score 0.534 Round 5: 99 peptides, 15 chains. Longest chain 13 peptides. Score 0.558 Taking the results from Round 3 Chains 15, Residues 88, Estimated correctness of the model 24.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.76 % complete ) and 2679 restraints for refining 1221 atoms. 2342 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2648 (Rfree = 0.000) for 1221 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 27: After refmac, R = 0.2420 (Rfree = 0.000) for 1215 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.2076 (Rfree = 0.000) for 1211 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.2008 (Rfree = 0.000) for 1213 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.2052 (Rfree = 0.000) for 1210 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.94 3.46 Search for helices and strands: 0 residues in 0 chains, 1256 seeds are put forward Round 1: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.412 Round 2: 91 peptides, 14 chains. Longest chain 13 peptides. Score 0.528 Round 3: 91 peptides, 13 chains. Longest chain 14 peptides. Score 0.564 Round 4: 81 peptides, 11 chains. Longest chain 16 peptides. Score 0.554 Round 5: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.487 Taking the results from Round 3 Chains 13, Residues 78, Estimated correctness of the model 16.3 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.76 % complete ) and 2726 restraints for refining 1247 atoms. 2410 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2642 (Rfree = 0.000) for 1247 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 32: After refmac, R = 0.2483 (Rfree = 0.000) for 1241 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2511 (Rfree = 0.000) for 1238 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.2386 (Rfree = 0.000) for 1237 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2355 (Rfree = 0.000) for 1233 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.84 3.34 Search for helices and strands: 0 residues in 0 chains, 1270 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.320 Round 2: 65 peptides, 9 chains. Longest chain 15 peptides. Score 0.493 Round 3: 65 peptides, 12 chains. Longest chain 12 peptides. Score 0.363 Round 4: 77 peptides, 12 chains. Longest chain 13 peptides. Score 0.481 Round 5: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.414 Taking the results from Round 2 Chains 9, Residues 56, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.76 % complete ) and 2952 restraints for refining 1255 atoms. 2720 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2606 (Rfree = 0.000) for 1255 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 37: After refmac, R = 0.2554 (Rfree = 0.000) for 1247 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.1870 (Rfree = 0.000) for 1250 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.1837 (Rfree = 0.000) for 1251 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2145 (Rfree = 0.000) for 1248 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.79 3.28 Search for helices and strands: 0 residues in 0 chains, 1291 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 7 peptides. Score 0.259 Round 2: 79 peptides, 14 chains. Longest chain 16 peptides. Score 0.419 Round 3: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.394 Round 4: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.363 Round 5: 55 peptides, 11 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 2 Chains 14, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.76 % complete ) and 2941 restraints for refining 1256 atoms. 2695 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2414 (Rfree = 0.000) for 1256 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2207 (Rfree = 0.000) for 1256 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.2078 (Rfree = 0.000) for 1251 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.1717 (Rfree = 0.000) for 1254 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1997 (Rfree = 0.000) for 1250 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.83 3.33 Search for helices and strands: 0 residues in 0 chains, 1297 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 9 peptides. Score 0.270 Round 2: 78 peptides, 15 chains. Longest chain 14 peptides. Score 0.366 Round 3: 82 peptides, 15 chains. Longest chain 8 peptides. Score 0.406 Round 4: 70 peptides, 14 chains. Longest chain 10 peptides. Score 0.326 Round 5: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 67, 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 1vjf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2474 reflections ( 99.76 % complete ) and 2917 restraints for refining 1268 atoms. 2664 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2078 (Rfree = 0.000) for 1268 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2055 (Rfree = 0.000) for 1264 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2371 (Rfree = 0.000) for 1258 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1961 (Rfree = 0.000) for 1253 atoms. TimeTaking 26.83