null 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 1vjf-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-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/1vjf-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-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 22:23:15 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/1vjf-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-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 125 and 0 Target number of residues in the AU: 125 Target solvent content: 0.5699 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-3.6-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: 96 Cell parameters: 50.903 50.903 121.411 90.000 90.000 90.000 Input sequence file: 1vjf-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1440 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 Loops will be built when appropriate and at the last cycle Resolution range: 46.944 3.601 Wilson plot Bfac: 41.47 2099 reflections ( 99.72 % complete ) and 0 restraints for refining 1592 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3208 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2265 (Rfree = 0.000) for 1592 atoms. Found 3 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.97 3.50 Search for helices and strands: 0 residues in 0 chains, 1611 seeds are put forward Round 1: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.346 Round 2: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.452 Round 3: 101 peptides, 16 chains. Longest chain 11 peptides. Score 0.539 Round 4: 103 peptides, 15 chains. Longest chain 14 peptides. Score 0.589 Round 5: 97 peptides, 14 chains. Longest chain 13 peptides. Score 0.577 Taking the results from Round 4 Chains 15, Residues 88, Estimated correctness of the model 10.2 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2099 reflections ( 99.72 % complete ) and 2838 restraints for refining 1305 atoms. 2477 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2419 (Rfree = 0.000) for 1305 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 2: After refmac, R = 0.2270 (Rfree = 0.000) for 1288 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.2173 (Rfree = 0.000) for 1281 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2159 (Rfree = 0.000) for 1274 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2120 (Rfree = 0.000) for 1270 atoms. Found 2 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 1291 seeds are put forward Round 1: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.409 Round 2: 105 peptides, 16 chains. Longest chain 15 peptides. Score 0.571 Round 3: 99 peptides, 17 chains. Longest chain 11 peptides. Score 0.486 Round 4: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.464 Round 5: 89 peptides, 14 chains. Longest chain 10 peptides. Score 0.511 Taking the results from Round 2 Chains 16, Residues 89, Estimated correctness of the model 2.9 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2099 reflections ( 99.72 % complete ) and 2857 restraints for refining 1264 atoms. 2506 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2225 (Rfree = 0.000) for 1264 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 7: After refmac, R = 0.2036 (Rfree = 0.000) for 1258 atoms. Found 6 (8 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2010 (Rfree = 0.000) for 1244 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.1935 (Rfree = 0.000) for 1240 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1905 (Rfree = 0.000) for 1234 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 1277 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 10 peptides. Score 0.385 Round 2: 95 peptides, 14 chains. Longest chain 11 peptides. Score 0.561 Round 3: 96 peptides, 13 chains. Longest chain 12 peptides. Score 0.602 Round 4: 103 peptides, 13 chains. Longest chain 15 peptides. Score 0.652 Round 5: 106 peptides, 14 chains. Longest chain 14 peptides. Score 0.642 Taking the results from Round 4 Chains 13, Residues 90, Estimated correctness of the model 33.8 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 2099 reflections ( 99.72 % complete ) and 2687 restraints for refining 1305 atoms. 2252 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2673 (Rfree = 0.000) for 1305 atoms. Found 3 (8 requested) and removed 14 (4 requested) atoms. Cycle 12: After refmac, R = 0.2318 (Rfree = 0.000) for 1278 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2222 (Rfree = 0.000) for 1265 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2163 (Rfree = 0.000) for 1258 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2153 (Rfree = 0.000) for 1250 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.87 3.38 Search for helices and strands: 0 residues in 0 chains, 1288 seeds are put forward Round 1: 82 peptides, 14 chains. Longest chain 9 peptides. Score 0.447 Round 2: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.354 Round 3: 93 peptides, 16 chains. Longest chain 9 peptides. Score 0.470 Round 4: 87 peptides, 14 chains. Longest chain 13 peptides. Score 0.493 Round 5: 88 peptides, 14 chains. Longest chain 9 peptides. Score 0.502 Taking the results from Round 5 Chains 14, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2099 reflections ( 99.72 % complete ) and 2936 restraints for refining 1290 atoms. 2654 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2421 (Rfree = 0.000) for 1290 atoms. Found 3 (8 requested) and removed 13 (4 requested) atoms. Cycle 17: After refmac, R = 0.2206 (Rfree = 0.000) for 1267 atoms. Found 2 (8 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.2132 (Rfree = 0.000) for 1255 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2249 (Rfree = 0.000) for 1252 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2208 (Rfree = 0.000) for 1246 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.62 3.08 Search for helices and strands: 0 residues in 0 chains, 1282 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 8 peptides. Score 0.290 Round 2: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.344 Round 3: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.397 Round 4: 85 peptides, 15 chains. Longest chain 13 peptides. Score 0.435 Round 5: 96 peptides, 17 chains. Longest chain 11 peptides. Score 0.459 Taking the results from Round 5 Chains 17, Residues 79, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2099 reflections ( 99.72 % complete ) and 2783 restraints for refining 1275 atoms. 2468 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2523 (Rfree = 0.000) for 1275 atoms. Found 5 (8 requested) and removed 10 (4 requested) atoms. Cycle 22: After refmac, R = 0.2492 (Rfree = 0.000) for 1266 atoms. Found 0 (8 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.2348 (Rfree = 0.000) for 1255 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2323 (Rfree = 0.000) for 1253 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. Cycle 25: After refmac, R = 0.2279 (Rfree = 0.000) for 1245 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.95 3.47 Search for helices and strands: 0 residues in 0 chains, 1277 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 11 peptides. Score 0.339 Round 2: 82 peptides, 15 chains. Longest chain 12 peptides. Score 0.406 Round 3: 74 peptides, 13 chains. Longest chain 12 peptides. Score 0.411 Round 4: 76 peptides, 14 chains. Longest chain 11 peptides. Score 0.389 Round 5: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.331 Taking the results from Round 3 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2099 reflections ( 99.72 % complete ) and 3010 restraints for refining 1262 atoms. 2779 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2573 (Rfree = 0.000) for 1262 atoms. Found 4 (8 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.2166 (Rfree = 0.000) for 1250 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.1901 (Rfree = 0.000) for 1244 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2239 (Rfree = 0.000) for 1240 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2125 (Rfree = 0.000) for 1240 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.04 3.58 Search for helices and strands: 0 residues in 0 chains, 1284 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.239 Round 2: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.335 Round 3: 78 peptides, 15 chains. Longest chain 10 peptides. Score 0.366 Round 4: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.325 Round 5: 73 peptides, 13 chains. Longest chain 9 peptides. Score 0.401 Taking the results from Round 5 Chains 13, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2099 reflections ( 99.72 % complete ) and 2850 restraints for refining 1235 atoms. 2623 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2254 (Rfree = 0.000) for 1235 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.2204 (Rfree = 0.000) for 1227 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2107 (Rfree = 0.000) for 1221 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.2078 (Rfree = 0.000) for 1221 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2026 (Rfree = 0.000) for 1220 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 1250 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 8 peptides. Score 0.272 Round 2: 71 peptides, 14 chains. Longest chain 7 peptides. Score 0.337 Round 3: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.447 Round 4: 73 peptides, 13 chains. Longest chain 9 peptides. Score 0.401 Round 5: 73 peptides, 13 chains. Longest chain 8 peptides. Score 0.401 Taking the results from Round 3 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2099 reflections ( 99.72 % complete ) and 2836 restraints for refining 1217 atoms. 2615 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2529 (Rfree = 0.000) for 1217 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 37: After refmac, R = 0.2340 (Rfree = 0.000) for 1208 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 38: After refmac, R = 0.2227 (Rfree = 0.000) for 1202 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2295 (Rfree = 0.000) for 1197 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.2143 (Rfree = 0.000) for 1195 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 3.51 Search for helices and strands: 0 residues in 0 chains, 1217 seeds are put forward Round 1: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.321 Round 2: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.380 Round 3: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.397 Round 4: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.363 Round 5: 75 peptides, 12 chains. Longest chain 14 peptides. Score 0.463 Taking the results from Round 5 Chains 12, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2099 reflections ( 99.72 % complete ) and 2873 restraints for refining 1244 atoms. 2633 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2222 (Rfree = 0.000) for 1244 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 42: After refmac, R = 0.2051 (Rfree = 0.000) for 1239 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2006 (Rfree = 0.000) for 1234 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.2021 (Rfree = 0.000) for 1235 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1981 (Rfree = 0.000) for 1235 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 3.53 Search for helices and strands: 0 residues in 0 chains, 1272 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 9 peptides. Score 0.255 Round 2: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.291 Round 3: 58 peptides, 10 chains. Longest chain 8 peptides. Score 0.380 Round 4: 60 peptides, 10 chains. Longest chain 9 peptides. Score 0.400 Round 5: 62 peptides, 11 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 50, 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. 2099 reflections ( 99.72 % complete ) and 2933 restraints for refining 1229 atoms. 2743 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2296 (Rfree = 0.000) for 1229 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2253 (Rfree = 0.000) for 1223 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2208 (Rfree = 0.000) for 1220 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2191 (Rfree = 0.000) for 1217 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:17 GMT 2018 Job finished. TimeTaking 26.2 Used memory is bytes: 20090336