Sun 23 Dec 22:22:58 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 1vr3-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.8-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/1vr3-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.8-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 22:23:07 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/1vr3-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.8-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 225 and 0 Target number of residues in the AU: 225 Target solvent content: 0.6592 Checking the provided sequence file Detected sequence length: 191 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 191 Adjusted target solvent content: 0.71 Input MTZ file: 1vr3-3.8-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: 79.137 79.137 114.115 90.000 90.000 90.000 Input sequence file: 1vr3-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1528 target number of atoms Had to go as low as 1.15 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: 65.030 3.800 Wilson plot Bfac: 83.56 3888 reflections ( 99.64 % complete ) and 0 restraints for refining 1688 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3502 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2936 (Rfree = 0.000) for 1688 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 2.66 Search for helices and strands: 0 residues in 0 chains, 1719 seeds are put forward Round 1: 128 peptides, 16 chains. Longest chain 20 peptides. Score 0.495 Round 2: 144 peptides, 9 chains. Longest chain 43 peptides. Score 0.673 Round 3: 141 peptides, 9 chains. Longest chain 47 peptides. Score 0.664 Round 4: 133 peptides, 14 chains. Longest chain 23 peptides. Score 0.552 Round 5: 136 peptides, 14 chains. Longest chain 45 peptides. Score 0.563 Taking the results from Round 2 Chains 12, Residues 135, Estimated correctness of the model 30.1 % 2 chains (50 residues) have been docked in sequence ------------------------------------------------------ 3888 reflections ( 99.64 % complete ) and 2726 restraints for refining 1552 atoms. 1956 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2666 (Rfree = 0.000) for 1552 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 2: After refmac, R = 0.2541 (Rfree = 0.000) for 1495 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.2504 (Rfree = 0.000) for 1472 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 4: After refmac, R = 0.2395 (Rfree = 0.000) for 1466 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2308 (Rfree = 0.000) for 1465 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 2.72 Search for helices and strands: 0 residues in 0 chains, 1525 seeds are put forward Round 1: 130 peptides, 11 chains. Longest chain 27 peptides. Score 0.594 Round 2: 134 peptides, 10 chains. Longest chain 36 peptides. Score 0.625 Round 3: 130 peptides, 9 chains. Longest chain 34 peptides. Score 0.629 Round 4: 133 peptides, 11 chains. Longest chain 28 peptides. Score 0.605 Round 5: 136 peptides, 11 chains. Longest chain 33 peptides. Score 0.615 Taking the results from Round 3 Chains 10, Residues 121, Estimated correctness of the model 11.9 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 3888 reflections ( 99.64 % complete ) and 2470 restraints for refining 1400 atoms. 1777 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2717 (Rfree = 0.000) for 1400 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 7: After refmac, R = 0.2515 (Rfree = 0.000) for 1358 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 8: After refmac, R = 0.2393 (Rfree = 0.000) for 1343 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.2358 (Rfree = 0.000) for 1335 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2340 (Rfree = 0.000) for 1330 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 2.65 Search for helices and strands: 0 residues in 0 chains, 1369 seeds are put forward Round 1: 129 peptides, 14 chains. Longest chain 29 peptides. Score 0.537 Round 2: 136 peptides, 11 chains. Longest chain 32 peptides. Score 0.615 Round 3: 133 peptides, 13 chains. Longest chain 30 peptides. Score 0.570 Round 4: 128 peptides, 11 chains. Longest chain 42 peptides. Score 0.587 Round 5: 139 peptides, 14 chains. Longest chain 20 peptides. Score 0.574 Taking the results from Round 2 Chains 13, Residues 125, Estimated correctness of the model 5.7 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 3888 reflections ( 99.64 % complete ) and 2415 restraints for refining 1382 atoms. 1744 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2666 (Rfree = 0.000) for 1382 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 12: After refmac, R = 0.2482 (Rfree = 0.000) for 1355 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 13: After refmac, R = 0.2449 (Rfree = 0.000) for 1340 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2332 (Rfree = 0.000) for 1338 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.2270 (Rfree = 0.000) for 1333 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 2.70 Search for helices and strands: 0 residues in 0 chains, 1374 seeds are put forward Round 1: 137 peptides, 16 chains. Longest chain 25 peptides. Score 0.531 Round 2: 140 peptides, 11 chains. Longest chain 34 peptides. Score 0.629 Round 3: 128 peptides, 14 chains. Longest chain 19 peptides. Score 0.533 Round 4: 129 peptides, 13 chains. Longest chain 26 peptides. Score 0.555 Round 5: 126 peptides, 8 chains. Longest chain 39 peptides. Score 0.633 Taking the results from Round 5 Chains 8, Residues 118, Estimated correctness of the model 13.6 % 1 chains (38 residues) have been docked in sequence ------------------------------------------------------ 3888 reflections ( 99.64 % complete ) and 2501 restraints for refining 1382 atoms. 1860 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2702 (Rfree = 0.000) for 1382 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 17: After refmac, R = 0.2596 (Rfree = 0.000) for 1364 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 18: After refmac, R = 0.2418 (Rfree = 0.000) for 1352 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2407 (Rfree = 0.000) for 1351 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2331 (Rfree = 0.000) for 1349 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 2.68 Search for helices and strands: 0 residues in 0 chains, 1397 seeds are put forward Round 1: 128 peptides, 12 chains. Longest chain 33 peptides. Score 0.569 Round 2: 130 peptides, 12 chains. Longest chain 21 peptides. Score 0.577 Round 3: 136 peptides, 10 chains. Longest chain 25 peptides. Score 0.632 Round 4: 134 peptides, 8 chains. Longest chain 34 peptides. Score 0.658 Round 5: 140 peptides, 9 chains. Longest chain 47 peptides. Score 0.661 Taking the results from Round 5 Chains 11, Residues 131, Estimated correctness of the model 25.3 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3888 reflections ( 99.64 % complete ) and 2590 restraints for refining 1382 atoms. 1952 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2686 (Rfree = 0.000) for 1382 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 22: After refmac, R = 0.2484 (Rfree = 0.000) for 1361 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 23: After refmac, R = 0.2427 (Rfree = 0.000) for 1349 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.2366 (Rfree = 0.000) for 1346 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2330 (Rfree = 0.000) for 1341 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 1392 seeds are put forward Round 1: 126 peptides, 14 chains. Longest chain 32 peptides. Score 0.525 Round 2: 129 peptides, 14 chains. Longest chain 24 peptides. Score 0.537 Round 3: 125 peptides, 13 chains. Longest chain 19 peptides. Score 0.540 Round 4: 125 peptides, 14 chains. Longest chain 17 peptides. Score 0.521 Round 5: 120 peptides, 10 chains. Longest chain 22 peptides. Score 0.576 Taking the results from Round 5 Chains 11, Residues 110, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 3888 reflections ( 99.64 % complete ) and 2620 restraints for refining 1382 atoms. 2028 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2652 (Rfree = 0.000) for 1382 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 27: After refmac, R = 0.2455 (Rfree = 0.000) for 1362 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.2402 (Rfree = 0.000) for 1353 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2464 (Rfree = 0.000) for 1353 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2383 (Rfree = 0.000) for 1356 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 2.70 Search for helices and strands: 0 residues in 0 chains, 1413 seeds are put forward Round 1: 126 peptides, 17 chains. Longest chain 14 peptides. Score 0.467 Round 2: 127 peptides, 15 chains. Longest chain 17 peptides. Score 0.510 Round 3: 128 peptides, 16 chains. Longest chain 17 peptides. Score 0.495 Round 4: 131 peptides, 13 chains. Longest chain 24 peptides. Score 0.562 Round 5: 128 peptides, 12 chains. Longest chain 26 peptides. Score 0.569 Taking the results from Round 5 Chains 14, Residues 116, Estimated correctness of the model 0.0 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 3888 reflections ( 99.64 % complete ) and 2654 restraints for refining 1398 atoms. 2029 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2615 (Rfree = 0.000) for 1398 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.2436 (Rfree = 0.000) for 1391 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.2401 (Rfree = 0.000) for 1381 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2370 (Rfree = 0.000) for 1375 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.2342 (Rfree = 0.000) for 1372 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 1415 seeds are put forward Round 1: 104 peptides, 12 chains. Longest chain 14 peptides. Score 0.473 Round 2: 121 peptides, 14 chains. Longest chain 18 peptides. Score 0.505 Round 3: 126 peptides, 11 chains. Longest chain 26 peptides. Score 0.580 Round 4: 129 peptides, 12 chains. Longest chain 21 peptides. Score 0.573 Round 5: 130 peptides, 13 chains. Longest chain 21 peptides. Score 0.559 Taking the results from Round 3 Chains 11, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3888 reflections ( 99.64 % complete ) and 3046 restraints for refining 1381 atoms. 2597 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2369 (Rfree = 0.000) for 1381 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 37: After refmac, R = 0.2212 (Rfree = 0.000) for 1376 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.2252 (Rfree = 0.000) for 1374 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.2090 (Rfree = 0.000) for 1371 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.2117 (Rfree = 0.000) for 1374 atoms. Found 6 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 2.65 Search for helices and strands: 0 residues in 0 chains, 1442 seeds are put forward Round 1: 128 peptides, 17 chains. Longest chain 12 peptides. Score 0.476 Round 2: 138 peptides, 16 chains. Longest chain 17 peptides. Score 0.535 Round 3: 139 peptides, 16 chains. Longest chain 18 peptides. Score 0.539 Round 4: 135 peptides, 16 chains. Longest chain 26 peptides. Score 0.523 Round 5: 124 peptides, 15 chains. Longest chain 20 peptides. Score 0.498 Taking the results from Round 3 Chains 18, Residues 123, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3888 reflections ( 99.64 % complete ) and 2731 restraints for refining 1382 atoms. 2204 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2442 (Rfree = 0.000) for 1382 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 42: After refmac, R = 0.2311 (Rfree = 0.000) for 1380 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.2248 (Rfree = 0.000) for 1377 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2249 (Rfree = 0.000) for 1375 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2237 (Rfree = 0.000) for 1370 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 2.70 Search for helices and strands: 0 residues in 0 chains, 1422 seeds are put forward Round 1: 128 peptides, 19 chains. Longest chain 16 peptides. Score 0.437 Round 2: 130 peptides, 14 chains. Longest chain 17 peptides. Score 0.540 Round 3: 127 peptides, 13 chains. Longest chain 35 peptides. Score 0.547 Round 4: 119 peptides, 9 chains. Longest chain 41 peptides. Score 0.591 Round 5: 128 peptides, 13 chains. Longest chain 25 peptides. Score 0.551 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 110, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 1vr3-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3888 reflections ( 99.64 % complete ) and 2596 restraints for refining 1382 atoms. 2034 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2547 (Rfree = 0.000) for 1382 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2320 (Rfree = 0.000) for 1367 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2218 (Rfree = 0.000) for 1355 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2163 (Rfree = 0.000) for 1347 atoms. TimeTaking 31.73