Tue 25 Dec 19:27:57 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 1vqr-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.2-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/1vqr-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.2-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 ============================================================ Tue 25 Dec 19:28:07 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/1vqr-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.2-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 967 and 0 Target number of residues in the AU: 967 Target solvent content: 0.5827 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-3.2-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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.75 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 83.418 3.200 Wilson plot Bfac: 45.87 18027 reflections ( 88.16 % complete ) and 0 restraints for refining 10560 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3553 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3188 (Rfree = 0.000) for 10560 atoms. Found 76 (94 requested) and removed 183 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.06 3.10 Search for helices and strands: 0 residues in 0 chains, 10623 seeds are put forward NCS extension: 0 residues added, 10623 seeds are put forward Round 1: 328 peptides, 73 chains. Longest chain 8 peptides. Score 0.226 Round 2: 422 peptides, 87 chains. Longest chain 10 peptides. Score 0.280 Round 3: 462 peptides, 87 chains. Longest chain 14 peptides. Score 0.337 Round 4: 461 peptides, 88 chains. Longest chain 13 peptides. Score 0.329 Round 5: 481 peptides, 91 chains. Longest chain 13 peptides. Score 0.339 Taking the results from Round 5 Chains 91, Residues 390, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20584 restraints for refining 8675 atoms. 19115 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2669 (Rfree = 0.000) for 8675 atoms. Found 44 (77 requested) and removed 61 (38 requested) atoms. Cycle 2: After refmac, R = 0.2596 (Rfree = 0.000) for 8592 atoms. Found 39 (77 requested) and removed 49 (38 requested) atoms. Cycle 3: After refmac, R = 0.2524 (Rfree = 0.000) for 8547 atoms. Found 42 (77 requested) and removed 48 (38 requested) atoms. Cycle 4: After refmac, R = 0.2473 (Rfree = 0.000) for 8512 atoms. Found 43 (76 requested) and removed 51 (38 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2210 (Rfree = 0.000) for 8472 atoms. Found 10 (76 requested) and removed 43 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.96 3.00 Search for helices and strands: 0 residues in 0 chains, 8692 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8704 seeds are put forward Round 1: 407 peptides, 88 chains. Longest chain 8 peptides. Score 0.252 Round 2: 469 peptides, 90 chains. Longest chain 10 peptides. Score 0.329 Round 3: 466 peptides, 88 chains. Longest chain 11 peptides. Score 0.336 Round 4: 473 peptides, 85 chains. Longest chain 10 peptides. Score 0.363 Round 5: 466 peptides, 79 chains. Longest chain 16 peptides. Score 0.388 Taking the results from Round 5 Chains 79, Residues 387, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20292 restraints for refining 8542 atoms. 18776 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2494 (Rfree = 0.000) for 8542 atoms. Found 37 (76 requested) and removed 54 (38 requested) atoms. Cycle 7: After refmac, R = 0.2511 (Rfree = 0.000) for 8492 atoms. Found 39 (76 requested) and removed 53 (38 requested) atoms. Cycle 8: After refmac, R = 0.2416 (Rfree = 0.000) for 8458 atoms. Found 42 (76 requested) and removed 52 (38 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2397 (Rfree = 0.000) for 8435 atoms. Found 37 (75 requested) and removed 50 (37 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2127 (Rfree = 0.000) for 8408 atoms. Found 9 (75 requested) and removed 46 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.94 2.98 Search for helices and strands: 0 residues in 0 chains, 8605 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 8628 seeds are put forward Round 1: 412 peptides, 83 chains. Longest chain 9 peptides. Score 0.290 Round 2: 447 peptides, 80 chains. Longest chain 11 peptides. Score 0.357 Round 3: 465 peptides, 79 chains. Longest chain 12 peptides. Score 0.387 Round 4: 479 peptides, 81 chains. Longest chain 21 peptides. Score 0.394 Round 5: 490 peptides, 85 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 4 Chains 82, Residues 398, Estimated correctness of the model 0.0 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 18027 reflections ( 88.16 % complete ) and 20244 restraints for refining 8631 atoms. 18627 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2400 (Rfree = 0.000) for 8631 atoms. Found 57 (77 requested) and removed 68 (38 requested) atoms. Cycle 12: After refmac, R = 0.2343 (Rfree = 0.000) for 8590 atoms. Found 51 (77 requested) and removed 45 (38 requested) atoms. Cycle 13: After refmac, R = 0.2324 (Rfree = 0.000) for 8572 atoms. Found 44 (77 requested) and removed 43 (38 requested) atoms. Cycle 14: After refmac, R = 0.2253 (Rfree = 0.000) for 8553 atoms. Found 40 (76 requested) and removed 44 (38 requested) atoms. Cycle 15: After refmac, R = 0.1994 (Rfree = 0.000) for 8535 atoms. Found 12 (76 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.93 2.97 Search for helices and strands: 0 residues in 0 chains, 8730 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 8757 seeds are put forward Round 1: 440 peptides, 87 chains. Longest chain 11 peptides. Score 0.306 Round 2: 490 peptides, 86 chains. Longest chain 14 peptides. Score 0.380 Round 3: 515 peptides, 93 chains. Longest chain 12 peptides. Score 0.373 Round 4: 528 peptides, 92 chains. Longest chain 13 peptides. Score 0.396 Round 5: 518 peptides, 87 chains. Longest chain 18 peptides. Score 0.410 Taking the results from Round 5 Chains 87, Residues 431, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20374 restraints for refining 8675 atoms. 18717 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2303 (Rfree = 0.000) for 8675 atoms. Found 49 (77 requested) and removed 50 (38 requested) atoms. Cycle 17: After refmac, R = 0.2281 (Rfree = 0.000) for 8639 atoms. Found 37 (77 requested) and removed 46 (38 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2227 (Rfree = 0.000) for 8609 atoms. Found 38 (77 requested) and removed 43 (38 requested) atoms. Cycle 19: After refmac, R = 0.1979 (Rfree = 0.000) for 8591 atoms. Found 22 (77 requested) and removed 42 (38 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2036 (Rfree = 0.000) for 8565 atoms. Found 19 (76 requested) and removed 43 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.95 2.99 Search for helices and strands: 0 residues in 0 chains, 8775 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 8799 seeds are put forward Round 1: 419 peptides, 81 chains. Longest chain 12 peptides. Score 0.312 Round 2: 478 peptides, 83 chains. Longest chain 12 peptides. Score 0.381 Round 3: 496 peptides, 79 chains. Longest chain 17 peptides. Score 0.427 Round 4: 503 peptides, 77 chains. Longest chain 19 peptides. Score 0.446 Round 5: 466 peptides, 79 chains. Longest chain 15 peptides. Score 0.388 Taking the results from Round 4 Chains 77, Residues 426, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20199 restraints for refining 8674 atoms. 18572 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2206 (Rfree = 0.000) for 8674 atoms. Found 52 (77 requested) and removed 45 (38 requested) atoms. Cycle 22: After refmac, R = 0.2191 (Rfree = 0.000) for 8667 atoms. Found 47 (77 requested) and removed 46 (38 requested) atoms. Cycle 23: After refmac, R = 0.2152 (Rfree = 0.000) for 8654 atoms. Found 39 (77 requested) and removed 44 (38 requested) atoms. Cycle 24: After refmac, R = 0.2103 (Rfree = 0.000) for 8640 atoms. Found 43 (77 requested) and removed 44 (38 requested) atoms. Cycle 25: After refmac, R = 0.2078 (Rfree = 0.000) for 8632 atoms. Found 35 (77 requested) and removed 43 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.97 3.01 Search for helices and strands: 0 residues in 0 chains, 8831 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 8852 seeds are put forward Round 1: 415 peptides, 85 chains. Longest chain 12 peptides. Score 0.282 Round 2: 470 peptides, 83 chains. Longest chain 22 peptides. Score 0.371 Round 3: 462 peptides, 77 chains. Longest chain 22 peptides. Score 0.394 Round 4: 481 peptides, 76 chains. Longest chain 19 peptides. Score 0.424 Round 5: 479 peptides, 81 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 4 Chains 76, Residues 405, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20231 restraints for refining 8675 atoms. 18658 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2198 (Rfree = 0.000) for 8675 atoms. Found 45 (77 requested) and removed 42 (38 requested) atoms. Cycle 27: After refmac, R = 0.2200 (Rfree = 0.000) for 8658 atoms. Found 52 (77 requested) and removed 41 (38 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2146 (Rfree = 0.000) for 8654 atoms. Found 28 (77 requested) and removed 43 (38 requested) atoms. Cycle 29: After refmac, R = 0.2131 (Rfree = 0.000) for 8632 atoms. Found 40 (77 requested) and removed 47 (38 requested) atoms. Cycle 30: After refmac, R = 0.2066 (Rfree = 0.000) for 8615 atoms. Found 30 (77 requested) and removed 42 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.96 3.00 Search for helices and strands: 0 residues in 0 chains, 8820 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 8843 seeds are put forward Round 1: 401 peptides, 82 chains. Longest chain 9 peptides. Score 0.280 Round 2: 478 peptides, 87 chains. Longest chain 21 peptides. Score 0.358 Round 3: 500 peptides, 87 chains. Longest chain 19 peptides. Score 0.387 Round 4: 484 peptides, 83 chains. Longest chain 12 peptides. Score 0.389 Round 5: 483 peptides, 77 chains. Longest chain 16 peptides. Score 0.421 Taking the results from Round 5 Chains 78, Residues 406, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20205 restraints for refining 8673 atoms. 18629 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2211 (Rfree = 0.000) for 8673 atoms. Found 58 (77 requested) and removed 41 (38 requested) atoms. Cycle 32: After refmac, R = 0.2159 (Rfree = 0.000) for 8672 atoms. Found 42 (77 requested) and removed 40 (38 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1973 (Rfree = 0.000) for 8667 atoms. Found 25 (77 requested) and removed 41 (38 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2019 (Rfree = 0.000) for 8638 atoms. Found 22 (77 requested) and removed 39 (38 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2021 (Rfree = 0.000) for 8615 atoms. Found 33 (77 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.96 3.00 Search for helices and strands: 0 residues in 0 chains, 8817 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 8836 seeds are put forward Round 1: 396 peptides, 83 chains. Longest chain 12 peptides. Score 0.266 Round 2: 444 peptides, 79 chains. Longest chain 12 peptides. Score 0.359 Round 3: 420 peptides, 72 chains. Longest chain 17 peptides. Score 0.367 Round 4: 428 peptides, 75 chains. Longest chain 12 peptides. Score 0.361 Round 5: 440 peptides, 70 chains. Longest chain 17 peptides. Score 0.406 Taking the results from Round 5 Chains 70, Residues 370, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20121 restraints for refining 8675 atoms. 18650 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2217 (Rfree = 0.000) for 8675 atoms. Found 62 (77 requested) and removed 42 (38 requested) atoms. Cycle 37: After refmac, R = 0.2140 (Rfree = 0.000) for 8679 atoms. Found 54 (78 requested) and removed 45 (39 requested) atoms. Cycle 38: After refmac, R = 0.2057 (Rfree = 0.000) for 8673 atoms. Found 37 (77 requested) and removed 42 (38 requested) atoms. Cycle 39: After refmac, R = 0.2060 (Rfree = 0.000) for 8658 atoms. Found 44 (77 requested) and removed 42 (38 requested) atoms. Cycle 40: After refmac, R = 0.2031 (Rfree = 0.000) for 8655 atoms. Found 36 (77 requested) and removed 42 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.96 3.00 Search for helices and strands: 0 residues in 0 chains, 8846 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 8870 seeds are put forward Round 1: 396 peptides, 81 chains. Longest chain 10 peptides. Score 0.279 Round 2: 434 peptides, 79 chains. Longest chain 14 peptides. Score 0.345 Round 3: 428 peptides, 72 chains. Longest chain 16 peptides. Score 0.378 Round 4: 434 peptides, 73 chains. Longest chain 15 peptides. Score 0.380 Round 5: 434 peptides, 71 chains. Longest chain 16 peptides. Score 0.392 Taking the results from Round 5 Chains 71, Residues 363, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20679 restraints for refining 8676 atoms. 19298 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2091 (Rfree = 0.000) for 8676 atoms. Found 50 (77 requested) and removed 40 (38 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2028 (Rfree = 0.000) for 8670 atoms. Found 46 (77 requested) and removed 39 (38 requested) atoms. Cycle 43: After refmac, R = 0.1987 (Rfree = 0.000) for 8669 atoms. Found 45 (77 requested) and removed 39 (38 requested) atoms. Cycle 44: After refmac, R = 0.1952 (Rfree = 0.000) for 8671 atoms. Found 30 (77 requested) and removed 40 (38 requested) atoms. Cycle 45: After refmac, R = 0.1927 (Rfree = 0.000) for 8658 atoms. Found 36 (77 requested) and removed 41 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.94 2.98 Search for helices and strands: 0 residues in 0 chains, 8868 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 8890 seeds are put forward Round 1: 354 peptides, 77 chains. Longest chain 10 peptides. Score 0.241 Round 2: 401 peptides, 75 chains. Longest chain 11 peptides. Score 0.323 Round 3: 409 peptides, 73 chains. Longest chain 14 peptides. Score 0.346 Round 4: 406 peptides, 72 chains. Longest chain 12 peptides. Score 0.348 Round 5: 387 peptides, 73 chains. Longest chain 15 peptides. Score 0.315 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 72, Residues 334, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 1vqr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18027 reflections ( 88.16 % complete ) and 20426 restraints for refining 8676 atoms. 19142 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2110 (Rfree = 0.000) for 8676 atoms. Found 0 (77 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.2131 (Rfree = 0.000) for 8619 atoms. Found 0 (77 requested) and removed 38 (38 requested) atoms. Cycle 48: After refmac, R = 0.2117 (Rfree = 0.000) for 8573 atoms. Found 0 (77 requested) and removed 38 (38 requested) atoms. Cycle 49: After refmac, R = 0.2040 (Rfree = 0.000) for 8531 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 124.66