Sun 23 Dec 22:22:49 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 1vlu-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-4.0-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/1vlu-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-4.0-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 22:22:59 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/1vlu-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-4.0-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 909 and 0 Target number of residues in the AU: 909 Target solvent content: 0.6653 Checking the provided sequence file Detected sequence length: 468 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 936 Adjusted target solvent content: 0.66 Input MTZ file: 1vlu-4.0-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.90 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: 44.569 4.000 Wilson plot Bfac: 88.66 12767 reflections ( 99.80 % complete ) and 0 restraints for refining 8285 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3393 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3400 (Rfree = 0.000) for 8285 atoms. Found 39 (39 requested) and removed 555 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.08 Search for helices and strands: 0 residues in 0 chains, 7839 seeds are put forward NCS extension: 0 residues added, 7839 seeds are put forward Round 1: 251 peptides, 50 chains. Longest chain 11 peptides. Score 0.250 Round 2: 328 peptides, 54 chains. Longest chain 13 peptides. Score 0.332 Round 3: 375 peptides, 61 chains. Longest chain 12 peptides. Score 0.351 Round 4: 394 peptides, 61 chains. Longest chain 18 peptides. Score 0.374 Round 5: 398 peptides, 60 chains. Longest chain 19 peptides. Score 0.384 Taking the results from Round 5 Chains 61, Residues 338, Estimated correctness of the model 0.0 % 8 chains (42 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 16049 restraints for refining 6761 atoms. 14637 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2905 (Rfree = 0.000) for 6761 atoms. Found 32 (32 requested) and removed 157 (16 requested) atoms. Cycle 2: After refmac, R = 0.2620 (Rfree = 0.000) for 6488 atoms. Found 31 (31 requested) and removed 66 (15 requested) atoms. Cycle 3: After refmac, R = 0.2464 (Rfree = 0.000) for 6382 atoms. Found 30 (30 requested) and removed 58 (15 requested) atoms. Cycle 4: After refmac, R = 0.2483 (Rfree = 0.000) for 6310 atoms. Found 30 (30 requested) and removed 56 (15 requested) atoms. Cycle 5: After refmac, R = 0.2403 (Rfree = 0.000) for 6251 atoms. Found 29 (29 requested) and removed 45 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.06 Search for helices and strands: 0 residues in 0 chains, 6496 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 6534 seeds are put forward Round 1: 442 peptides, 65 chains. Longest chain 31 peptides. Score 0.409 Round 2: 492 peptides, 59 chains. Longest chain 24 peptides. Score 0.492 Round 3: 523 peptides, 60 chains. Longest chain 27 peptides. Score 0.518 Round 4: 498 peptides, 50 chains. Longest chain 38 peptides. Score 0.540 Round 5: 501 peptides, 52 chains. Longest chain 24 peptides. Score 0.534 Taking the results from Round 4 Chains 59, Residues 448, Estimated correctness of the model 0.0 % 9 chains (99 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14348 restraints for refining 6760 atoms. 12308 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2656 (Rfree = 0.000) for 6760 atoms. Found 32 (32 requested) and removed 100 (16 requested) atoms. Cycle 7: After refmac, R = 0.2523 (Rfree = 0.000) for 6577 atoms. Found 31 (31 requested) and removed 63 (15 requested) atoms. Cycle 8: After refmac, R = 0.2379 (Rfree = 0.000) for 6505 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 9: After refmac, R = 0.2383 (Rfree = 0.000) for 6417 atoms. Found 30 (30 requested) and removed 60 (15 requested) atoms. Cycle 10: After refmac, R = 0.2327 (Rfree = 0.000) for 6351 atoms. Found 30 (30 requested) and removed 37 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.80 3.05 Search for helices and strands: 0 residues in 0 chains, 6592 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6616 seeds are put forward Round 1: 480 peptides, 65 chains. Longest chain 16 peptides. Score 0.451 Round 2: 501 peptides, 60 chains. Longest chain 24 peptides. Score 0.496 Round 3: 518 peptides, 59 chains. Longest chain 33 peptides. Score 0.518 Round 4: 510 peptides, 60 chains. Longest chain 20 peptides. Score 0.505 Round 5: 513 peptides, 50 chains. Longest chain 32 peptides. Score 0.554 Taking the results from Round 5 Chains 57, Residues 463, Estimated correctness of the model 0.0 % 9 chains (114 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14222 restraints for refining 6762 atoms. 12050 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2500 (Rfree = 0.000) for 6762 atoms. Found 32 (32 requested) and removed 67 (16 requested) atoms. Cycle 12: After refmac, R = 0.2457 (Rfree = 0.000) for 6617 atoms. Found 31 (31 requested) and removed 52 (15 requested) atoms. Cycle 13: After refmac, R = 0.2403 (Rfree = 0.000) for 6541 atoms. Found 31 (31 requested) and removed 44 (15 requested) atoms. Cycle 14: After refmac, R = 0.2371 (Rfree = 0.000) for 6479 atoms. Found 31 (31 requested) and removed 51 (15 requested) atoms. Cycle 15: After refmac, R = 0.2334 (Rfree = 0.000) for 6416 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.02 Search for helices and strands: 0 residues in 0 chains, 6673 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 6702 seeds are put forward Round 1: 458 peptides, 71 chains. Longest chain 14 peptides. Score 0.396 Round 2: 509 peptides, 62 chains. Longest chain 22 peptides. Score 0.495 Round 3: 511 peptides, 61 chains. Longest chain 18 peptides. Score 0.502 Round 4: 513 peptides, 61 chains. Longest chain 17 peptides. Score 0.504 Round 5: 481 peptides, 59 chains. Longest chain 30 peptides. Score 0.481 Taking the results from Round 4 Failed to save intermediate PDB Chains 64, Residues 452, Estimated correctness of the model 0.0 % 7 chains (79 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14371 restraints for refining 6762 atoms. 12353 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2509 (Rfree = 0.000) for 6762 atoms. Found 32 (32 requested) and removed 68 (16 requested) atoms. Cycle 17: After refmac, R = 0.2450 (Rfree = 0.000) for 6606 atoms. Found 31 (31 requested) and removed 57 (15 requested) atoms. Cycle 18: After refmac, R = 0.2335 (Rfree = 0.000) for 6526 atoms. Found 31 (31 requested) and removed 42 (15 requested) atoms. Cycle 19: After refmac, R = 0.2350 (Rfree = 0.000) for 6464 atoms. Found 30 (30 requested) and removed 43 (15 requested) atoms. Cycle 20: After refmac, R = 0.2044 (Rfree = 0.000) for 6412 atoms. Found 10 (30 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.01 Search for helices and strands: 0 residues in 0 chains, 6652 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6667 seeds are put forward Round 1: 446 peptides, 65 chains. Longest chain 16 peptides. Score 0.413 Round 2: 482 peptides, 62 chains. Longest chain 18 peptides. Score 0.467 Round 3: 476 peptides, 65 chains. Longest chain 19 peptides. Score 0.446 Round 4: 476 peptides, 57 chains. Longest chain 18 peptides. Score 0.485 Round 5: 477 peptides, 59 chains. Longest chain 24 peptides. Score 0.477 Taking the results from Round 4 Chains 61, Residues 419, Estimated correctness of the model 0.0 % 5 chains (44 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 15042 restraints for refining 6759 atoms. 13300 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2675 (Rfree = 0.000) for 6759 atoms. Found 32 (32 requested) and removed 67 (16 requested) atoms. Cycle 22: After refmac, R = 0.2489 (Rfree = 0.000) for 6608 atoms. Found 31 (31 requested) and removed 42 (15 requested) atoms. Cycle 23: After refmac, R = 0.2068 (Rfree = 0.000) for 6528 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 24: After refmac, R = 0.2227 (Rfree = 0.000) for 6497 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 25: After refmac, R = 0.2253 (Rfree = 0.000) for 6477 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.01 Search for helices and strands: 0 residues in 0 chains, 6733 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 6755 seeds are put forward Round 1: 444 peptides, 72 chains. Longest chain 16 peptides. Score 0.375 Round 2: 472 peptides, 61 chains. Longest chain 17 peptides. Score 0.462 Round 3: 487 peptides, 65 chains. Longest chain 17 peptides. Score 0.458 Round 4: 493 peptides, 61 chains. Longest chain 21 peptides. Score 0.483 Round 5: 491 peptides, 54 chains. Longest chain 21 peptides. Score 0.515 Taking the results from Round 5 Chains 60, Residues 437, Estimated correctness of the model 0.0 % 7 chains (65 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 14699 restraints for refining 6762 atoms. 12783 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2545 (Rfree = 0.000) for 6762 atoms. Found 32 (32 requested) and removed 56 (16 requested) atoms. Cycle 27: After refmac, R = 0.2395 (Rfree = 0.000) for 6628 atoms. Found 32 (32 requested) and removed 50 (16 requested) atoms. Cycle 28: After refmac, R = 0.2506 (Rfree = 0.000) for 6544 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. Cycle 29: After refmac, R = 0.2411 (Rfree = 0.000) for 6465 atoms. Found 31 (31 requested) and removed 42 (15 requested) atoms. Cycle 30: After refmac, R = 0.2368 (Rfree = 0.000) for 6409 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 2.98 Search for helices and strands: 0 residues in 0 chains, 6716 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6735 seeds are put forward Round 1: 424 peptides, 76 chains. Longest chain 19 peptides. Score 0.330 Round 2: 459 peptides, 63 chains. Longest chain 17 peptides. Score 0.438 Round 3: 465 peptides, 63 chains. Longest chain 18 peptides. Score 0.444 Round 4: 483 peptides, 67 chains. Longest chain 18 peptides. Score 0.444 Round 5: 472 peptides, 61 chains. Longest chain 32 peptides. Score 0.462 Taking the results from Round 5 Chains 62, Residues 411, Estimated correctness of the model 0.0 % 6 chains (56 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 15033 restraints for refining 6761 atoms. 13242 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2448 (Rfree = 0.000) for 6761 atoms. Found 32 (32 requested) and removed 78 (16 requested) atoms. Cycle 32: After refmac, R = 0.2262 (Rfree = 0.000) for 6631 atoms. Found 31 (31 requested) and removed 41 (15 requested) atoms. Cycle 33: After refmac, R = 0.2206 (Rfree = 0.000) for 6578 atoms. Found 24 (31 requested) and removed 54 (15 requested) atoms. Cycle 34: After refmac, R = 0.2173 (Rfree = 0.000) for 6520 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 35: After refmac, R = 0.2193 (Rfree = 0.000) for 6494 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.01 Search for helices and strands: 0 residues in 0 chains, 6720 seeds are put forward NCS extension: 55 residues added (14 deleted due to clashes), 6775 seeds are put forward Round 1: 442 peptides, 71 chains. Longest chain 15 peptides. Score 0.378 Round 2: 483 peptides, 67 chains. Longest chain 19 peptides. Score 0.444 Round 3: 489 peptides, 61 chains. Longest chain 37 peptides. Score 0.479 Round 4: 493 peptides, 60 chains. Longest chain 24 peptides. Score 0.488 Round 5: 488 peptides, 62 chains. Longest chain 16 peptides. Score 0.474 Taking the results from Round 4 Chains 66, Residues 433, Estimated correctness of the model 0.0 % 11 chains (118 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 13865 restraints for refining 6762 atoms. 11746 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2548 (Rfree = 0.000) for 6762 atoms. Found 32 (32 requested) and removed 52 (16 requested) atoms. Cycle 37: After refmac, R = 0.2381 (Rfree = 0.000) for 6667 atoms. Found 32 (32 requested) and removed 44 (16 requested) atoms. Cycle 38: After refmac, R = 0.2289 (Rfree = 0.000) for 6597 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 39: After refmac, R = 0.2228 (Rfree = 0.000) for 6537 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 40: After refmac, R = 0.2155 (Rfree = 0.000) for 6488 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.02 Search for helices and strands: 0 residues in 0 chains, 6712 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6734 seeds are put forward Round 1: 412 peptides, 75 chains. Longest chain 12 peptides. Score 0.320 Round 2: 441 peptides, 65 chains. Longest chain 20 peptides. Score 0.408 Round 3: 480 peptides, 67 chains. Longest chain 22 peptides. Score 0.441 Round 4: 488 peptides, 67 chains. Longest chain 23 peptides. Score 0.449 Round 5: 470 peptides, 63 chains. Longest chain 23 peptides. Score 0.450 Taking the results from Round 5 Chains 63, Residues 407, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12767 reflections ( 99.80 % complete ) and 15445 restraints for refining 6762 atoms. 13846 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2511 (Rfree = 0.000) for 6762 atoms. Found 32 (32 requested) and removed 60 (16 requested) atoms. Cycle 42: After refmac, R = 0.2340 (Rfree = 0.000) for 6665 atoms. Found 31 (31 requested) and removed 46 (15 requested) atoms. Cycle 43: After refmac, R = 0.2217 (Rfree = 0.000) for 6616 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 44: After refmac, R = 0.2183 (Rfree = 0.000) for 6583 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 45: After refmac, R = 0.1906 (Rfree = 0.000) for 6560 atoms. Found 10 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 2.99 Search for helices and strands: 0 residues in 0 chains, 6792 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6815 seeds are put forward Round 1: 386 peptides, 71 chains. Longest chain 15 peptides. Score 0.309 Round 2: 447 peptides, 68 chains. Longest chain 19 peptides. Score 0.399 Round 3: 455 peptides, 61 chains. Longest chain 33 peptides. Score 0.444 Round 4: 463 peptides, 64 chains. Longest chain 24 peptides. Score 0.437 Round 5: 464 peptides, 61 chains. Longest chain 25 peptides. Score 0.453 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 403, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vlu-4_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (403 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12767 reflections ( 99.80 % complete ) and 15206 restraints for refining 6760 atoms. 13636 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2469 (Rfree = 0.000) for 6760 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2393 (Rfree = 0.000) for 6689 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2320 (Rfree = 0.000) for 6635 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2260 (Rfree = 0.000) for 6580 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... TimeTaking 90.65