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 1vl5-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-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/1vl5-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-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 ============================================================ 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/1vl5-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-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 783 and 0 Target number of residues in the AU: 783 Target solvent content: 0.6342 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-3.6-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: 4 Cell parameters: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 8320 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: 49.849 3.600 Wilson plot Bfac: 68.61 13375 reflections ( 99.90 % complete ) and 0 restraints for refining 9229 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3147 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2790 (Rfree = 0.000) for 9229 atoms. Found 59 (59 requested) and removed 56 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 9378 seeds are put forward NCS extension: 0 residues added, 9378 seeds are put forward Round 1: 439 peptides, 86 chains. Longest chain 13 peptides. Score 0.319 Round 2: 540 peptides, 82 chains. Longest chain 19 peptides. Score 0.482 Round 3: 564 peptides, 73 chains. Longest chain 19 peptides. Score 0.558 Round 4: 583 peptides, 75 chains. Longest chain 23 peptides. Score 0.569 Round 5: 580 peptides, 76 chains. Longest chain 21 peptides. Score 0.561 Taking the results from Round 4 Chains 75, Residues 508, Estimated correctness of the model 2.2 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17157 restraints for refining 7539 atoms. 15151 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2407 (Rfree = 0.000) for 7539 atoms. Found 46 (48 requested) and removed 57 (24 requested) atoms. Cycle 2: After refmac, R = 0.2260 (Rfree = 0.000) for 7376 atoms. Found 44 (48 requested) and removed 42 (24 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2171 (Rfree = 0.000) for 7289 atoms. Found 41 (47 requested) and removed 36 (23 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2067 (Rfree = 0.000) for 7240 atoms. Found 27 (46 requested) and removed 33 (23 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2023 (Rfree = 0.000) for 7186 atoms. Found 28 (46 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 7460 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 7484 seeds are put forward Round 1: 524 peptides, 87 chains. Longest chain 16 peptides. Score 0.433 Round 2: 574 peptides, 83 chains. Longest chain 23 peptides. Score 0.518 Round 3: 588 peptides, 84 chains. Longest chain 26 peptides. Score 0.529 Round 4: 593 peptides, 78 chains. Longest chain 21 peptides. Score 0.565 Round 5: 614 peptides, 83 chains. Longest chain 22 peptides. Score 0.564 Taking the results from Round 4 Chains 83, Residues 515, Estimated correctness of the model 0.5 % 6 chains (52 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 16235 restraints for refining 7372 atoms. 14094 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2175 (Rfree = 0.000) for 7372 atoms. Found 29 (47 requested) and removed 53 (23 requested) atoms. Cycle 7: After refmac, R = 0.2041 (Rfree = 0.000) for 7282 atoms. Found 28 (47 requested) and removed 43 (23 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1958 (Rfree = 0.000) for 7234 atoms. Found 16 (46 requested) and removed 44 (23 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1946 (Rfree = 0.000) for 7186 atoms. Found 12 (46 requested) and removed 34 (23 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1864 (Rfree = 0.000) for 7149 atoms. Found 4 (45 requested) and removed 32 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 7417 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 7438 seeds are put forward Round 1: 496 peptides, 84 chains. Longest chain 11 peptides. Score 0.413 Round 2: 578 peptides, 85 chains. Longest chain 19 peptides. Score 0.512 Round 3: 563 peptides, 80 chains. Longest chain 18 peptides. Score 0.521 Round 4: 579 peptides, 76 chains. Longest chain 23 peptides. Score 0.559 Round 5: 576 peptides, 78 chains. Longest chain 20 peptides. Score 0.546 Taking the results from Round 4 Chains 79, Residues 503, Estimated correctness of the model 0.0 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13375 reflections ( 99.90 % complete ) and 16809 restraints for refining 7523 atoms. 14722 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2136 (Rfree = 0.000) for 7523 atoms. Found 32 (48 requested) and removed 47 (24 requested) atoms. Cycle 12: After refmac, R = 0.1972 (Rfree = 0.000) for 7456 atoms. Found 15 (48 requested) and removed 33 (24 requested) atoms. Cycle 13: After refmac, R = 0.1925 (Rfree = 0.000) for 7409 atoms. Found 12 (47 requested) and removed 32 (23 requested) atoms. Cycle 14: After refmac, R = 0.1854 (Rfree = 0.000) for 7369 atoms. Found 7 (47 requested) and removed 30 (23 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1900 (Rfree = 0.000) for 7332 atoms. Found 17 (47 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 7564 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 7586 seeds are put forward Round 1: 497 peptides, 80 chains. Longest chain 15 peptides. Score 0.438 Round 2: 569 peptides, 81 chains. Longest chain 25 peptides. Score 0.522 Round 3: 565 peptides, 72 chains. Longest chain 28 peptides. Score 0.564 Round 4: 566 peptides, 76 chains. Longest chain 18 peptides. Score 0.545 Round 5: 598 peptides, 73 chains. Longest chain 28 peptides. Score 0.595 Taking the results from Round 5 Chains 80, Residues 525, Estimated correctness of the model 12.7 % 10 chains (95 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13375 reflections ( 99.90 % complete ) and 15976 restraints for refining 7542 atoms. 13548 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2307 (Rfree = 0.000) for 7542 atoms. Found 44 (48 requested) and removed 53 (24 requested) atoms. Cycle 17: After refmac, R = 0.2166 (Rfree = 0.000) for 7474 atoms. Found 20 (48 requested) and removed 29 (24 requested) atoms. Cycle 18: After refmac, R = 0.2119 (Rfree = 0.000) for 7437 atoms. Found 13 (47 requested) and removed 27 (23 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2039 (Rfree = 0.000) for 7410 atoms. Found 21 (47 requested) and removed 28 (23 requested) atoms. Cycle 20: After refmac, R = 0.1987 (Rfree = 0.000) for 7384 atoms. Found 17 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 7631 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 7664 seeds are put forward Round 1: 489 peptides, 84 chains. Longest chain 15 peptides. Score 0.403 Round 2: 554 peptides, 74 chains. Longest chain 32 peptides. Score 0.541 Round 3: 534 peptides, 72 chains. Longest chain 27 peptides. Score 0.528 Round 4: 543 peptides, 71 chains. Longest chain 25 peptides. Score 0.544 Round 5: 535 peptides, 72 chains. Longest chain 29 peptides. Score 0.530 Taking the results from Round 4 Chains 72, Residues 472, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17443 restraints for refining 7540 atoms. 15582 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2306 (Rfree = 0.000) for 7540 atoms. Found 42 (48 requested) and removed 40 (24 requested) atoms. Cycle 22: After refmac, R = 0.2114 (Rfree = 0.000) for 7490 atoms. Found 38 (48 requested) and removed 40 (24 requested) atoms. Cycle 23: After refmac, R = 0.1787 (Rfree = 0.000) for 7463 atoms. Found 4 (48 requested) and removed 26 (24 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1734 (Rfree = 0.000) for 7426 atoms. Found 7 (47 requested) and removed 28 (23 requested) atoms. Cycle 25: After refmac, R = 0.1712 (Rfree = 0.000) for 7395 atoms. Found 13 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 7624 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 7648 seeds are put forward Round 1: 452 peptides, 80 chains. Longest chain 15 peptides. Score 0.376 Round 2: 541 peptides, 77 chains. Longest chain 21 peptides. Score 0.510 Round 3: 553 peptides, 75 chains. Longest chain 20 peptides. Score 0.535 Round 4: 537 peptides, 78 chains. Longest chain 20 peptides. Score 0.500 Round 5: 559 peptides, 76 chains. Longest chain 26 peptides. Score 0.537 Taking the results from Round 5 Chains 80, Residues 483, Estimated correctness of the model 0.0 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17015 restraints for refining 7540 atoms. 14991 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2343 (Rfree = 0.000) for 7540 atoms. Found 48 (48 requested) and removed 41 (24 requested) atoms. Cycle 27: After refmac, R = 0.2202 (Rfree = 0.000) for 7478 atoms. Found 34 (48 requested) and removed 33 (24 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2045 (Rfree = 0.000) for 7449 atoms. Found 28 (47 requested) and removed 31 (23 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1957 (Rfree = 0.000) for 7423 atoms. Found 24 (47 requested) and removed 29 (23 requested) atoms. Cycle 30: After refmac, R = 0.1931 (Rfree = 0.000) for 7410 atoms. Found 25 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 7671 seeds are put forward NCS extension: 17 residues added (8 deleted due to clashes), 7688 seeds are put forward Round 1: 435 peptides, 83 chains. Longest chain 14 peptides. Score 0.332 Round 2: 496 peptides, 82 chains. Longest chain 16 peptides. Score 0.425 Round 3: 498 peptides, 75 chains. Longest chain 14 peptides. Score 0.468 Round 4: 515 peptides, 74 chains. Longest chain 17 peptides. Score 0.495 Round 5: 506 peptides, 77 chains. Longest chain 20 peptides. Score 0.467 Taking the results from Round 4 Chains 74, Residues 441, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17584 restraints for refining 7541 atoms. 15874 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2167 (Rfree = 0.000) for 7541 atoms. Found 29 (48 requested) and removed 41 (24 requested) atoms. Cycle 32: After refmac, R = 0.2217 (Rfree = 0.000) for 7491 atoms. Found 33 (48 requested) and removed 37 (24 requested) atoms. Cycle 33: After refmac, R = 0.2069 (Rfree = 0.000) for 7475 atoms. Found 19 (48 requested) and removed 41 (24 requested) atoms. Cycle 34: After refmac, R = 0.1763 (Rfree = 0.000) for 7427 atoms. Found 6 (47 requested) and removed 25 (23 requested) atoms. Cycle 35: After refmac, R = 0.1707 (Rfree = 0.000) for 7398 atoms. Found 6 (47 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 7637 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 7659 seeds are put forward Round 1: 416 peptides, 78 chains. Longest chain 12 peptides. Score 0.336 Round 2: 468 peptides, 81 chains. Longest chain 15 peptides. Score 0.392 Round 3: 491 peptides, 77 chains. Longest chain 16 peptides. Score 0.447 Round 4: 495 peptides, 72 chains. Longest chain 16 peptides. Score 0.481 Round 5: 486 peptides, 77 chains. Longest chain 15 peptides. Score 0.440 Taking the results from Round 4 Chains 73, Residues 423, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17398 restraints for refining 7540 atoms. 15691 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2159 (Rfree = 0.000) for 7540 atoms. Found 32 (48 requested) and removed 44 (24 requested) atoms. Cycle 37: After refmac, R = 0.2082 (Rfree = 0.000) for 7502 atoms. Found 34 (48 requested) and removed 33 (24 requested) atoms. Cycle 38: After refmac, R = 0.1991 (Rfree = 0.000) for 7491 atoms. Found 26 (48 requested) and removed 33 (24 requested) atoms. Cycle 39: After refmac, R = 0.1683 (Rfree = 0.000) for 7478 atoms. Found 6 (48 requested) and removed 25 (24 requested) atoms. Cycle 40: After refmac, R = 0.1636 (Rfree = 0.000) for 7450 atoms. Found 8 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 7658 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 7679 seeds are put forward Round 1: 397 peptides, 77 chains. Longest chain 12 peptides. Score 0.313 Round 2: 448 peptides, 72 chains. Longest chain 15 peptides. Score 0.419 Round 3: 476 peptides, 74 chains. Longest chain 16 peptides. Score 0.445 Round 4: 465 peptides, 71 chains. Longest chain 18 peptides. Score 0.448 Round 5: 473 peptides, 67 chains. Longest chain 18 peptides. Score 0.481 Taking the results from Round 5 Chains 68, Residues 406, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17418 restraints for refining 7542 atoms. 15778 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2241 (Rfree = 0.000) for 7542 atoms. Found 39 (48 requested) and removed 35 (24 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2060 (Rfree = 0.000) for 7508 atoms. Found 43 (48 requested) and removed 30 (24 requested) atoms. Cycle 43: After refmac, R = 0.1870 (Rfree = 0.000) for 7481 atoms. Found 16 (48 requested) and removed 29 (24 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1860 (Rfree = 0.000) for 7443 atoms. Found 25 (47 requested) and removed 27 (23 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1844 (Rfree = 0.000) for 7423 atoms. Found 23 (47 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 7630 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7645 seeds are put forward Round 1: 351 peptides, 70 chains. Longest chain 9 peptides. Score 0.288 Round 2: 407 peptides, 67 chains. Longest chain 18 peptides. Score 0.392 Round 3: 422 peptides, 68 chains. Longest chain 13 peptides. Score 0.407 Round 4: 419 peptides, 70 chains. Longest chain 13 peptides. Score 0.390 Round 5: 422 peptides, 67 chains. Longest chain 14 peptides. Score 0.413 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 67, Residues 355, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input Building loops using Loopy2018 67 chains (355 residues) following loop building 3 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13375 reflections ( 99.90 % complete ) and 17799 restraints for refining 7542 atoms. 16420 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2020 (Rfree = 0.000) for 7542 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.1990 (Rfree = 0.000) for 7496 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.1948 (Rfree = 0.000) for 7454 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1881 (Rfree = 0.000) for 7419 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:13:05 GMT 2018 Job finished. TimeTaking 105.14