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 2f4l-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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/2f4l-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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 ============================================================ Tue 25 Dec 19:28:06 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/2f4l-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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 842 and 0 Target number of residues in the AU: 842 Target solvent content: 0.6470 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: 0.50 Input MTZ file: 2f4l-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: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.70 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: 86.372 3.800 Wilson plot Bfac: 76.13 13249 reflections ( 99.60 % complete ) and 0 restraints for refining 10463 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3091 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3218 (Rfree = 0.000) for 10463 atoms. Found 57 (57 requested) and removed 61 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.56 Search for helices and strands: 0 residues in 0 chains, 10580 seeds are put forward NCS extension: 0 residues added, 10580 seeds are put forward Round 1: 473 peptides, 90 chains. Longest chain 11 peptides. Score 0.331 Round 2: 655 peptides, 90 chains. Longest chain 21 peptides. Score 0.545 Round 3: 709 peptides, 92 chains. Longest chain 23 peptides. Score 0.589 Round 4: 729 peptides, 83 chains. Longest chain 27 peptides. Score 0.643 Round 5: 757 peptides, 86 chains. Longest chain 24 peptides. Score 0.655 Taking the results from Round 5 Chains 95, Residues 671, Estimated correctness of the model 22.9 % 10 chains (88 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 18529 restraints for refining 8592 atoms. 15639 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2681 (Rfree = 0.000) for 8592 atoms. Found 46 (47 requested) and removed 81 (23 requested) atoms. Cycle 2: After refmac, R = 0.2545 (Rfree = 0.000) for 8307 atoms. Found 47 (47 requested) and removed 51 (23 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2470 (Rfree = 0.000) for 8177 atoms. Found 45 (45 requested) and removed 42 (22 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2342 (Rfree = 0.000) for 8089 atoms. Found 40 (44 requested) and removed 40 (22 requested) atoms. Cycle 5: After refmac, R = 0.2250 (Rfree = 0.000) for 8034 atoms. Found 33 (44 requested) and removed 38 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.52 Search for helices and strands: 0 residues in 0 chains, 8220 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 8232 seeds are put forward Round 1: 622 peptides, 102 chains. Longest chain 20 peptides. Score 0.452 Round 2: 693 peptides, 89 chains. Longest chain 29 peptides. Score 0.587 Round 3: 694 peptides, 96 chains. Longest chain 21 peptides. Score 0.558 Round 4: 701 peptides, 95 chains. Longest chain 27 peptides. Score 0.569 Round 5: 703 peptides, 90 chains. Longest chain 22 peptides. Score 0.592 Taking the results from Round 5 Chains 96, Residues 613, Estimated correctness of the model 0.0 % 10 chains (84 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 18713 restraints for refining 8477 atoms. 16078 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2492 (Rfree = 0.000) for 8477 atoms. Found 45 (46 requested) and removed 103 (23 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2176 (Rfree = 0.000) for 8291 atoms. Found 37 (46 requested) and removed 46 (23 requested) atoms. Cycle 8: After refmac, R = 0.2138 (Rfree = 0.000) for 8202 atoms. Found 38 (45 requested) and removed 36 (22 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2057 (Rfree = 0.000) for 8152 atoms. Found 40 (45 requested) and removed 29 (22 requested) atoms. Cycle 10: After refmac, R = 0.2019 (Rfree = 0.000) for 8126 atoms. Found 36 (44 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 8303 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 8326 seeds are put forward Round 1: 594 peptides, 96 chains. Longest chain 18 peptides. Score 0.450 Round 2: 678 peptides, 94 chains. Longest chain 25 peptides. Score 0.550 Round 3: 669 peptides, 91 chains. Longest chain 29 peptides. Score 0.555 Round 4: 674 peptides, 85 chains. Longest chain 35 peptides. Score 0.586 Round 5: 702 peptides, 88 chains. Longest chain 24 peptides. Score 0.600 Taking the results from Round 5 Chains 90, Residues 614, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 19567 restraints for refining 8595 atoms. 17126 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2465 (Rfree = 0.000) for 8595 atoms. Found 47 (47 requested) and removed 50 (23 requested) atoms. Cycle 12: After refmac, R = 0.2232 (Rfree = 0.000) for 8472 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. Cycle 13: After refmac, R = 0.2163 (Rfree = 0.000) for 8429 atoms. Found 38 (46 requested) and removed 44 (23 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2054 (Rfree = 0.000) for 8391 atoms. Found 45 (46 requested) and removed 36 (23 requested) atoms. Cycle 15: After refmac, R = 0.1988 (Rfree = 0.000) for 8376 atoms. Found 46 (46 requested) and removed 38 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 8538 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 8556 seeds are put forward Round 1: 593 peptides, 104 chains. Longest chain 18 peptides. Score 0.407 Round 2: 613 peptides, 91 chains. Longest chain 29 peptides. Score 0.496 Round 3: 631 peptides, 89 chains. Longest chain 42 peptides. Score 0.525 Round 4: 620 peptides, 87 chains. Longest chain 22 peptides. Score 0.523 Round 5: 620 peptides, 83 chains. Longest chain 27 peptides. Score 0.541 Taking the results from Round 5 Chains 87, Residues 537, Estimated correctness of the model 0.0 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13249 reflections ( 99.60 % complete ) and 19583 restraints for refining 8595 atoms. 17346 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2498 (Rfree = 0.000) for 8595 atoms. Found 47 (47 requested) and removed 59 (23 requested) atoms. Cycle 17: After refmac, R = 0.2459 (Rfree = 0.000) for 8497 atoms. Found 47 (47 requested) and removed 40 (23 requested) atoms. Cycle 18: After refmac, R = 0.2219 (Rfree = 0.000) for 8432 atoms. Found 46 (46 requested) and removed 39 (23 requested) atoms. Cycle 19: After refmac, R = 0.1800 (Rfree = 0.000) for 8394 atoms. Found 24 (46 requested) and removed 32 (23 requested) atoms. Cycle 20: After refmac, R = 0.1981 (Rfree = 0.000) for 8358 atoms. Found 46 (46 requested) and removed 41 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 8524 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 8538 seeds are put forward Round 1: 525 peptides, 91 chains. Longest chain 17 peptides. Score 0.392 Round 2: 548 peptides, 88 chains. Longest chain 24 peptides. Score 0.436 Round 3: 577 peptides, 86 chains. Longest chain 35 peptides. Score 0.480 Round 4: 587 peptides, 78 chains. Longest chain 35 peptides. Score 0.530 Round 5: 607 peptides, 85 chains. Longest chain 29 peptides. Score 0.518 Taking the results from Round 4 Chains 81, Residues 509, Estimated correctness of the model 0.0 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 19401 restraints for refining 8593 atoms. 17229 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2333 (Rfree = 0.000) for 8593 atoms. Found 47 (47 requested) and removed 86 (23 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1975 (Rfree = 0.000) for 8485 atoms. Found 47 (47 requested) and removed 46 (23 requested) atoms. Cycle 23: After refmac, R = 0.1953 (Rfree = 0.000) for 8446 atoms. Found 46 (46 requested) and removed 33 (23 requested) atoms. Cycle 24: After refmac, R = 0.1969 (Rfree = 0.000) for 8433 atoms. Found 46 (46 requested) and removed 27 (23 requested) atoms. Cycle 25: After refmac, R = 0.1880 (Rfree = 0.000) for 8431 atoms. Found 46 (46 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.60 Search for helices and strands: 0 residues in 0 chains, 8586 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 8598 seeds are put forward Round 1: 500 peptides, 95 chains. Longest chain 14 peptides. Score 0.338 Round 2: 582 peptides, 90 chains. Longest chain 37 peptides. Score 0.466 Round 3: 601 peptides, 94 chains. Longest chain 25 peptides. Score 0.468 Round 4: 582 peptides, 83 chains. Longest chain 29 peptides. Score 0.501 Round 5: 589 peptides, 85 chains. Longest chain 29 peptides. Score 0.499 Taking the results from Round 4 Chains 85, Residues 499, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20098 restraints for refining 8594 atoms. 18134 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2295 (Rfree = 0.000) for 8594 atoms. Found 43 (47 requested) and removed 54 (23 requested) atoms. Cycle 27: After refmac, R = 0.2134 (Rfree = 0.000) for 8506 atoms. Found 47 (47 requested) and removed 33 (23 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1802 (Rfree = 0.000) for 8480 atoms. Found 14 (46 requested) and removed 32 (23 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1723 (Rfree = 0.000) for 8429 atoms. Found 12 (46 requested) and removed 27 (23 requested) atoms. Cycle 30: After refmac, R = 0.1983 (Rfree = 0.000) for 8393 atoms. Found 46 (46 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 8560 seeds are put forward NCS extension: 40 residues added (3 deleted due to clashes), 8600 seeds are put forward Round 1: 492 peptides, 97 chains. Longest chain 13 peptides. Score 0.316 Round 2: 537 peptides, 84 chains. Longest chain 20 peptides. Score 0.444 Round 3: 529 peptides, 84 chains. Longest chain 17 peptides. Score 0.435 Round 4: 531 peptides, 80 chains. Longest chain 18 peptides. Score 0.458 Round 5: 551 peptides, 81 chains. Longest chain 16 peptides. Score 0.476 Taking the results from Round 5 Chains 82, Residues 470, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20146 restraints for refining 8594 atoms. 18317 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2167 (Rfree = 0.000) for 8594 atoms. Found 47 (47 requested) and removed 61 (23 requested) atoms. Cycle 32: After refmac, R = 0.2016 (Rfree = 0.000) for 8508 atoms. Found 47 (47 requested) and removed 32 (23 requested) atoms. Cycle 33: After refmac, R = 0.2010 (Rfree = 0.000) for 8500 atoms. Found 46 (46 requested) and removed 26 (23 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1614 (Rfree = 0.000) for 8495 atoms. Found 31 (46 requested) and removed 28 (23 requested) atoms. Cycle 35: After refmac, R = 0.1512 (Rfree = 0.000) for 8481 atoms. Found 19 (46 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 8596 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8611 seeds are put forward Round 1: 420 peptides, 86 chains. Longest chain 10 peptides. Score 0.281 Round 2: 494 peptides, 81 chains. Longest chain 15 peptides. Score 0.408 Round 3: 498 peptides, 77 chains. Longest chain 15 peptides. Score 0.434 Round 4: 481 peptides, 70 chains. Longest chain 20 peptides. Score 0.451 Round 5: 510 peptides, 80 chains. Longest chain 16 peptides. Score 0.433 Taking the results from Round 4 Chains 71, Residues 411, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20371 restraints for refining 8553 atoms. 18760 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2083 (Rfree = 0.000) for 8553 atoms. Found 47 (47 requested) and removed 47 (23 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2092 (Rfree = 0.000) for 8506 atoms. Found 47 (47 requested) and removed 32 (23 requested) atoms. Cycle 38: After refmac, R = 0.1970 (Rfree = 0.000) for 8482 atoms. Found 46 (46 requested) and removed 40 (23 requested) atoms. Cycle 39: After refmac, R = 0.1515 (Rfree = 0.000) for 8468 atoms. Found 18 (46 requested) and removed 33 (23 requested) atoms. Cycle 40: After refmac, R = 0.1389 (Rfree = 0.000) for 8443 atoms. Found 15 (46 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 8563 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 8590 seeds are put forward Round 1: 418 peptides, 83 chains. Longest chain 15 peptides. Score 0.296 Round 2: 469 peptides, 82 chains. Longest chain 19 peptides. Score 0.370 Round 3: 503 peptides, 83 chains. Longest chain 19 peptides. Score 0.408 Round 4: 509 peptides, 86 chains. Longest chain 19 peptides. Score 0.399 Round 5: 514 peptides, 85 chains. Longest chain 19 peptides. Score 0.411 Taking the results from Round 5 Chains 85, Residues 429, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13249 reflections ( 99.60 % complete ) and 20369 restraints for refining 8595 atoms. 18738 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2100 (Rfree = 0.000) for 8595 atoms. Found 47 (47 requested) and removed 48 (23 requested) atoms. Cycle 42: After refmac, R = 0.2052 (Rfree = 0.000) for 8559 atoms. Found 47 (47 requested) and removed 47 (23 requested) atoms. Cycle 43: After refmac, R = 0.1998 (Rfree = 0.000) for 8533 atoms. Found 47 (47 requested) and removed 31 (23 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 44: After refmac, R = 0.2087 (Rfree = 0.000) for 8523 atoms. Found 47 (47 requested) and removed 37 (23 requested) atoms. Cycle 45: After refmac, R = 0.1971 (Rfree = 0.000) for 8509 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 8671 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 8693 seeds are put forward Round 1: 345 peptides, 74 chains. Longest chain 14 peptides. Score 0.245 Round 2: 412 peptides, 77 chains. Longest chain 19 peptides. Score 0.323 Round 3: 416 peptides, 73 chains. Longest chain 16 peptides. Score 0.352 Round 4: 436 peptides, 75 chains. Longest chain 16 peptides. Score 0.367 Round 5: 429 peptides, 71 chains. Longest chain 18 peptides. Score 0.381 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 71, Residues 358, 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 2f4l-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13249 reflections ( 99.60 % complete ) and 20674 restraints for refining 8573 atoms. 19300 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2260 (Rfree = 0.000) for 8573 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2214 (Rfree = 0.000) for 8494 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.2146 (Rfree = 0.000) for 8441 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1734 (Rfree = 0.000) for 8392 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:24:02 GMT 2018 Job finished. TimeTaking 116.1