Mon 24 Dec 00:43:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2f4l-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.8-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:43:29 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/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.8-parrot-mrncs/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-mrncs.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-mrncs.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 Failed to save intermediate PDB 13249 reflections ( 99.60 % complete ) and 0 restraints for refining 10571 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3043 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3221 (Rfree = 0.000) for 10571 atoms. Found 58 (58 requested) and removed 129 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.51 Search for helices and strands: 0 residues in 0 chains, 10622 seeds are put forward NCS extension: 0 residues added, 10622 seeds are put forward Round 1: 506 peptides, 92 chains. Longest chain 14 peptides. Score 0.363 Round 2: 681 peptides, 103 chains. Longest chain 24 peptides. Score 0.513 Round 3: 733 peptides, 101 chains. Longest chain 21 peptides. Score 0.574 Round 4: 754 peptides, 89 chains. Longest chain 23 peptides. Score 0.641 Round 5: 752 peptides, 89 chains. Longest chain 29 peptides. Score 0.640 Taking the results from Round 4 Chains 90, Residues 665, Estimated correctness of the model 17.0 % 9 chains (74 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 18748 restraints for refining 8596 atoms. 15945 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2576 (Rfree = 0.000) for 8596 atoms. Found 36 (47 requested) and removed 96 (23 requested) atoms. Cycle 2: After refmac, R = 0.2484 (Rfree = 0.000) for 8332 atoms. Found 29 (46 requested) and removed 95 (23 requested) atoms. Cycle 3: After refmac, R = 0.2282 (Rfree = 0.000) for 8209 atoms. Found 36 (45 requested) and removed 69 (22 requested) atoms. Cycle 4: After refmac, R = 0.2155 (Rfree = 0.000) for 8133 atoms. Found 21 (44 requested) and removed 46 (22 requested) atoms. Cycle 5: After refmac, R = 0.2077 (Rfree = 0.000) for 8087 atoms. Found 30 (44 requested) and removed 65 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 8279 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8295 seeds are put forward Round 1: 633 peptides, 102 chains. Longest chain 16 peptides. Score 0.465 Round 2: 718 peptides, 93 chains. Longest chain 22 peptides. Score 0.594 Round 3: 721 peptides, 91 chains. Longest chain 31 peptides. Score 0.605 Round 4: 754 peptides, 85 chains. Longest chain 44 peptides. Score 0.657 Round 5: 741 peptides, 87 chains. Longest chain 26 peptides. Score 0.638 Taking the results from Round 4 Chains 95, Residues 669, Estimated correctness of the model 23.7 % 11 chains (110 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 18230 restraints for refining 8596 atoms. 15260 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2415 (Rfree = 0.000) for 8596 atoms. Found 38 (47 requested) and removed 76 (23 requested) atoms. Cycle 7: After refmac, R = 0.2238 (Rfree = 0.000) for 8472 atoms. Found 47 (47 requested) and removed 79 (23 requested) atoms. Cycle 8: After refmac, R = 0.2173 (Rfree = 0.000) for 8390 atoms. Found 43 (46 requested) and removed 54 (23 requested) atoms. Cycle 9: After refmac, R = 0.2104 (Rfree = 0.000) for 8346 atoms. Found 35 (46 requested) and removed 38 (23 requested) atoms. Cycle 10: After refmac, R = 0.1817 (Rfree = 0.000) for 8306 atoms. Found 19 (45 requested) and removed 33 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 8458 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 8482 seeds are put forward Round 1: 674 peptides, 104 chains. Longest chain 33 peptides. Score 0.500 Round 2: 727 peptides, 92 chains. Longest chain 26 peptides. Score 0.606 Round 3: 739 peptides, 91 chains. Longest chain 32 peptides. Score 0.621 Round 4: 743 peptides, 85 chains. Longest chain 40 peptides. Score 0.648 Round 5: 720 peptides, 83 chains. Longest chain 32 peptides. Score 0.636 Taking the results from Round 4 Chains 89, Residues 658, Estimated correctness of the model 20.0 % 6 chains (109 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 18378 restraints for refining 8596 atoms. 15422 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2430 (Rfree = 0.000) for 8596 atoms. Found 41 (47 requested) and removed 64 (23 requested) atoms. Cycle 12: After refmac, R = 0.2316 (Rfree = 0.000) for 8475 atoms. Found 38 (47 requested) and removed 52 (23 requested) atoms. Cycle 13: After refmac, R = 0.2153 (Rfree = 0.000) for 8392 atoms. Found 35 (46 requested) and removed 35 (23 requested) atoms. Cycle 14: After refmac, R = 0.2118 (Rfree = 0.000) for 8338 atoms. Found 44 (46 requested) and removed 38 (23 requested) atoms. Cycle 15: After refmac, R = 0.1998 (Rfree = 0.000) for 8320 atoms. Found 31 (45 requested) and removed 34 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.53 Search for helices and strands: 0 residues in 0 chains, 8476 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 8513 seeds are put forward Round 1: 620 peptides, 105 chains. Longest chain 27 peptides. Score 0.435 Round 2: 680 peptides, 92 chains. Longest chain 29 peptides. Score 0.561 Round 3: 666 peptides, 88 chains. Longest chain 25 peptides. Score 0.565 Round 4: 693 peptides, 94 chains. Longest chain 25 peptides. Score 0.565 Round 5: 670 peptides, 81 chains. Longest chain 23 peptides. Score 0.599 Taking the results from Round 5 Chains 86, Residues 589, Estimated correctness of the model 0.0 % 5 chains (53 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 19547 restraints for refining 8595 atoms. 17098 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2408 (Rfree = 0.000) for 8595 atoms. Found 47 (47 requested) and removed 115 (23 requested) atoms. Cycle 17: After refmac, R = 0.2262 (Rfree = 0.000) for 8470 atoms. Found 45 (46 requested) and removed 64 (23 requested) atoms. Cycle 18: After refmac, R = 0.2178 (Rfree = 0.000) for 8418 atoms. Found 46 (46 requested) and removed 61 (23 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2074 (Rfree = 0.000) for 8376 atoms. Found 38 (46 requested) and removed 40 (23 requested) atoms. Cycle 20: After refmac, R = 0.1978 (Rfree = 0.000) for 8355 atoms. Found 42 (46 requested) and removed 35 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.56 Search for helices and strands: 0 residues in 0 chains, 8503 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 8527 seeds are put forward Round 1: 539 peptides, 92 chains. Longest chain 17 peptides. Score 0.404 Round 2: 587 peptides, 84 chains. Longest chain 21 peptides. Score 0.501 Round 3: 636 peptides, 95 chains. Longest chain 21 peptides. Score 0.502 Round 4: 632 peptides, 90 chains. Longest chain 23 peptides. Score 0.521 Round 5: 635 peptides, 87 chains. Longest chain 21 peptides. Score 0.538 Taking the results from Round 5 Chains 88, Residues 548, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13249 reflections ( 99.60 % complete ) and 19962 restraints for refining 8595 atoms. 17791 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2422 (Rfree = 0.000) for 8595 atoms. Found 47 (47 requested) and removed 47 (23 requested) atoms. Cycle 22: After refmac, R = 0.2261 (Rfree = 0.000) for 8523 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 23: After refmac, R = 0.2173 (Rfree = 0.000) for 8486 atoms. Found 46 (46 requested) and removed 47 (23 requested) atoms. Cycle 24: After refmac, R = 0.1792 (Rfree = 0.000) for 8455 atoms. Found 27 (46 requested) and removed 33 (23 requested) atoms. Cycle 25: After refmac, R = 0.2076 (Rfree = 0.000) for 8436 atoms. Found 44 (46 requested) and removed 35 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 8611 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8632 seeds are put forward Round 1: 533 peptides, 101 chains. Longest chain 17 peptides. Score 0.348 Round 2: 592 peptides, 96 chains. Longest chain 19 peptides. Score 0.447 Round 3: 616 peptides, 97 chains. Longest chain 22 peptides. Score 0.470 Round 4: 582 peptides, 85 chains. Longest chain 20 peptides. Score 0.491 Round 5: 598 peptides, 89 chains. Longest chain 31 peptides. Score 0.489 Taking the results from Round 4 Chains 85, Residues 497, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20227 restraints for refining 8596 atoms. 18297 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2468 (Rfree = 0.000) for 8596 atoms. Found 47 (47 requested) and removed 59 (23 requested) atoms. Cycle 27: After refmac, R = 0.2242 (Rfree = 0.000) for 8503 atoms. Found 47 (47 requested) and removed 42 (23 requested) atoms. Cycle 28: After refmac, R = 0.2265 (Rfree = 0.000) for 8466 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. Cycle 29: After refmac, R = 0.2160 (Rfree = 0.000) for 8432 atoms. Found 46 (46 requested) and removed 28 (23 requested) atoms. Cycle 30: After refmac, R = 0.2248 (Rfree = 0.000) for 8426 atoms. Found 46 (46 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.57 Search for helices and strands: 0 residues in 0 chains, 8627 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 8661 seeds are put forward Round 1: 447 peptides, 90 chains. Longest chain 10 peptides. Score 0.295 Round 2: 548 peptides, 91 chains. Longest chain 14 peptides. Score 0.421 Round 3: 538 peptides, 82 chains. Longest chain 17 peptides. Score 0.456 Round 4: 558 peptides, 88 chains. Longest chain 16 peptides. Score 0.448 Round 5: 563 peptides, 84 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 5 Chains 84, Residues 479, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20016 restraints for refining 8536 atoms. 18158 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2355 (Rfree = 0.000) for 8536 atoms. Found 46 (46 requested) and removed 70 (23 requested) atoms. Cycle 32: After refmac, R = 0.2234 (Rfree = 0.000) for 8460 atoms. Found 46 (46 requested) and removed 61 (23 requested) atoms. Cycle 33: After refmac, R = 0.2156 (Rfree = 0.000) for 8411 atoms. Found 46 (46 requested) and removed 44 (23 requested) atoms. Cycle 34: After refmac, R = 0.2074 (Rfree = 0.000) for 8375 atoms. Found 46 (46 requested) and removed 32 (23 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2044 (Rfree = 0.000) for 8371 atoms. Found 44 (46 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 8560 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8573 seeds are put forward Round 1: 405 peptides, 85 chains. Longest chain 11 peptides. Score 0.265 Round 2: 467 peptides, 85 chains. Longest chain 16 peptides. Score 0.351 Round 3: 498 peptides, 88 chains. Longest chain 12 peptides. Score 0.375 Round 4: 506 peptides, 88 chains. Longest chain 16 peptides. Score 0.385 Round 5: 510 peptides, 83 chains. Longest chain 20 peptides. Score 0.417 Taking the results from Round 5 Chains 83, Residues 427, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20327 restraints for refining 8593 atoms. 18632 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2340 (Rfree = 0.000) for 8593 atoms. Found 47 (47 requested) and removed 51 (23 requested) atoms. Cycle 37: After refmac, R = 0.2106 (Rfree = 0.000) for 8518 atoms. Found 47 (47 requested) and removed 60 (23 requested) atoms. Cycle 38: After refmac, R = 0.1639 (Rfree = 0.000) for 8453 atoms. Found 24 (46 requested) and removed 26 (23 requested) atoms. Cycle 39: After refmac, R = 0.1514 (Rfree = 0.000) for 8423 atoms. Found 18 (46 requested) and removed 28 (23 requested) atoms. Cycle 40: After refmac, R = 0.1510 (Rfree = 0.000) for 8408 atoms. Found 17 (46 requested) and removed 38 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.60 Search for helices and strands: 0 residues in 0 chains, 8571 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 8591 seeds are put forward Round 1: 395 peptides, 80 chains. Longest chain 10 peptides. Score 0.281 Round 2: 455 peptides, 79 chains. Longest chain 19 peptides. Score 0.369 Round 3: 464 peptides, 76 chains. Longest chain 21 peptides. Score 0.398 Round 4: 460 peptides, 77 chains. Longest chain 14 peptides. Score 0.387 Round 5: 477 peptides, 76 chains. Longest chain 22 peptides. Score 0.414 Taking the results from Round 5 Chains 76, Residues 401, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20404 restraints for refining 8595 atoms. 18815 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2121 (Rfree = 0.000) for 8595 atoms. Found 47 (47 requested) and removed 61 (23 requested) atoms. Cycle 42: After refmac, R = 0.2036 (Rfree = 0.000) for 8523 atoms. Found 47 (47 requested) and removed 56 (23 requested) atoms. Cycle 43: After refmac, R = 0.2076 (Rfree = 0.000) for 8458 atoms. Found 46 (46 requested) and removed 42 (23 requested) atoms. Cycle 44: After refmac, R = 0.2132 (Rfree = 0.000) for 8418 atoms. Found 46 (46 requested) and removed 41 (23 requested) atoms. Cycle 45: After refmac, R = 0.2154 (Rfree = 0.000) for 8388 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 8598 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8616 seeds are put forward Round 1: 354 peptides, 77 chains. Longest chain 11 peptides. Score 0.239 Round 2: 438 peptides, 80 chains. Longest chain 16 peptides. Score 0.341 Round 3: 439 peptides, 81 chains. Longest chain 11 peptides. Score 0.336 Round 4: 440 peptides, 78 chains. Longest chain 13 peptides. Score 0.355 Round 5: 432 peptides, 73 chains. Longest chain 12 peptides. Score 0.373 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 73, Residues 359, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input Building loops using Loopy2018 73 chains (359 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13249 reflections ( 99.60 % complete ) and 19668 restraints for refining 8281 atoms. 18264 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2310 (Rfree = 0.000) for 8281 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2204 (Rfree = 0.000) for 8210 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2153 (Rfree = 0.000) for 8162 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1801 (Rfree = 0.000) for 8126 atoms. TimeTaking 76.08