null Mon 24 Dec 07:48:51 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2f4l-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-parrot-noncs ############### 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 07:48:55 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/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-parrot-noncs/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 850 and 0 Target number of residues in the AU: 850 Target solvent content: 0.6436 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-3.6-parrot-noncs.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-3.6-parrot-noncs.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 3.600 Wilson plot Bfac: 74.06 15528 reflections ( 99.66 % complete ) and 0 restraints for refining 10516 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3340 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3052 (Rfree = 0.000) for 10516 atoms. Found 67 (67 requested) and removed 133 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 10592 seeds are put forward NCS extension: 0 residues added, 10592 seeds are put forward Round 1: 499 peptides, 95 chains. Longest chain 11 peptides. Score 0.337 Round 2: 642 peptides, 104 chains. Longest chain 16 peptides. Score 0.465 Round 3: 694 peptides, 91 chains. Longest chain 21 peptides. Score 0.579 Round 4: 707 peptides, 101 chains. Longest chain 18 peptides. Score 0.549 Round 5: 728 peptides, 100 chains. Longest chain 23 peptides. Score 0.574 Taking the results from Round 3 Chains 97, Residues 603, Estimated correctness of the model 6.3 % 11 chains (96 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 18501 restraints for refining 8611 atoms. 15882 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2551 (Rfree = 0.000) for 8611 atoms. Found 44 (55 requested) and removed 67 (27 requested) atoms. Cycle 2: After refmac, R = 0.2432 (Rfree = 0.000) for 8428 atoms. Found 45 (55 requested) and removed 51 (27 requested) atoms. Cycle 3: After refmac, R = 0.2342 (Rfree = 0.000) for 8354 atoms. Found 50 (54 requested) and removed 46 (27 requested) atoms. Cycle 4: After refmac, R = 0.2259 (Rfree = 0.000) for 8311 atoms. Found 26 (53 requested) and removed 51 (26 requested) atoms. Cycle 5: After refmac, R = 0.2007 (Rfree = 0.000) for 8248 atoms. Found 19 (53 requested) and removed 36 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 8429 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8450 seeds are put forward Round 1: 570 peptides, 101 chains. Longest chain 13 peptides. Score 0.395 Round 2: 683 peptides, 93 chains. Longest chain 22 peptides. Score 0.560 Round 3: 709 peptides, 98 chains. Longest chain 26 peptides. Score 0.564 Round 4: 689 peptides, 94 chains. Longest chain 18 peptides. Score 0.561 Round 5: 697 peptides, 91 chains. Longest chain 27 peptides. Score 0.582 Taking the results from Round 5 Chains 92, Residues 606, Estimated correctness of the model 7.5 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19227 restraints for refining 8614 atoms. 16804 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2379 (Rfree = 0.000) for 8614 atoms. Found 53 (55 requested) and removed 65 (27 requested) atoms. Cycle 7: After refmac, R = 0.2179 (Rfree = 0.000) for 8521 atoms. Found 24 (55 requested) and removed 46 (27 requested) atoms. Cycle 8: After refmac, R = 0.2110 (Rfree = 0.000) for 8462 atoms. Found 22 (54 requested) and removed 42 (27 requested) atoms. Cycle 9: After refmac, R = 0.2076 (Rfree = 0.000) for 8421 atoms. Found 13 (54 requested) and removed 38 (27 requested) atoms. Cycle 10: After refmac, R = 0.2147 (Rfree = 0.000) for 8386 atoms. Found 26 (53 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 8557 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 8597 seeds are put forward Round 1: 590 peptides, 99 chains. Longest chain 20 peptides. Score 0.430 Round 2: 649 peptides, 92 chains. Longest chain 23 peptides. Score 0.530 Round 3: 666 peptides, 91 chains. Longest chain 27 peptides. Score 0.552 Round 4: 673 peptides, 91 chains. Longest chain 22 peptides. Score 0.559 Round 5: 677 peptides, 84 chains. Longest chain 27 peptides. Score 0.593 Taking the results from Round 5 Chains 90, Residues 593, Estimated correctness of the model 11.9 % 6 chains (71 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 18848 restraints for refining 8614 atoms. 16318 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2316 (Rfree = 0.000) for 8614 atoms. Found 45 (55 requested) and removed 41 (27 requested) atoms. Cycle 12: After refmac, R = 0.2203 (Rfree = 0.000) for 8556 atoms. Found 31 (55 requested) and removed 37 (27 requested) atoms. Cycle 13: After refmac, R = 0.2151 (Rfree = 0.000) for 8517 atoms. Found 31 (54 requested) and removed 34 (27 requested) atoms. Cycle 14: After refmac, R = 0.2122 (Rfree = 0.000) for 8493 atoms. Found 29 (54 requested) and removed 36 (27 requested) atoms. Cycle 15: After refmac, R = 0.2074 (Rfree = 0.000) for 8463 atoms. Found 27 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 8630 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 8647 seeds are put forward Round 1: 544 peptides, 100 chains. Longest chain 13 peptides. Score 0.368 Round 2: 630 peptides, 88 chains. Longest chain 18 peptides. Score 0.529 Round 3: 640 peptides, 95 chains. Longest chain 18 peptides. Score 0.506 Round 4: 659 peptides, 99 chains. Longest chain 20 peptides. Score 0.508 Round 5: 639 peptides, 90 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 5 Chains 92, Residues 549, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19684 restraints for refining 8612 atoms. 17492 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2278 (Rfree = 0.000) for 8612 atoms. Found 44 (55 requested) and removed 55 (27 requested) atoms. Cycle 17: After refmac, R = 0.2230 (Rfree = 0.000) for 8539 atoms. Found 50 (55 requested) and removed 49 (27 requested) atoms. Cycle 18: After refmac, R = 0.2197 (Rfree = 0.000) for 8526 atoms. Found 54 (54 requested) and removed 37 (27 requested) atoms. Cycle 19: After refmac, R = 0.2182 (Rfree = 0.000) for 8525 atoms. Found 54 (54 requested) and removed 39 (27 requested) atoms. Cycle 20: After refmac, R = 0.2198 (Rfree = 0.000) for 8521 atoms. Found 44 (54 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 8679 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 8700 seeds are put forward Round 1: 539 peptides, 100 chains. Longest chain 10 peptides. Score 0.361 Round 2: 590 peptides, 88 chains. Longest chain 19 peptides. Score 0.485 Round 3: 609 peptides, 90 chains. Longest chain 25 peptides. Score 0.496 Round 4: 621 peptides, 90 chains. Longest chain 16 peptides. Score 0.509 Round 5: 622 peptides, 89 chains. Longest chain 22 peptides. Score 0.515 Taking the results from Round 5 Chains 93, Residues 533, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19753 restraints for refining 8614 atoms. 17597 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2414 (Rfree = 0.000) for 8614 atoms. Found 55 (55 requested) and removed 55 (27 requested) atoms. Cycle 22: After refmac, R = 0.2172 (Rfree = 0.000) for 8534 atoms. Found 48 (55 requested) and removed 30 (27 requested) atoms. Cycle 23: After refmac, R = 0.2053 (Rfree = 0.000) for 8490 atoms. Found 44 (54 requested) and removed 32 (27 requested) atoms. Cycle 24: After refmac, R = 0.1989 (Rfree = 0.000) for 8464 atoms. Found 35 (54 requested) and removed 33 (27 requested) atoms. Cycle 25: After refmac, R = 0.1993 (Rfree = 0.000) for 8458 atoms. Found 38 (54 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 8655 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 8681 seeds are put forward Round 1: 525 peptides, 102 chains. Longest chain 15 peptides. Score 0.332 Round 2: 591 peptides, 97 chains. Longest chain 13 peptides. Score 0.441 Round 3: 608 peptides, 95 chains. Longest chain 21 peptides. Score 0.471 Round 4: 599 peptides, 95 chains. Longest chain 17 peptides. Score 0.460 Round 5: 615 peptides, 90 chains. Longest chain 17 peptides. Score 0.503 Taking the results from Round 5 Chains 90, Residues 525, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 20149 restraints for refining 8615 atoms. 18117 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2347 (Rfree = 0.000) for 8615 atoms. Found 50 (55 requested) and removed 70 (27 requested) atoms. Cycle 27: After refmac, R = 0.2315 (Rfree = 0.000) for 8542 atoms. Found 51 (55 requested) and removed 36 (27 requested) atoms. Cycle 28: After refmac, R = 0.1993 (Rfree = 0.000) for 8521 atoms. Found 15 (54 requested) and removed 31 (27 requested) atoms. Cycle 29: After refmac, R = 0.2064 (Rfree = 0.000) for 8478 atoms. Found 30 (54 requested) and removed 29 (27 requested) atoms. Cycle 30: After refmac, R = 0.1899 (Rfree = 0.000) for 8464 atoms. Found 15 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 8584 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8600 seeds are put forward Round 1: 506 peptides, 99 chains. Longest chain 15 peptides. Score 0.324 Round 2: 582 peptides, 97 chains. Longest chain 14 peptides. Score 0.430 Round 3: 573 peptides, 93 chains. Longest chain 21 peptides. Score 0.440 Round 4: 578 peptides, 92 chains. Longest chain 18 peptides. Score 0.451 Round 5: 591 peptides, 99 chains. Longest chain 14 peptides. Score 0.431 Taking the results from Round 4 Chains 94, Residues 486, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19982 restraints for refining 8615 atoms. 18086 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2309 (Rfree = 0.000) for 8615 atoms. Found 55 (55 requested) and removed 54 (27 requested) atoms. Cycle 32: After refmac, R = 0.2242 (Rfree = 0.000) for 8581 atoms. Found 55 (55 requested) and removed 39 (27 requested) atoms. Cycle 33: After refmac, R = 0.2050 (Rfree = 0.000) for 8579 atoms. Found 18 (55 requested) and removed 29 (27 requested) atoms. Cycle 34: After refmac, R = 0.2097 (Rfree = 0.000) for 8558 atoms. Found 41 (54 requested) and removed 33 (27 requested) atoms. Cycle 35: After refmac, R = 0.1977 (Rfree = 0.000) for 8555 atoms. Found 11 (54 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 8703 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 8716 seeds are put forward Round 1: 438 peptides, 86 chains. Longest chain 13 peptides. Score 0.306 Round 2: 499 peptides, 84 chains. Longest chain 13 peptides. Score 0.398 Round 3: 500 peptides, 86 chains. Longest chain 17 peptides. Score 0.388 Round 4: 498 peptides, 81 chains. Longest chain 15 peptides. Score 0.413 Round 5: 500 peptides, 82 chains. Longest chain 15 peptides. Score 0.410 Taking the results from Round 4 Chains 82, Residues 417, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 20414 restraints for refining 8613 atoms. 18787 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2261 (Rfree = 0.000) for 8613 atoms. Found 55 (55 requested) and removed 45 (27 requested) atoms. Cycle 37: After refmac, R = 0.2326 (Rfree = 0.000) for 8596 atoms. Found 55 (55 requested) and removed 35 (27 requested) atoms. Cycle 38: After refmac, R = 0.2224 (Rfree = 0.000) for 8598 atoms. Found 55 (55 requested) and removed 34 (27 requested) atoms. Cycle 39: After refmac, R = 0.2210 (Rfree = 0.000) for 8597 atoms. Found 50 (55 requested) and removed 31 (27 requested) atoms. Cycle 40: After refmac, R = 0.2153 (Rfree = 0.000) for 8595 atoms. Found 54 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 8766 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 8783 seeds are put forward Round 1: 412 peptides, 87 chains. Longest chain 8 peptides. Score 0.263 Round 2: 512 peptides, 90 chains. Longest chain 16 peptides. Score 0.381 Round 3: 503 peptides, 86 chains. Longest chain 12 peptides. Score 0.392 Round 4: 505 peptides, 81 chains. Longest chain 15 peptides. Score 0.421 Round 5: 529 peptides, 85 chains. Longest chain 15 peptides. Score 0.429 Taking the results from Round 5 Chains 85, Residues 444, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 20290 restraints for refining 8614 atoms. 18551 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2518 (Rfree = 0.000) for 8614 atoms. Found 55 (55 requested) and removed 60 (27 requested) atoms. Cycle 42: After refmac, R = 0.2432 (Rfree = 0.000) for 8538 atoms. Found 55 (55 requested) and removed 34 (27 requested) atoms. Cycle 43: After refmac, R = 0.2322 (Rfree = 0.000) for 8535 atoms. Found 54 (54 requested) and removed 35 (27 requested) atoms. Cycle 44: After refmac, R = 0.2301 (Rfree = 0.000) for 8528 atoms. Found 51 (54 requested) and removed 30 (27 requested) atoms. Cycle 45: After refmac, R = 0.2312 (Rfree = 0.000) for 8528 atoms. Found 54 (54 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.40 Search for helices and strands: 0 residues in 0 chains, 8664 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8678 seeds are put forward Round 1: 403 peptides, 87 chains. Longest chain 9 peptides. Score 0.250 Round 2: 471 peptides, 88 chains. Longest chain 12 peptides. Score 0.339 Round 3: 478 peptides, 87 chains. Longest chain 12 peptides. Score 0.354 Round 4: 482 peptides, 81 chains. Longest chain 13 peptides. Score 0.393 Round 5: 486 peptides, 83 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 81, Residues 401, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15528 reflections ( 99.66 % complete ) and 20429 restraints for refining 8595 atoms. 18906 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2570 (Rfree = 0.000) for 8595 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2615 (Rfree = 0.000) for 8512 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.2423 (Rfree = 0.000) for 8460 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.2303 (Rfree = 0.000) for 8414 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:11:01 GMT 2018 Job finished. TimeTaking 82.16 Used memory is bytes: 17062400