Sun 23 Dec 23:47:30 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 2pbl-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.6-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/2pbl-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.6-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 ============================================================ Sun 23 Dec 23:47:35 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/2pbl-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.6-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 689 and 0 Target number of residues in the AU: 689 Target solvent content: 0.6307 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-3.6-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8384 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: 87.858 3.600 Wilson plot Bfac: 66.84 11642 reflections ( 99.06 % complete ) and 0 restraints for refining 9252 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3576 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4184 (Rfree = 0.000) for 9252 atoms. Found 59 (59 requested) and removed 112 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.50 Search for helices and strands: 0 residues in 0 chains, 9381 seeds are put forward NCS extension: 0 residues added, 9381 seeds are put forward Round 1: 310 peptides, 65 chains. Longest chain 14 peptides. Score 0.264 Round 2: 425 peptides, 80 chains. Longest chain 12 peptides. Score 0.355 Round 3: 476 peptides, 84 chains. Longest chain 13 peptides. Score 0.409 Round 4: 481 peptides, 81 chains. Longest chain 12 peptides. Score 0.436 Round 5: 525 peptides, 83 chains. Longest chain 16 peptides. Score 0.488 Taking the results from Round 5 Chains 87, Residues 442, Estimated correctness of the model 0.0 % 14 chains (106 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16550 restraints for refining 7597 atoms. 14528 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3506 (Rfree = 0.000) for 7597 atoms. Found 48 (48 requested) and removed 106 (24 requested) atoms. Cycle 2: After refmac, R = 0.3542 (Rfree = 0.000) for 7347 atoms. Found 48 (48 requested) and removed 69 (24 requested) atoms. Cycle 3: After refmac, R = 0.3394 (Rfree = 0.000) for 7237 atoms. Found 47 (47 requested) and removed 57 (23 requested) atoms. Cycle 4: After refmac, R = 0.3250 (Rfree = 0.000) for 7153 atoms. Found 46 (46 requested) and removed 45 (23 requested) atoms. Cycle 5: After refmac, R = 0.3068 (Rfree = 0.000) for 7107 atoms. Found 45 (45 requested) and removed 45 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 7420 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7433 seeds are put forward Round 1: 429 peptides, 83 chains. Longest chain 12 peptides. Score 0.340 Round 2: 524 peptides, 89 chains. Longest chain 17 peptides. Score 0.449 Round 3: 539 peptides, 84 chains. Longest chain 15 peptides. Score 0.501 Round 4: 560 peptides, 77 chains. Longest chain 16 peptides. Score 0.569 Round 5: 536 peptides, 74 chains. Longest chain 20 peptides. Score 0.555 Taking the results from Round 4 Chains 80, Residues 483, Estimated correctness of the model 2.2 % 10 chains (67 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 15781 restraints for refining 7324 atoms. 13722 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3190 (Rfree = 0.000) for 7324 atoms. Found 47 (47 requested) and removed 92 (23 requested) atoms. Cycle 7: After refmac, R = 0.2955 (Rfree = 0.000) for 7177 atoms. Found 46 (46 requested) and removed 55 (23 requested) atoms. Cycle 8: After refmac, R = 0.2804 (Rfree = 0.000) for 7122 atoms. Found 45 (45 requested) and removed 42 (22 requested) atoms. Cycle 9: After refmac, R = 0.2806 (Rfree = 0.000) for 7083 atoms. Found 45 (45 requested) and removed 42 (22 requested) atoms. Cycle 10: After refmac, R = 0.2727 (Rfree = 0.000) for 7053 atoms. Found 45 (45 requested) and removed 35 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.58 Search for helices and strands: 0 residues in 0 chains, 7329 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 7342 seeds are put forward Round 1: 434 peptides, 80 chains. Longest chain 15 peptides. Score 0.369 Round 2: 490 peptides, 75 chains. Longest chain 17 peptides. Score 0.487 Round 3: 556 peptides, 82 chains. Longest chain 16 peptides. Score 0.535 Round 4: 548 peptides, 80 chains. Longest chain 18 peptides. Score 0.536 Round 5: 555 peptides, 81 chains. Longest chain 17 peptides. Score 0.540 Taking the results from Round 5 Chains 82, Residues 474, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16620 restraints for refining 7411 atoms. 14714 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3023 (Rfree = 0.000) for 7411 atoms. Found 47 (47 requested) and removed 79 (23 requested) atoms. Cycle 12: After refmac, R = 0.2749 (Rfree = 0.000) for 7301 atoms. Found 47 (47 requested) and removed 46 (23 requested) atoms. Cycle 13: After refmac, R = 0.2610 (Rfree = 0.000) for 7272 atoms. Found 46 (46 requested) and removed 38 (23 requested) atoms. Cycle 14: After refmac, R = 0.2557 (Rfree = 0.000) for 7251 atoms. Found 46 (46 requested) and removed 31 (23 requested) atoms. Cycle 15: After refmac, R = 0.2626 (Rfree = 0.000) for 7247 atoms. Found 46 (46 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 7573 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 7583 seeds are put forward Round 1: 426 peptides, 79 chains. Longest chain 14 peptides. Score 0.363 Round 2: 500 peptides, 78 chains. Longest chain 15 peptides. Score 0.483 Round 3: 528 peptides, 86 chains. Longest chain 14 peptides. Score 0.473 Round 4: 526 peptides, 79 chains. Longest chain 14 peptides. Score 0.513 Round 5: 509 peptides, 78 chains. Longest chain 14 peptides. Score 0.496 Taking the results from Round 4 Chains 80, Residues 447, Estimated correctness of the model 0.0 % 7 chains (40 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16633 restraints for refining 7419 atoms. 14805 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2936 (Rfree = 0.000) for 7419 atoms. Found 47 (47 requested) and removed 70 (23 requested) atoms. Cycle 17: After refmac, R = 0.2899 (Rfree = 0.000) for 7330 atoms. Found 47 (47 requested) and removed 41 (23 requested) atoms. Cycle 18: After refmac, R = 0.2807 (Rfree = 0.000) for 7295 atoms. Found 47 (47 requested) and removed 41 (23 requested) atoms. Cycle 19: After refmac, R = 0.2080 (Rfree = 0.000) for 7268 atoms. Found 45 (46 requested) and removed 25 (23 requested) atoms. Cycle 20: After refmac, R = 0.1860 (Rfree = 0.000) for 7265 atoms. Found 23 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.63 Search for helices and strands: 0 residues in 0 chains, 7503 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 7515 seeds are put forward Round 1: 433 peptides, 81 chains. Longest chain 13 peptides. Score 0.361 Round 2: 500 peptides, 88 chains. Longest chain 13 peptides. Score 0.419 Round 3: 501 peptides, 84 chains. Longest chain 15 peptides. Score 0.447 Round 4: 478 peptides, 74 chains. Longest chain 24 peptides. Score 0.476 Round 5: 491 peptides, 77 chains. Longest chain 15 peptides. Score 0.476 Taking the results from Round 5 Chains 77, Residues 414, Estimated correctness of the model 0.0 % 9 chains (43 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16964 restraints for refining 7461 atoms. 15266 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2876 (Rfree = 0.000) for 7461 atoms. Found 47 (47 requested) and removed 86 (23 requested) atoms. Cycle 22: After refmac, R = 0.2808 (Rfree = 0.000) for 7363 atoms. Found 47 (47 requested) and removed 52 (23 requested) atoms. Cycle 23: After refmac, R = 0.2744 (Rfree = 0.000) for 7309 atoms. Found 47 (47 requested) and removed 36 (23 requested) atoms. Cycle 24: After refmac, R = 0.2727 (Rfree = 0.000) for 7294 atoms. Found 46 (46 requested) and removed 44 (23 requested) atoms. Cycle 25: After refmac, R = 0.2685 (Rfree = 0.000) for 7267 atoms. Found 46 (46 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 7551 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7568 seeds are put forward Round 1: 432 peptides, 86 chains. Longest chain 12 peptides. Score 0.324 Round 2: 489 peptides, 88 chains. Longest chain 11 peptides. Score 0.403 Round 3: 512 peptides, 80 chains. Longest chain 12 peptides. Score 0.488 Round 4: 499 peptides, 80 chains. Longest chain 14 peptides. Score 0.469 Round 5: 500 peptides, 83 chains. Longest chain 12 peptides. Score 0.452 Taking the results from Round 3 Chains 80, Residues 432, Estimated correctness of the model 0.0 % 7 chains (34 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16240 restraints for refining 7336 atoms. 14495 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2954 (Rfree = 0.000) for 7336 atoms. Found 47 (47 requested) and removed 51 (23 requested) atoms. Cycle 27: After refmac, R = 0.2845 (Rfree = 0.000) for 7284 atoms. Found 47 (47 requested) and removed 32 (23 requested) atoms. Cycle 28: After refmac, R = 0.2826 (Rfree = 0.000) for 7252 atoms. Found 46 (46 requested) and removed 30 (23 requested) atoms. Cycle 29: After refmac, R = 0.2168 (Rfree = 0.000) for 7232 atoms. Found 46 (46 requested) and removed 27 (23 requested) atoms. Cycle 30: After refmac, R = 0.1970 (Rfree = 0.000) for 7233 atoms. Found 35 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.66 Search for helices and strands: 0 residues in 0 chains, 7441 seeds are put forward NCS extension: 9 residues added (4 deleted due to clashes), 7450 seeds are put forward Round 1: 396 peptides, 77 chains. Longest chain 12 peptides. Score 0.327 Round 2: 465 peptides, 88 chains. Longest chain 14 peptides. Score 0.365 Round 3: 486 peptides, 85 chains. Longest chain 12 peptides. Score 0.418 Round 4: 468 peptides, 80 chains. Longest chain 12 peptides. Score 0.423 Round 5: 460 peptides, 78 chains. Longest chain 12 peptides. Score 0.424 Taking the results from Round 5 Chains 78, Residues 382, Estimated correctness of the model 0.0 % 6 chains (22 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 17017 restraints for refining 7395 atoms. 15502 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3146 (Rfree = 0.000) for 7395 atoms. Found 47 (47 requested) and removed 70 (23 requested) atoms. Cycle 32: After refmac, R = 0.2971 (Rfree = 0.000) for 7314 atoms. Found 47 (47 requested) and removed 47 (23 requested) atoms. Cycle 33: After refmac, R = 0.3026 (Rfree = 0.000) for 7278 atoms. Found 46 (46 requested) and removed 36 (23 requested) atoms. Cycle 34: After refmac, R = 0.2900 (Rfree = 0.000) for 7258 atoms. Found 46 (46 requested) and removed 32 (23 requested) atoms. Cycle 35: After refmac, R = 0.2882 (Rfree = 0.000) for 7244 atoms. Found 46 (46 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 7499 seeds are put forward NCS extension: 6 residues added (8 deleted due to clashes), 7505 seeds are put forward Round 1: 317 peptides, 69 chains. Longest chain 10 peptides. Score 0.246 Round 2: 421 peptides, 79 chains. Longest chain 11 peptides. Score 0.355 Round 3: 426 peptides, 80 chains. Longest chain 15 peptides. Score 0.356 Round 4: 420 peptides, 73 chains. Longest chain 14 peptides. Score 0.395 Round 5: 432 peptides, 77 chains. Longest chain 15 peptides. Score 0.387 Taking the results from Round 4 Chains 73, Residues 347, Estimated correctness of the model 0.0 % 11 chains (57 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 15878 restraints for refining 7163 atoms. 14403 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3024 (Rfree = 0.000) for 7163 atoms. Found 45 (45 requested) and removed 72 (22 requested) atoms. Cycle 37: After refmac, R = 0.2822 (Rfree = 0.000) for 7081 atoms. Found 45 (45 requested) and removed 30 (22 requested) atoms. Cycle 38: After refmac, R = 0.2824 (Rfree = 0.000) for 7054 atoms. Found 45 (45 requested) and removed 33 (22 requested) atoms. Cycle 39: After refmac, R = 0.2791 (Rfree = 0.000) for 7049 atoms. Found 45 (45 requested) and removed 30 (22 requested) atoms. Cycle 40: After refmac, R = 0.2793 (Rfree = 0.000) for 7048 atoms. Found 45 (45 requested) and removed 31 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.58 Search for helices and strands: 0 residues in 0 chains, 7307 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 7319 seeds are put forward Round 1: 314 peptides, 68 chains. Longest chain 9 peptides. Score 0.248 Round 2: 378 peptides, 73 chains. Longest chain 12 peptides. Score 0.325 Round 3: 387 peptides, 69 chains. Longest chain 11 peptides. Score 0.369 Round 4: 378 peptides, 68 chains. Longest chain 12 peptides. Score 0.361 Round 5: 378 peptides, 63 chains. Longest chain 13 peptides. Score 0.397 Taking the results from Round 5 Chains 64, Residues 315, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 15978 restraints for refining 7065 atoms. 14670 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3294 (Rfree = 0.000) for 7065 atoms. Found 45 (45 requested) and removed 52 (22 requested) atoms. Cycle 42: After refmac, R = 0.3055 (Rfree = 0.000) for 7008 atoms. Found 45 (45 requested) and removed 34 (22 requested) atoms. Cycle 43: After refmac, R = 0.3165 (Rfree = 0.000) for 6990 atoms. Found 45 (45 requested) and removed 35 (22 requested) atoms. Cycle 44: After refmac, R = 0.3040 (Rfree = 0.000) for 6970 atoms. Found 44 (44 requested) and removed 26 (22 requested) atoms. Cycle 45: After refmac, R = 0.2347 (Rfree = 0.000) for 6966 atoms. Found 44 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 7176 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 7188 seeds are put forward Round 1: 249 peptides, 54 chains. Longest chain 10 peptides. Score 0.236 Round 2: 312 peptides, 62 chains. Longest chain 15 peptides. Score 0.291 Round 3: 331 peptides, 64 chains. Longest chain 11 peptides. Score 0.310 Round 4: 322 peptides, 59 chains. Longest chain 14 peptides. Score 0.332 Round 5: 332 peptides, 60 chains. Longest chain 14 peptides. Score 0.342 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 272, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11642 reflections ( 99.06 % complete ) and 15295 restraints for refining 6738 atoms. 14235 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2968 (Rfree = 0.000) for 6738 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.3044 (Rfree = 0.000) for 6698 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2812 (Rfree = 0.000) for 6660 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2908 (Rfree = 0.000) for 6623 atoms. TimeTaking 84.25