Sun 23 Dec 22:23:05 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 2pbl-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-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/2pbl-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-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 ============================================================ Sun 23 Dec 22:23:13 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/2pbl-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-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 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-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: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 8384 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: 87.858 3.600 Wilson plot Bfac: 66.84 11642 reflections ( 99.06 % complete ) and 0 restraints for refining 9292 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3511 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4145 (Rfree = 0.000) for 9292 atoms. Found 59 (59 requested) and removed 67 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.50 Search for helices and strands: 0 residues in 0 chains, 9508 seeds are put forward NCS extension: 0 residues added, 9508 seeds are put forward Round 1: 363 peptides, 73 chains. Longest chain 10 peptides. Score 0.299 Round 2: 463 peptides, 78 chains. Longest chain 16 peptides. Score 0.428 Round 3: 516 peptides, 78 chains. Longest chain 14 peptides. Score 0.505 Round 4: 544 peptides, 78 chains. Longest chain 16 peptides. Score 0.543 Round 5: 525 peptides, 73 chains. Longest chain 21 peptides. Score 0.547 Taking the results from Round 5 Chains 76, Residues 452, Estimated correctness of the model 0.0 % 8 chains (63 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 17054 restraints for refining 7596 atoms. 15147 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3567 (Rfree = 0.000) for 7596 atoms. Found 48 (48 requested) and removed 97 (24 requested) atoms. Cycle 2: After refmac, R = 0.3551 (Rfree = 0.000) for 7353 atoms. Found 48 (48 requested) and removed 53 (24 requested) atoms. Cycle 3: After refmac, R = 0.3462 (Rfree = 0.000) for 7257 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. Cycle 4: After refmac, R = 0.3415 (Rfree = 0.000) for 7188 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. Cycle 5: After refmac, R = 0.3322 (Rfree = 0.000) for 7162 atoms. Found 46 (46 requested) and removed 38 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.58 Search for helices and strands: 0 residues in 0 chains, 7516 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7529 seeds are put forward Round 1: 446 peptides, 83 chains. Longest chain 13 peptides. Score 0.368 Round 2: 538 peptides, 82 chains. Longest chain 21 peptides. Score 0.512 Round 3: 568 peptides, 78 chains. Longest chain 23 peptides. Score 0.573 Round 4: 588 peptides, 78 chains. Longest chain 21 peptides. Score 0.597 Round 5: 550 peptides, 74 chains. Longest chain 33 peptides. Score 0.573 Taking the results from Round 4 Chains 84, Residues 510, Estimated correctness of the model 13.5 % 14 chains (121 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 15600 restraints for refining 7421 atoms. 13226 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3273 (Rfree = 0.000) for 7421 atoms. Found 47 (47 requested) and removed 93 (23 requested) atoms. Cycle 7: After refmac, R = 0.3150 (Rfree = 0.000) for 7222 atoms. Found 47 (47 requested) and removed 56 (23 requested) atoms. Cycle 8: After refmac, R = 0.3125 (Rfree = 0.000) for 7137 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. Cycle 9: After refmac, R = 0.2985 (Rfree = 0.000) for 7099 atoms. Found 45 (45 requested) and removed 43 (22 requested) atoms. Cycle 10: After refmac, R = 0.2934 (Rfree = 0.000) for 7057 atoms. Found 45 (45 requested) and removed 31 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 7375 seeds are put forward NCS extension: 17 residues added (11 deleted due to clashes), 7392 seeds are put forward Round 1: 475 peptides, 83 chains. Longest chain 14 peptides. Score 0.414 Round 2: 548 peptides, 78 chains. Longest chain 21 peptides. Score 0.548 Round 3: 554 peptides, 75 chains. Longest chain 23 peptides. Score 0.572 Round 4: 541 peptides, 74 chains. Longest chain 28 peptides. Score 0.562 Round 5: 558 peptides, 68 chains. Longest chain 21 peptides. Score 0.614 Taking the results from Round 5 Chains 74, Residues 490, Estimated correctness of the model 20.0 % 6 chains (55 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16509 restraints for refining 7473 atoms. 14437 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3449 (Rfree = 0.000) for 7473 atoms. Found 47 (47 requested) and removed 73 (23 requested) atoms. Cycle 12: After refmac, R = 0.3285 (Rfree = 0.000) for 7342 atoms. Found 47 (47 requested) and removed 62 (23 requested) atoms. Cycle 13: After refmac, R = 0.3227 (Rfree = 0.000) for 7261 atoms. Found 47 (47 requested) and removed 42 (23 requested) atoms. Cycle 14: After refmac, R = 0.3159 (Rfree = 0.000) for 7224 atoms. Found 46 (46 requested) and removed 37 (23 requested) atoms. Cycle 15: After refmac, R = 0.2401 (Rfree = 0.000) for 7199 atoms. Found 46 (46 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 7510 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 7528 seeds are put forward Round 1: 455 peptides, 87 chains. Longest chain 19 peptides. Score 0.355 Round 2: 512 peptides, 79 chains. Longest chain 22 peptides. Score 0.494 Round 3: 516 peptides, 78 chains. Longest chain 18 peptides. Score 0.505 Round 4: 536 peptides, 80 chains. Longest chain 22 peptides. Score 0.521 Round 5: 537 peptides, 84 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 4 Chains 83, Residues 456, Estimated correctness of the model 0.0 % 6 chains (49 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16291 restraints for refining 7353 atoms. 14380 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3049 (Rfree = 0.000) for 7353 atoms. Found 47 (47 requested) and removed 66 (23 requested) atoms. Cycle 17: After refmac, R = 0.3122 (Rfree = 0.000) for 7281 atoms. Found 47 (47 requested) and removed 42 (23 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2939 (Rfree = 0.000) for 7235 atoms. Found 46 (46 requested) and removed 37 (23 requested) atoms. Cycle 19: After refmac, R = 0.2862 (Rfree = 0.000) for 7212 atoms. Found 46 (46 requested) and removed 38 (23 requested) atoms. Cycle 20: After refmac, R = 0.2753 (Rfree = 0.000) for 7199 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 7462 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 7478 seeds are put forward Round 1: 448 peptides, 81 chains. Longest chain 21 peptides. Score 0.385 Round 2: 525 peptides, 78 chains. Longest chain 26 peptides. Score 0.518 Round 3: 530 peptides, 74 chains. Longest chain 27 peptides. Score 0.548 Round 4: 555 peptides, 81 chains. Longest chain 29 peptides. Score 0.540 Round 5: 536 peptides, 68 chains. Longest chain 33 peptides. Score 0.589 Taking the results from Round 5 Chains 71, Residues 468, Estimated correctness of the model 10.3 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16761 restraints for refining 7511 atoms. 14847 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3114 (Rfree = 0.000) for 7511 atoms. Found 48 (48 requested) and removed 84 (24 requested) atoms. Cycle 22: After refmac, R = 0.2914 (Rfree = 0.000) for 7392 atoms. Found 47 (47 requested) and removed 41 (23 requested) atoms. Cycle 23: After refmac, R = 0.2902 (Rfree = 0.000) for 7354 atoms. Found 47 (47 requested) and removed 36 (23 requested) atoms. Cycle 24: After refmac, R = 0.2782 (Rfree = 0.000) for 7327 atoms. Found 47 (47 requested) and removed 28 (23 requested) atoms. Cycle 25: After refmac, R = 0.2759 (Rfree = 0.000) for 7328 atoms. Found 47 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 7593 seeds are put forward NCS extension: 23 residues added (6 deleted due to clashes), 7616 seeds are put forward Round 1: 424 peptides, 79 chains. Longest chain 15 peptides. Score 0.360 Round 2: 476 peptides, 73 chains. Longest chain 27 peptides. Score 0.480 Round 3: 486 peptides, 78 chains. Longest chain 18 peptides. Score 0.463 Round 4: 499 peptides, 75 chains. Longest chain 21 peptides. Score 0.500 Round 5: 516 peptides, 76 chains. Longest chain 27 peptides. Score 0.517 Taking the results from Round 5 Chains 80, Residues 440, Estimated correctness of the model 0.0 % 8 chains (64 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16670 restraints for refining 7530 atoms. 14774 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3042 (Rfree = 0.000) for 7530 atoms. Found 48 (48 requested) and removed 72 (24 requested) atoms. Cycle 27: After refmac, R = 0.2925 (Rfree = 0.000) for 7423 atoms. Found 48 (48 requested) and removed 51 (24 requested) atoms. Cycle 28: After refmac, R = 0.3011 (Rfree = 0.000) for 7378 atoms. Found 47 (47 requested) and removed 36 (23 requested) atoms. Cycle 29: After refmac, R = 0.2855 (Rfree = 0.000) for 7362 atoms. Found 47 (47 requested) and removed 38 (23 requested) atoms. Cycle 30: After refmac, R = 0.3013 (Rfree = 0.000) for 7345 atoms. Found 47 (47 requested) and removed 40 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 7542 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 7566 seeds are put forward Round 1: 341 peptides, 69 chains. Longest chain 11 peptides. Score 0.290 Round 2: 442 peptides, 78 chains. Longest chain 12 peptides. Score 0.396 Round 3: 436 peptides, 70 chains. Longest chain 17 peptides. Score 0.440 Round 4: 460 peptides, 75 chains. Longest chain 17 peptides. Score 0.443 Round 5: 455 peptides, 73 chains. Longest chain 19 peptides. Score 0.449 Taking the results from Round 5 Chains 74, Residues 382, Estimated correctness of the model 0.0 % 8 chains (51 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16708 restraints for refining 7416 atoms. 15082 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3153 (Rfree = 0.000) for 7416 atoms. Found 47 (47 requested) and removed 70 (23 requested) atoms. Cycle 32: After refmac, R = 0.3028 (Rfree = 0.000) for 7328 atoms. Found 47 (47 requested) and removed 45 (23 requested) atoms. Cycle 33: After refmac, R = 0.3006 (Rfree = 0.000) for 7277 atoms. Found 47 (47 requested) and removed 31 (23 requested) atoms. Cycle 34: After refmac, R = 0.2922 (Rfree = 0.000) for 7250 atoms. Found 46 (46 requested) and removed 30 (23 requested) atoms. Cycle 35: After refmac, R = 0.2935 (Rfree = 0.000) for 7236 atoms. Found 46 (46 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 7458 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 7476 seeds are put forward Round 1: 384 peptides, 78 chains. Longest chain 15 peptides. Score 0.299 Round 2: 392 peptides, 70 chains. Longest chain 15 peptides. Score 0.370 Round 3: 432 peptides, 74 chains. Longest chain 17 peptides. Score 0.407 Round 4: 422 peptides, 70 chains. Longest chain 17 peptides. Score 0.418 Round 5: 412 peptides, 63 chains. Longest chain 19 peptides. Score 0.450 Taking the results from Round 5 Chains 63, Residues 349, Estimated correctness of the model 0.0 % 7 chains (36 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 16424 restraints for refining 7234 atoms. 14980 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3261 (Rfree = 0.000) for 7234 atoms. Found 46 (46 requested) and removed 59 (23 requested) atoms. Cycle 37: After refmac, R = 0.3142 (Rfree = 0.000) for 7143 atoms. Found 46 (46 requested) and removed 40 (23 requested) atoms. Cycle 38: After refmac, R = 0.3031 (Rfree = 0.000) for 7105 atoms. Found 45 (45 requested) and removed 31 (22 requested) atoms. Cycle 39: After refmac, R = 0.2903 (Rfree = 0.000) for 7088 atoms. Found 45 (45 requested) and removed 34 (22 requested) atoms. Cycle 40: After refmac, R = 0.2107 (Rfree = 0.000) for 7086 atoms. Found 45 (45 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.62 Search for helices and strands: 0 residues in 0 chains, 7281 seeds are put forward NCS extension: 15 residues added (9 deleted due to clashes), 7296 seeds are put forward Round 1: 310 peptides, 64 chains. Longest chain 12 peptides. Score 0.272 Round 2: 385 peptides, 68 chains. Longest chain 17 peptides. Score 0.373 Round 3: 380 peptides, 64 chains. Longest chain 12 peptides. Score 0.393 Round 4: 381 peptides, 66 chains. Longest chain 17 peptides. Score 0.381 Round 5: 385 peptides, 66 chains. Longest chain 16 peptides. Score 0.387 Taking the results from Round 3 Chains 64, Residues 316, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 11642 reflections ( 99.06 % complete ) and 15681 restraints for refining 6957 atoms. 14445 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2731 (Rfree = 0.000) for 6957 atoms. Found 44 (44 requested) and removed 40 (22 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2928 (Rfree = 0.000) for 6921 atoms. Found 44 (44 requested) and removed 38 (22 requested) atoms. Cycle 43: After refmac, R = 0.2808 (Rfree = 0.000) for 6907 atoms. Found 44 (44 requested) and removed 28 (22 requested) atoms. Cycle 44: After refmac, R = 0.2920 (Rfree = 0.000) for 6906 atoms. Found 44 (44 requested) and removed 29 (22 requested) atoms. Cycle 45: After refmac, R = 0.2825 (Rfree = 0.000) for 6907 atoms. Found 44 (44 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 7122 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7137 seeds are put forward Round 1: 283 peptides, 62 chains. Longest chain 8 peptides. Score 0.237 Round 2: 336 peptides, 67 chains. Longest chain 10 peptides. Score 0.296 Round 3: 347 peptides, 66 chains. Longest chain 12 peptides. Score 0.323 Round 4: 358 peptides, 66 chains. Longest chain 11 peptides. Score 0.342 Round 5: 351 peptides, 68 chains. Longest chain 10 peptides. Score 0.315 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 292, Estimated correctness of the model 0.0 % 5 chains (17 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (292 residues) following loop building 5 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11642 reflections ( 99.06 % complete ) and 15005 restraints for refining 6733 atoms. 13866 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2985 (Rfree = 0.000) for 6733 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.2792 (Rfree = 0.000) for 6671 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2781 (Rfree = 0.000) for 6638 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2672 (Rfree = 0.000) for 6608 atoms. TimeTaking 89.98