Mon 24 Dec 07:25:52 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 2hr2-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-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/2hr2-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-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 07:25:56 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/2hr2-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-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 901 and 0 Target number of residues in the AU: 901 Target solvent content: 0.6596 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-3.8-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: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.85 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: 88.085 3.800 Wilson plot Bfac: 84.55 14444 reflections ( 98.08 % complete ) and 0 restraints for refining 8471 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3308 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3530 (Rfree = 0.000) for 8471 atoms. Found 46 (46 requested) and removed 36 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.08 Search for helices and strands: 0 residues in 0 chains, 8754 seeds are put forward NCS extension: 0 residues added, 8754 seeds are put forward Round 1: 407 peptides, 67 chains. Longest chain 16 peptides. Score 0.361 Round 2: 486 peptides, 63 chains. Longest chain 18 peptides. Score 0.472 Round 3: 520 peptides, 56 chains. Longest chain 24 peptides. Score 0.540 Round 4: 533 peptides, 56 chains. Longest chain 28 peptides. Score 0.552 Round 5: 532 peptides, 57 chains. Longest chain 24 peptides. Score 0.547 Taking the results from Round 4 Chains 62, Residues 477, Estimated correctness of the model 0.0 % 5 chains (55 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15204 restraints for refining 6900 atoms. 13162 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2759 (Rfree = 0.000) for 6900 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. Cycle 2: After refmac, R = 0.2668 (Rfree = 0.000) for 6719 atoms. Found 37 (37 requested) and removed 48 (18 requested) atoms. Cycle 3: After refmac, R = 0.2354 (Rfree = 0.000) for 6598 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. Cycle 4: After refmac, R = 0.2493 (Rfree = 0.000) for 6539 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. Cycle 5: After refmac, R = 0.2175 (Rfree = 0.000) for 6495 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 6920 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6941 seeds are put forward Round 1: 483 peptides, 70 chains. Longest chain 18 peptides. Score 0.434 Round 2: 530 peptides, 62 chains. Longest chain 22 peptides. Score 0.522 Round 3: 533 peptides, 65 chains. Longest chain 20 peptides. Score 0.511 Round 4: 539 peptides, 61 chains. Longest chain 26 peptides. Score 0.535 Round 5: 536 peptides, 52 chains. Longest chain 35 peptides. Score 0.573 Taking the results from Round 5 Chains 54, Residues 484, Estimated correctness of the model 0.0 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14794 restraints for refining 6898 atoms. 12714 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2593 (Rfree = 0.000) for 6898 atoms. Found 37 (37 requested) and removed 56 (18 requested) atoms. Cycle 7: After refmac, R = 0.2404 (Rfree = 0.000) for 6760 atoms. Found 37 (37 requested) and removed 43 (18 requested) atoms. Cycle 8: After refmac, R = 0.2276 (Rfree = 0.000) for 6684 atoms. Found 37 (37 requested) and removed 43 (18 requested) atoms. Cycle 9: After refmac, R = 0.2242 (Rfree = 0.000) for 6648 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. Cycle 10: After refmac, R = 0.2140 (Rfree = 0.000) for 6623 atoms. Found 36 (36 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.03 Search for helices and strands: 0 residues in 0 chains, 7034 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 7053 seeds are put forward Round 1: 488 peptides, 74 chains. Longest chain 14 peptides. Score 0.419 Round 2: 529 peptides, 62 chains. Longest chain 18 peptides. Score 0.521 Round 3: 505 peptides, 60 chains. Longest chain 22 peptides. Score 0.506 Round 4: 514 peptides, 59 chains. Longest chain 25 peptides. Score 0.520 Round 5: 516 peptides, 59 chains. Longest chain 22 peptides. Score 0.522 Taking the results from Round 5 Chains 64, Residues 457, Estimated correctness of the model 0.0 % 8 chains (70 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14568 restraints for refining 6902 atoms. 12567 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2382 (Rfree = 0.000) for 6902 atoms. Found 37 (37 requested) and removed 53 (18 requested) atoms. Cycle 12: After refmac, R = 0.2162 (Rfree = 0.000) for 6816 atoms. Found 32 (37 requested) and removed 43 (18 requested) atoms. Cycle 13: After refmac, R = 0.2193 (Rfree = 0.000) for 6777 atoms. Found 37 (37 requested) and removed 47 (18 requested) atoms. Cycle 14: After refmac, R = 0.2070 (Rfree = 0.000) for 6747 atoms. Found 37 (37 requested) and removed 39 (18 requested) atoms. Cycle 15: After refmac, R = 0.2053 (Rfree = 0.000) for 6725 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.00 Search for helices and strands: 0 residues in 0 chains, 7126 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 7146 seeds are put forward Round 1: 498 peptides, 77 chains. Longest chain 23 peptides. Score 0.415 Round 2: 535 peptides, 68 chains. Longest chain 20 peptides. Score 0.499 Round 3: 530 peptides, 69 chains. Longest chain 28 peptides. Score 0.489 Round 4: 496 peptides, 61 chains. Longest chain 26 peptides. Score 0.492 Round 5: 499 peptides, 58 chains. Longest chain 23 peptides. Score 0.510 Taking the results from Round 5 Chains 58, Residues 441, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15374 restraints for refining 6903 atoms. 13600 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2494 (Rfree = 0.000) for 6903 atoms. Found 37 (37 requested) and removed 35 (18 requested) atoms. Cycle 17: After refmac, R = 0.2332 (Rfree = 0.000) for 6834 atoms. Found 37 (37 requested) and removed 41 (18 requested) atoms. Cycle 18: After refmac, R = 0.2240 (Rfree = 0.000) for 6789 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Cycle 19: After refmac, R = 0.2184 (Rfree = 0.000) for 6754 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 20: After refmac, R = 0.2113 (Rfree = 0.000) for 6726 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.00 Search for helices and strands: 0 residues in 0 chains, 7128 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 7140 seeds are put forward Round 1: 462 peptides, 79 chains. Longest chain 19 peptides. Score 0.363 Round 2: 535 peptides, 71 chains. Longest chain 21 peptides. Score 0.485 Round 3: 524 peptides, 73 chains. Longest chain 26 peptides. Score 0.464 Round 4: 501 peptides, 67 chains. Longest chain 18 peptides. Score 0.468 Round 5: 501 peptides, 65 chains. Longest chain 19 peptides. Score 0.478 Taking the results from Round 2 Chains 73, Residues 464, Estimated correctness of the model 0.0 % 6 chains (58 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14727 restraints for refining 6900 atoms. 12760 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2396 (Rfree = 0.000) for 6900 atoms. Found 37 (37 requested) and removed 60 (18 requested) atoms. Cycle 22: After refmac, R = 0.2249 (Rfree = 0.000) for 6816 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. Cycle 23: After refmac, R = 0.2227 (Rfree = 0.000) for 6783 atoms. Found 37 (37 requested) and removed 44 (18 requested) atoms. Cycle 24: After refmac, R = 0.2169 (Rfree = 0.000) for 6750 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. Cycle 25: After refmac, R = 0.2111 (Rfree = 0.000) for 6738 atoms. Found 27 (37 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 2.98 Search for helices and strands: 0 residues in 0 chains, 7102 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 7122 seeds are put forward Round 1: 459 peptides, 81 chains. Longest chain 13 peptides. Score 0.349 Round 2: 510 peptides, 72 chains. Longest chain 15 peptides. Score 0.454 Round 3: 505 peptides, 70 chains. Longest chain 20 peptides. Score 0.458 Round 4: 516 peptides, 75 chains. Longest chain 16 peptides. Score 0.445 Round 5: 499 peptides, 68 chains. Longest chain 21 peptides. Score 0.461 Taking the results from Round 5 Chains 69, Residues 431, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15218 restraints for refining 6898 atoms. 13508 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2539 (Rfree = 0.000) for 6898 atoms. Found 37 (37 requested) and removed 35 (18 requested) atoms. Cycle 27: After refmac, R = 0.2267 (Rfree = 0.000) for 6826 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. Cycle 28: After refmac, R = 0.1971 (Rfree = 0.000) for 6790 atoms. Found 37 (37 requested) and removed 23 (18 requested) atoms. Cycle 29: After refmac, R = 0.2090 (Rfree = 0.000) for 6781 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. Cycle 30: After refmac, R = 0.1867 (Rfree = 0.000) for 6769 atoms. Found 23 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 7138 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 7161 seeds are put forward Round 1: 438 peptides, 79 chains. Longest chain 12 peptides. Score 0.334 Round 2: 490 peptides, 71 chains. Longest chain 18 peptides. Score 0.437 Round 3: 479 peptides, 67 chains. Longest chain 18 peptides. Score 0.444 Round 4: 487 peptides, 63 chains. Longest chain 24 peptides. Score 0.473 Round 5: 475 peptides, 61 chains. Longest chain 22 peptides. Score 0.470 Taking the results from Round 4 Chains 65, Residues 424, Estimated correctness of the model 0.0 % 6 chains (46 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15114 restraints for refining 6903 atoms. 13301 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2603 (Rfree = 0.000) for 6903 atoms. Found 37 (37 requested) and removed 41 (18 requested) atoms. Cycle 32: After refmac, R = 0.2352 (Rfree = 0.000) for 6829 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. Cycle 33: After refmac, R = 0.2370 (Rfree = 0.000) for 6790 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. Cycle 34: After refmac, R = 0.2347 (Rfree = 0.000) for 6756 atoms. Found 37 (37 requested) and removed 21 (18 requested) atoms. Cycle 35: After refmac, R = 0.2270 (Rfree = 0.000) for 6743 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 7089 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 7115 seeds are put forward Round 1: 404 peptides, 78 chains. Longest chain 10 peptides. Score 0.296 Round 2: 465 peptides, 74 chains. Longest chain 14 peptides. Score 0.393 Round 3: 471 peptides, 75 chains. Longest chain 15 peptides. Score 0.395 Round 4: 472 peptides, 68 chains. Longest chain 17 peptides. Score 0.432 Round 5: 486 peptides, 75 chains. Longest chain 14 peptides. Score 0.412 Taking the results from Round 4 Chains 71, Residues 404, Estimated correctness of the model 0.0 % 6 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15152 restraints for refining 6902 atoms. 13418 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2564 (Rfree = 0.000) for 6902 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Cycle 37: After refmac, R = 0.2469 (Rfree = 0.000) for 6850 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. Cycle 38: After refmac, R = 0.2476 (Rfree = 0.000) for 6813 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 39: After refmac, R = 0.2390 (Rfree = 0.000) for 6780 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 40: After refmac, R = 0.2373 (Rfree = 0.000) for 6764 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.01 Search for helices and strands: 0 residues in 0 chains, 7101 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 7115 seeds are put forward Round 1: 391 peptides, 77 chains. Longest chain 17 peptides. Score 0.285 Round 2: 448 peptides, 77 chains. Longest chain 15 peptides. Score 0.357 Round 3: 452 peptides, 72 chains. Longest chain 17 peptides. Score 0.388 Round 4: 455 peptides, 71 chains. Longest chain 18 peptides. Score 0.397 Round 5: 482 peptides, 73 chains. Longest chain 18 peptides. Score 0.418 Taking the results from Round 5 Chains 73, Residues 409, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15331 restraints for refining 6903 atoms. 13689 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2671 (Rfree = 0.000) for 6903 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. Cycle 42: After refmac, R = 0.2413 (Rfree = 0.000) for 6848 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 43: After refmac, R = 0.2420 (Rfree = 0.000) for 6825 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 44: After refmac, R = 0.2355 (Rfree = 0.000) for 6802 atoms. Found 37 (37 requested) and removed 25 (18 requested) atoms. Cycle 45: After refmac, R = 0.2333 (Rfree = 0.000) for 6794 atoms. Found 37 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.05 Search for helices and strands: 0 residues in 0 chains, 7191 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 7209 seeds are put forward Round 1: 366 peptides, 73 chains. Longest chain 10 peptides. Score 0.274 Round 2: 423 peptides, 68 chains. Longest chain 18 peptides. Score 0.375 Round 3: 410 peptides, 65 chains. Longest chain 14 peptides. Score 0.375 Round 4: 405 peptides, 65 chains. Longest chain 16 peptides. Score 0.369 Round 5: 424 peptides, 67 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 67, Residues 357, Estimated correctness of the model 0.0 % 8 chains (34 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 67 chains (357 residues) following loop building 8 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14444 reflections ( 98.08 % complete ) and 15683 restraints for refining 6902 atoms. 14235 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2528 (Rfree = 0.000) for 6902 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2441 (Rfree = 0.000) for 6836 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2284 (Rfree = 0.000) for 6794 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1969 (Rfree = 0.000) for 6759 atoms. TimeTaking 69.4