Mon 24 Dec 00:54:13 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 2a2m-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.2-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/2a2m-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.2-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 00:54:18 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/2a2m-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.2-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 657 and 0 Target number of residues in the AU: 657 Target solvent content: 0.6247 Checking the provided sequence file Detected sequence length: 258 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 516 Adjusted target solvent content: 0.71 Input MTZ file: 2a2m-3.2-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: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4128 target number of atoms Had to go as low as 0.90 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: 163.559 3.200 Wilson plot Bfac: 63.52 16630 reflections ( 99.82 % complete ) and 0 restraints for refining 4628 atoms. Observations/parameters ratio is 0.90 ------------------------------------------------------ Starting model: R = 0.3194 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2342 (Rfree = 0.000) for 4628 atoms. Found 41 (41 requested) and removed 38 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 2.32 Search for helices and strands: 0 residues in 0 chains, 4770 seeds are put forward NCS extension: 0 residues added, 4770 seeds are put forward Round 1: 363 peptides, 49 chains. Longest chain 32 peptides. Score 0.485 Round 2: 373 peptides, 42 chains. Longest chain 24 peptides. Score 0.548 Round 3: 387 peptides, 42 chains. Longest chain 30 peptides. Score 0.568 Round 4: 396 peptides, 40 chains. Longest chain 43 peptides. Score 0.593 Round 5: 413 peptides, 40 chains. Longest chain 33 peptides. Score 0.614 Taking the results from Round 5 Chains 43, Residues 373, Estimated correctness of the model 44.8 % 11 chains (161 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6706 restraints for refining 4001 atoms. 4581 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2795 (Rfree = 0.000) for 4001 atoms. Found 35 (35 requested) and removed 38 (17 requested) atoms. Cycle 2: After refmac, R = 0.2624 (Rfree = 0.000) for 3929 atoms. Found 35 (35 requested) and removed 31 (17 requested) atoms. Cycle 3: After refmac, R = 0.2514 (Rfree = 0.000) for 3912 atoms. Found 35 (35 requested) and removed 21 (17 requested) atoms. Cycle 4: After refmac, R = 0.2421 (Rfree = 0.000) for 3916 atoms. Found 33 (35 requested) and removed 28 (17 requested) atoms. Cycle 5: After refmac, R = 0.2358 (Rfree = 0.000) for 3907 atoms. Found 28 (35 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 2.34 Search for helices and strands: 0 residues in 0 chains, 4067 seeds are put forward NCS extension: 20 residues added (23 deleted due to clashes), 4087 seeds are put forward Round 1: 359 peptides, 38 chains. Longest chain 28 peptides. Score 0.555 Round 2: 376 peptides, 30 chains. Longest chain 48 peptides. Score 0.629 Round 3: 375 peptides, 33 chains. Longest chain 47 peptides. Score 0.609 Round 4: 367 peptides, 38 chains. Longest chain 25 peptides. Score 0.566 Round 5: 365 peptides, 36 chains. Longest chain 35 peptides. Score 0.577 Taking the results from Round 2 Chains 39, Residues 346, Estimated correctness of the model 48.6 % 8 chains (134 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6614 restraints for refining 3768 atoms. 4670 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2761 (Rfree = 0.000) for 3768 atoms. Found 33 (33 requested) and removed 26 (16 requested) atoms. Cycle 7: After refmac, R = 0.2591 (Rfree = 0.000) for 3760 atoms. Found 33 (33 requested) and removed 28 (16 requested) atoms. Cycle 8: After refmac, R = 0.2509 (Rfree = 0.000) for 3758 atoms. Found 33 (33 requested) and removed 29 (16 requested) atoms. Cycle 9: After refmac, R = 0.2437 (Rfree = 0.000) for 3743 atoms. Found 22 (33 requested) and removed 21 (16 requested) atoms. Cycle 10: After refmac, R = 0.2369 (Rfree = 0.000) for 3731 atoms. Found 27 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.35 Search for helices and strands: 0 residues in 0 chains, 3893 seeds are put forward NCS extension: 14 residues added (12 deleted due to clashes), 3907 seeds are put forward Round 1: 354 peptides, 35 chains. Longest chain 31 peptides. Score 0.568 Round 2: 380 peptides, 37 chains. Longest chain 33 peptides. Score 0.590 Round 3: 370 peptides, 35 chains. Longest chain 29 peptides. Score 0.590 Round 4: 371 peptides, 35 chains. Longest chain 29 peptides. Score 0.591 Round 5: 362 peptides, 40 chains. Longest chain 22 peptides. Score 0.546 Taking the results from Round 4 Chains 38, Residues 336, Estimated correctness of the model 38.6 % 9 chains (120 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6824 restraints for refining 3767 atoms. 5021 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2729 (Rfree = 0.000) for 3767 atoms. Found 33 (33 requested) and removed 30 (16 requested) atoms. Cycle 12: After refmac, R = 0.2563 (Rfree = 0.000) for 3745 atoms. Found 33 (33 requested) and removed 23 (16 requested) atoms. Cycle 13: After refmac, R = 0.2509 (Rfree = 0.000) for 3734 atoms. Found 33 (33 requested) and removed 22 (16 requested) atoms. Cycle 14: After refmac, R = 0.2485 (Rfree = 0.000) for 3736 atoms. Found 33 (33 requested) and removed 22 (16 requested) atoms. Cycle 15: After refmac, R = 0.2745 (Rfree = 0.000) for 3734 atoms. Found 33 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 2.37 Search for helices and strands: 0 residues in 0 chains, 3933 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 3954 seeds are put forward Round 1: 367 peptides, 39 chains. Longest chain 26 peptides. Score 0.559 Round 2: 373 peptides, 33 chains. Longest chain 30 peptides. Score 0.607 Round 3: 371 peptides, 34 chains. Longest chain 32 peptides. Score 0.598 Round 4: 376 peptides, 31 chains. Longest chain 32 peptides. Score 0.623 Round 5: 346 peptides, 37 chains. Longest chain 34 peptides. Score 0.543 Taking the results from Round 4 Chains 35, Residues 345, Estimated correctness of the model 47.1 % 7 chains (134 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6621 restraints for refining 3768 atoms. 4712 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2724 (Rfree = 0.000) for 3768 atoms. Found 33 (33 requested) and removed 43 (16 requested) atoms. Cycle 17: After refmac, R = 0.2525 (Rfree = 0.000) for 3732 atoms. Found 30 (33 requested) and removed 28 (16 requested) atoms. Cycle 18: After refmac, R = 0.2495 (Rfree = 0.000) for 3714 atoms. Found 33 (33 requested) and removed 37 (16 requested) atoms. Cycle 19: After refmac, R = 0.2357 (Rfree = 0.000) for 3694 atoms. Found 24 (33 requested) and removed 25 (16 requested) atoms. Cycle 20: After refmac, R = 0.2324 (Rfree = 0.000) for 3689 atoms. Found 21 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 2.37 Search for helices and strands: 0 residues in 0 chains, 3872 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3891 seeds are put forward Round 1: 365 peptides, 40 chains. Longest chain 22 peptides. Score 0.550 Round 2: 359 peptides, 35 chains. Longest chain 34 peptides. Score 0.575 Round 3: 373 peptides, 38 chains. Longest chain 31 peptides. Score 0.574 Round 4: 371 peptides, 42 chains. Longest chain 32 peptides. Score 0.545 Round 5: 348 peptides, 35 chains. Longest chain 20 peptides. Score 0.560 Taking the results from Round 2 Chains 37, Residues 324, Estimated correctness of the model 34.1 % 5 chains (88 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 7150 restraints for refining 3769 atoms. 5522 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2676 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 27 (16 requested) atoms. Cycle 22: After refmac, R = 0.2693 (Rfree = 0.000) for 3765 atoms. Found 33 (33 requested) and removed 32 (16 requested) atoms. Cycle 23: After refmac, R = 0.2571 (Rfree = 0.000) for 3750 atoms. Found 33 (33 requested) and removed 25 (16 requested) atoms. Cycle 24: After refmac, R = 0.2615 (Rfree = 0.000) for 3746 atoms. Found 33 (33 requested) and removed 29 (16 requested) atoms. Cycle 25: After refmac, R = 0.2416 (Rfree = 0.000) for 3741 atoms. Found 27 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 2.37 Search for helices and strands: 0 residues in 0 chains, 3905 seeds are put forward NCS extension: 50 residues added (8 deleted due to clashes), 3955 seeds are put forward Round 1: 363 peptides, 40 chains. Longest chain 40 peptides. Score 0.547 Round 2: 371 peptides, 35 chains. Longest chain 25 peptides. Score 0.591 Round 3: 356 peptides, 36 chains. Longest chain 29 peptides. Score 0.564 Round 4: 362 peptides, 39 chains. Longest chain 25 peptides. Score 0.552 Round 5: 364 peptides, 38 chains. Longest chain 29 peptides. Score 0.562 Taking the results from Round 2 Chains 39, Residues 336, Estimated correctness of the model 38.6 % 7 chains (113 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6809 restraints for refining 3769 atoms. 5012 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2700 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 31 (16 requested) atoms. Cycle 27: After refmac, R = 0.2706 (Rfree = 0.000) for 3754 atoms. Found 33 (33 requested) and removed 33 (16 requested) atoms. Cycle 28: After refmac, R = 0.2421 (Rfree = 0.000) for 3745 atoms. Found 31 (33 requested) and removed 29 (16 requested) atoms. Cycle 29: After refmac, R = 0.2359 (Rfree = 0.000) for 3738 atoms. Found 17 (33 requested) and removed 19 (16 requested) atoms. Cycle 30: After refmac, R = 0.2438 (Rfree = 0.000) for 3731 atoms. Found 33 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 2.34 Search for helices and strands: 0 residues in 0 chains, 3902 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 3918 seeds are put forward Round 1: 355 peptides, 39 chains. Longest chain 25 peptides. Score 0.542 Round 2: 362 peptides, 34 chains. Longest chain 45 peptides. Score 0.586 Round 3: 353 peptides, 34 chains. Longest chain 42 peptides. Score 0.573 Round 4: 363 peptides, 34 chains. Longest chain 35 peptides. Score 0.587 Round 5: 372 peptides, 32 chains. Longest chain 42 peptides. Score 0.612 Taking the results from Round 5 Chains 33, Residues 340, Estimated correctness of the model 44.3 % 6 chains (131 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6678 restraints for refining 3769 atoms. 4762 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2694 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 30 (16 requested) atoms. Cycle 32: After refmac, R = 0.2490 (Rfree = 0.000) for 3745 atoms. Found 33 (33 requested) and removed 20 (16 requested) atoms. Cycle 33: After refmac, R = 0.2424 (Rfree = 0.000) for 3734 atoms. Found 32 (33 requested) and removed 23 (16 requested) atoms. Cycle 34: After refmac, R = 0.2306 (Rfree = 0.000) for 3727 atoms. Found 29 (33 requested) and removed 20 (16 requested) atoms. Cycle 35: After refmac, R = 0.2559 (Rfree = 0.000) for 3724 atoms. Found 33 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.36 Search for helices and strands: 0 residues in 0 chains, 3888 seeds are put forward NCS extension: 31 residues added (13 deleted due to clashes), 3919 seeds are put forward Round 1: 355 peptides, 37 chains. Longest chain 46 peptides. Score 0.556 Round 2: 366 peptides, 28 chains. Longest chain 46 peptides. Score 0.629 Round 3: 347 peptides, 32 chains. Longest chain 43 peptides. Score 0.578 Round 4: 355 peptides, 32 chains. Longest chain 36 peptides. Score 0.589 Round 5: 353 peptides, 39 chains. Longest chain 26 peptides. Score 0.539 Taking the results from Round 2 Chains 30, Residues 338, Estimated correctness of the model 48.6 % 8 chains (176 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6374 restraints for refining 3769 atoms. 4230 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2636 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 37 (16 requested) atoms. Cycle 37: After refmac, R = 0.2603 (Rfree = 0.000) for 3743 atoms. Found 33 (33 requested) and removed 29 (16 requested) atoms. Cycle 38: After refmac, R = 0.2335 (Rfree = 0.000) for 3729 atoms. Found 33 (33 requested) and removed 21 (16 requested) atoms. Cycle 39: After refmac, R = 0.2280 (Rfree = 0.000) for 3730 atoms. Found 25 (33 requested) and removed 23 (16 requested) atoms. Cycle 40: After refmac, R = 0.2281 (Rfree = 0.000) for 3726 atoms. Found 31 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.33 Search for helices and strands: 0 residues in 0 chains, 3872 seeds are put forward NCS extension: 53 residues added (8 deleted due to clashes), 3925 seeds are put forward Round 1: 374 peptides, 35 chains. Longest chain 54 peptides. Score 0.595 Round 2: 376 peptides, 31 chains. Longest chain 42 peptides. Score 0.623 Round 3: 381 peptides, 33 chains. Longest chain 33 peptides. Score 0.617 Round 4: 383 peptides, 31 chains. Longest chain 32 peptides. Score 0.632 Round 5: 361 peptides, 34 chains. Longest chain 46 peptides. Score 0.584 Taking the results from Round 4 Chains 33, Residues 352, Estimated correctness of the model 49.4 % 11 chains (196 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6001 restraints for refining 3769 atoms. 3808 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2627 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 45 (16 requested) atoms. Cycle 42: After refmac, R = 0.2506 (Rfree = 0.000) for 3726 atoms. Found 33 (33 requested) and removed 28 (16 requested) atoms. Cycle 43: After refmac, R = 0.2651 (Rfree = 0.000) for 3716 atoms. Found 33 (33 requested) and removed 33 (16 requested) atoms. Cycle 44: After refmac, R = 0.2391 (Rfree = 0.000) for 3701 atoms. Found 33 (33 requested) and removed 23 (16 requested) atoms. Cycle 45: After refmac, R = 0.2303 (Rfree = 0.000) for 3704 atoms. Found 24 (33 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.36 Search for helices and strands: 0 residues in 0 chains, 3858 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3881 seeds are put forward Round 1: 371 peptides, 31 chains. Longest chain 38 peptides. Score 0.617 Round 2: 371 peptides, 33 chains. Longest chain 32 peptides. Score 0.604 Round 3: 378 peptides, 32 chains. Longest chain 31 peptides. Score 0.619 Round 4: 385 peptides, 33 chains. Longest chain 40 peptides. Score 0.622 Round 5: 368 peptides, 36 chains. Longest chain 30 peptides. Score 0.581 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 352, Estimated correctness of the model 46.9 % 12 chains (171 residues) have been docked in sequence Sequence coverage is 48 % Consider running further cycles of model building using 2a2m-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 147 A and 153 A Built loop between residues 166 A and 169 A Built loop between residues 168 B and 180 B Built loop between residues 192 B and 202 B Built loop between residues 226 B and 229 B 26 chains (368 residues) following loop building 7 chains (200 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16630 reflections ( 99.82 % complete ) and 5956 restraints for refining 3769 atoms. 3670 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2757 (Rfree = 0.000) for 3769 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2558 (Rfree = 0.000) for 3722 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2507 (Rfree = 0.000) for 3696 atoms. Found 0 (33 requested) and removed 7 (16 requested) atoms. Cycle 49: After refmac, R = 0.2432 (Rfree = 0.000) for 3678 atoms. TimeTaking 433.27