Mon 24 Dec 00:12:16 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 2afb-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-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/2afb-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-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 00:12:20 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/2afb-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-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 521 and 0 Target number of residues in the AU: 521 Target solvent content: 0.6155 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 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: 97.203 3.200 Wilson plot Bfac: 59.24 12384 reflections ( 99.61 % complete ) and 0 restraints for refining 6189 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3110 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3278 (Rfree = 0.000) for 6189 atoms. Found 55 (55 requested) and removed 43 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 6344 seeds are put forward NCS extension: 0 residues added, 6344 seeds are put forward Round 1: 305 peptides, 57 chains. Longest chain 15 peptides. Score 0.357 Round 2: 409 peptides, 58 chains. Longest chain 23 peptides. Score 0.557 Round 3: 455 peptides, 51 chains. Longest chain 27 peptides. Score 0.676 Round 4: 461 peptides, 46 chains. Longest chain 31 peptides. Score 0.714 Round 5: 478 peptides, 47 chains. Longest chain 26 peptides. Score 0.729 Taking the results from Round 5 Chains 53, Residues 431, Estimated correctness of the model 71.1 % 12 chains (144 residues) have been docked in sequence Building loops using Loopy2018 53 chains (431 residues) following loop building 12 chains (144 residues) in sequence following loop building ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 9785 restraints for refining 5127 atoms. 7620 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2890 (Rfree = 0.000) for 5127 atoms. Found 46 (46 requested) and removed 79 (23 requested) atoms. Cycle 2: After refmac, R = 0.2777 (Rfree = 0.000) for 4989 atoms. Found 37 (44 requested) and removed 42 (22 requested) atoms. Cycle 3: After refmac, R = 0.2664 (Rfree = 0.000) for 4935 atoms. Found 29 (42 requested) and removed 36 (22 requested) atoms. Cycle 4: After refmac, R = 0.2443 (Rfree = 0.000) for 4900 atoms. Found 17 (41 requested) and removed 27 (22 requested) atoms. Cycle 5: After refmac, R = 0.2376 (Rfree = 0.000) for 4868 atoms. Found 13 (40 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 5040 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5053 seeds are put forward Round 1: 432 peptides, 54 chains. Longest chain 24 peptides. Score 0.624 Round 2: 471 peptides, 54 chains. Longest chain 24 peptides. Score 0.679 Round 3: 474 peptides, 51 chains. Longest chain 26 peptides. Score 0.701 Round 4: 482 peptides, 47 chains. Longest chain 26 peptides. Score 0.733 Round 5: 477 peptides, 51 chains. Longest chain 33 peptides. Score 0.705 Taking the results from Round 4 Chains 54, Residues 435, Estimated correctness of the model 71.9 % 10 chains (140 residues) have been docked in sequence Building loops using Loopy2018 54 chains (435 residues) following loop building 10 chains (140 residues) in sequence following loop building ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 9788 restraints for refining 5127 atoms. 7557 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2767 (Rfree = 0.000) for 5127 atoms. Found 33 (41 requested) and removed 50 (23 requested) atoms. Cycle 7: After refmac, R = 0.2670 (Rfree = 0.000) for 5062 atoms. Found 30 (40 requested) and removed 34 (22 requested) atoms. Cycle 8: After refmac, R = 0.2575 (Rfree = 0.000) for 5032 atoms. Found 18 (39 requested) and removed 34 (22 requested) atoms. Cycle 9: After refmac, R = 0.2513 (Rfree = 0.000) for 5000 atoms. Found 22 (37 requested) and removed 31 (22 requested) atoms. Cycle 10: After refmac, R = 0.2484 (Rfree = 0.000) for 4984 atoms. Found 21 (36 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.30 Search for helices and strands: 0 residues in 0 chains, 5149 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 5169 seeds are put forward Round 1: 431 peptides, 57 chains. Longest chain 24 peptides. Score 0.601 Round 2: 466 peptides, 51 chains. Longest chain 33 peptides. Score 0.691 Round 3: 468 peptides, 52 chains. Longest chain 25 peptides. Score 0.688 Round 4: 474 peptides, 54 chains. Longest chain 29 peptides. Score 0.683 Round 5: 477 peptides, 53 chains. Longest chain 26 peptides. Score 0.693 Taking the results from Round 5 Chains 57, Residues 424, Estimated correctness of the model 63.7 % 9 chains (123 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 9899 restraints for refining 5127 atoms. 7753 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2629 (Rfree = 0.000) for 5127 atoms. Found 24 (37 requested) and removed 47 (23 requested) atoms. Cycle 12: After refmac, R = 0.2453 (Rfree = 0.000) for 5068 atoms. Found 23 (36 requested) and removed 31 (22 requested) atoms. Cycle 13: After refmac, R = 0.2383 (Rfree = 0.000) for 5043 atoms. Found 19 (36 requested) and removed 26 (22 requested) atoms. Cycle 14: After refmac, R = 0.2374 (Rfree = 0.000) for 5022 atoms. Found 16 (36 requested) and removed 25 (22 requested) atoms. Cycle 15: After refmac, R = 0.2296 (Rfree = 0.000) for 5003 atoms. Found 15 (35 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 5166 seeds are put forward NCS extension: 14 residues added (11 deleted due to clashes), 5180 seeds are put forward Round 1: 415 peptides, 59 chains. Longest chain 17 peptides. Score 0.560 Round 2: 459 peptides, 56 chains. Longest chain 25 peptides. Score 0.650 Round 3: 468 peptides, 51 chains. Longest chain 27 peptides. Score 0.694 Round 4: 456 peptides, 49 chains. Longest chain 35 peptides. Score 0.690 Round 5: 456 peptides, 49 chains. Longest chain 32 peptides. Score 0.690 Taking the results from Round 3 Chains 57, Residues 417, Estimated correctness of the model 63.9 % 10 chains (117 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10031 restraints for refining 5126 atoms. 7932 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2579 (Rfree = 0.000) for 5126 atoms. Found 32 (37 requested) and removed 35 (23 requested) atoms. Cycle 17: After refmac, R = 0.2486 (Rfree = 0.000) for 5094 atoms. Found 31 (36 requested) and removed 34 (22 requested) atoms. Cycle 18: After refmac, R = 0.2413 (Rfree = 0.000) for 5076 atoms. Found 19 (36 requested) and removed 26 (22 requested) atoms. Cycle 19: After refmac, R = 0.2370 (Rfree = 0.000) for 5055 atoms. Found 17 (36 requested) and removed 25 (22 requested) atoms. Cycle 20: After refmac, R = 0.2302 (Rfree = 0.000) for 5031 atoms. Found 28 (36 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 5215 seeds are put forward NCS extension: 17 residues added (8 deleted due to clashes), 5232 seeds are put forward Round 1: 386 peptides, 51 chains. Longest chain 20 peptides. Score 0.571 Round 2: 432 peptides, 48 chains. Longest chain 25 peptides. Score 0.664 Round 3: 455 peptides, 50 chains. Longest chain 35 peptides. Score 0.683 Round 4: 460 peptides, 53 chains. Longest chain 22 peptides. Score 0.671 Round 5: 439 peptides, 51 chains. Longest chain 30 peptides. Score 0.654 Taking the results from Round 3 Chains 51, Residues 405, Estimated correctness of the model 61.5 % 8 chains (108 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10189 restraints for refining 5127 atoms. 8191 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2547 (Rfree = 0.000) for 5127 atoms. Found 37 (37 requested) and removed 36 (23 requested) atoms. Cycle 22: After refmac, R = 0.2490 (Rfree = 0.000) for 5108 atoms. Found 37 (37 requested) and removed 33 (23 requested) atoms. Cycle 23: After refmac, R = 0.2426 (Rfree = 0.000) for 5091 atoms. Found 34 (36 requested) and removed 29 (22 requested) atoms. Cycle 24: After refmac, R = 0.2452 (Rfree = 0.000) for 5081 atoms. Found 36 (36 requested) and removed 31 (22 requested) atoms. Cycle 25: After refmac, R = 0.2186 (Rfree = 0.000) for 5071 atoms. Found 13 (36 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 5233 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 5255 seeds are put forward Round 1: 391 peptides, 58 chains. Longest chain 18 peptides. Score 0.525 Round 2: 420 peptides, 51 chains. Longest chain 23 peptides. Score 0.626 Round 3: 418 peptides, 52 chains. Longest chain 21 peptides. Score 0.616 Round 4: 426 peptides, 52 chains. Longest chain 22 peptides. Score 0.628 Round 5: 446 peptides, 50 chains. Longest chain 28 peptides. Score 0.670 Taking the results from Round 5 Chains 54, Residues 396, Estimated correctness of the model 58.5 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10980 restraints for refining 5127 atoms. 9264 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2484 (Rfree = 0.000) for 5127 atoms. Found 37 (37 requested) and removed 35 (23 requested) atoms. Cycle 27: After refmac, R = 0.2481 (Rfree = 0.000) for 5118 atoms. Found 26 (37 requested) and removed 32 (23 requested) atoms. Cycle 28: After refmac, R = 0.2447 (Rfree = 0.000) for 5102 atoms. Found 27 (36 requested) and removed 28 (22 requested) atoms. Cycle 29: After refmac, R = 0.2349 (Rfree = 0.000) for 5090 atoms. Found 31 (36 requested) and removed 27 (22 requested) atoms. Cycle 30: After refmac, R = 0.2345 (Rfree = 0.000) for 5084 atoms. Found 32 (36 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 5246 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 5266 seeds are put forward Round 1: 377 peptides, 53 chains. Longest chain 20 peptides. Score 0.539 Round 2: 403 peptides, 49 chains. Longest chain 32 peptides. Score 0.614 Round 3: 429 peptides, 55 chains. Longest chain 20 peptides. Score 0.612 Round 4: 411 peptides, 47 chains. Longest chain 24 peptides. Score 0.640 Round 5: 422 peptides, 53 chains. Longest chain 21 peptides. Score 0.615 Taking the results from Round 4 Chains 49, Residues 364, Estimated correctness of the model 51.4 % 6 chains (76 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10506 restraints for refining 5126 atoms. 8772 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2522 (Rfree = 0.000) for 5126 atoms. Found 36 (37 requested) and removed 37 (23 requested) atoms. Cycle 32: After refmac, R = 0.2427 (Rfree = 0.000) for 5106 atoms. Found 26 (36 requested) and removed 27 (22 requested) atoms. Cycle 33: After refmac, R = 0.2398 (Rfree = 0.000) for 5083 atoms. Found 35 (36 requested) and removed 29 (22 requested) atoms. Cycle 34: After refmac, R = 0.2332 (Rfree = 0.000) for 5080 atoms. Found 26 (36 requested) and removed 24 (22 requested) atoms. Cycle 35: After refmac, R = 0.2306 (Rfree = 0.000) for 5071 atoms. Found 27 (36 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 5211 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 5233 seeds are put forward Round 1: 372 peptides, 57 chains. Longest chain 23 peptides. Score 0.497 Round 2: 407 peptides, 55 chains. Longest chain 23 peptides. Score 0.576 Round 3: 411 peptides, 54 chains. Longest chain 19 peptides. Score 0.590 Round 4: 425 peptides, 52 chains. Longest chain 20 peptides. Score 0.627 Round 5: 425 peptides, 57 chains. Longest chain 22 peptides. Score 0.591 Taking the results from Round 4 Chains 52, Residues 373, Estimated correctness of the model 48.1 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 11183 restraints for refining 5124 atoms. 9649 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2501 (Rfree = 0.000) for 5124 atoms. Found 37 (37 requested) and removed 33 (23 requested) atoms. Cycle 37: After refmac, R = 0.2400 (Rfree = 0.000) for 5116 atoms. Found 37 (37 requested) and removed 25 (23 requested) atoms. Cycle 38: After refmac, R = 0.2109 (Rfree = 0.000) for 5119 atoms. Found 13 (36 requested) and removed 23 (22 requested) atoms. Cycle 39: After refmac, R = 0.2032 (Rfree = 0.000) for 5104 atoms. Found 10 (36 requested) and removed 23 (22 requested) atoms. Cycle 40: After refmac, R = 0.2032 (Rfree = 0.000) for 5084 atoms. Found 5 (36 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 5222 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5240 seeds are put forward Round 1: 373 peptides, 54 chains. Longest chain 19 peptides. Score 0.524 Round 2: 408 peptides, 52 chains. Longest chain 20 peptides. Score 0.600 Round 3: 417 peptides, 49 chains. Longest chain 19 peptides. Score 0.635 Round 4: 403 peptides, 48 chains. Longest chain 17 peptides. Score 0.621 Round 5: 413 peptides, 47 chains. Longest chain 24 peptides. Score 0.643 Taking the results from Round 5 Chains 50, Residues 366, Estimated correctness of the model 52.1 % 8 chains (52 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10897 restraints for refining 5127 atoms. 9323 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2509 (Rfree = 0.000) for 5127 atoms. Found 37 (37 requested) and removed 33 (23 requested) atoms. Cycle 42: After refmac, R = 0.2424 (Rfree = 0.000) for 5111 atoms. Found 26 (37 requested) and removed 27 (23 requested) atoms. Cycle 43: After refmac, R = 0.2374 (Rfree = 0.000) for 5097 atoms. Found 34 (36 requested) and removed 25 (22 requested) atoms. Cycle 44: After refmac, R = 0.2329 (Rfree = 0.000) for 5098 atoms. Found 33 (36 requested) and removed 23 (22 requested) atoms. Cycle 45: After refmac, R = 0.2270 (Rfree = 0.000) for 5101 atoms. Found 31 (36 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 5277 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5297 seeds are put forward Round 1: 352 peptides, 55 chains. Longest chain 17 peptides. Score 0.475 Round 2: 405 peptides, 53 chains. Longest chain 19 peptides. Score 0.588 Round 3: 387 peptides, 46 chains. Longest chain 29 peptides. Score 0.610 Round 4: 377 peptides, 52 chains. Longest chain 19 peptides. Score 0.547 Round 5: 388 peptides, 49 chains. Longest chain 22 peptides. Score 0.589 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 341, Estimated correctness of the model 43.7 % 6 chains (79 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input Building loops using Loopy2018 48 chains (341 residues) following loop building 6 chains (79 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12384 reflections ( 99.61 % complete ) and 10480 restraints for refining 5127 atoms. 8799 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2460 (Rfree = 0.000) for 5127 atoms. Found 0 (37 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2427 (Rfree = 0.000) for 5079 atoms. Found 0 (36 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2390 (Rfree = 0.000) for 5045 atoms. Found 0 (36 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.2386 (Rfree = 0.000) for 5011 atoms. TimeTaking 65.3