null Sun 23 Dec 22:22:46 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 2a2m-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.2-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/2a2m-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.2-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 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.2-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 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-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: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-3.2-parrot-hancs.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 4558 atoms. Observations/parameters ratio is 0.91 ------------------------------------------------------ Starting model: R = 0.3261 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2692 (Rfree = 0.000) for 4558 atoms. Found 40 (40 requested) and removed 40 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 2.35 Search for helices and strands: 0 residues in 0 chains, 4704 seeds are put forward NCS extension: 0 residues added, 4704 seeds are put forward Round 1: 337 peptides, 50 chains. Longest chain 16 peptides. Score 0.435 Round 2: 366 peptides, 40 chains. Longest chain 36 peptides. Score 0.551 Round 3: 380 peptides, 45 chains. Longest chain 36 peptides. Score 0.538 Round 4: 378 peptides, 39 chains. Longest chain 25 peptides. Score 0.575 Round 5: 366 peptides, 37 chains. Longest chain 39 peptides. Score 0.571 Taking the results from Round 4 Chains 45, Residues 339, Estimated correctness of the model 34.1 % 7 chains (80 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 7471 restraints for refining 3885 atoms. 5862 conditional restraints added. Observations/parameters ratio is 1.07 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2845 (Rfree = 0.000) for 3885 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. Cycle 2: After refmac, R = 0.2760 (Rfree = 0.000) for 3832 atoms. Found 34 (34 requested) and removed 21 (17 requested) atoms. Cycle 3: After refmac, R = 0.2776 (Rfree = 0.000) for 3808 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 4: After refmac, R = 0.2716 (Rfree = 0.000) for 3788 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 5: After refmac, R = 0.2708 (Rfree = 0.000) for 3772 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 2.38 Search for helices and strands: 0 residues in 0 chains, 3940 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 3964 seeds are put forward Round 1: 368 peptides, 44 chains. Longest chain 25 peptides. Score 0.527 Round 2: 378 peptides, 38 chains. Longest chain 25 peptides. Score 0.581 Round 3: 382 peptides, 36 chains. Longest chain 29 peptides. Score 0.599 Round 4: 376 peptides, 38 chains. Longest chain 30 peptides. Score 0.579 Round 5: 382 peptides, 41 chains. Longest chain 27 peptides. Score 0.567 Taking the results from Round 3 Chains 42, Residues 346, Estimated correctness of the model 40.8 % 6 chains (108 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6992 restraints for refining 3769 atoms. 5200 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2847 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 31 (16 requested) atoms. Cycle 7: After refmac, R = 0.2702 (Rfree = 0.000) for 3746 atoms. Found 33 (33 requested) and removed 22 (16 requested) atoms. Cycle 8: After refmac, R = 0.2692 (Rfree = 0.000) for 3728 atoms. Found 33 (33 requested) and removed 25 (16 requested) atoms. Cycle 9: After refmac, R = 0.2561 (Rfree = 0.000) for 3721 atoms. Found 33 (33 requested) and removed 28 (16 requested) atoms. Cycle 10: After refmac, R = 0.2603 (Rfree = 0.000) for 3717 atoms. Found 33 (33 requested) and removed 38 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 2.35 Search for helices and strands: 0 residues in 0 chains, 3885 seeds are put forward NCS extension: 38 residues added (8 deleted due to clashes), 3923 seeds are put forward Round 1: 361 peptides, 42 chains. Longest chain 26 peptides. Score 0.530 Round 2: 367 peptides, 37 chains. Longest chain 51 peptides. Score 0.573 Round 3: 374 peptides, 39 chains. Longest chain 43 peptides. Score 0.569 Round 4: 370 peptides, 40 chains. Longest chain 27 peptides. Score 0.557 Round 5: 373 peptides, 38 chains. Longest chain 34 peptides. Score 0.574 Taking the results from Round 5 Chains 45, Residues 335, Estimated correctness of the model 33.9 % 7 chains (111 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 7028 restraints for refining 3768 atoms. 5284 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2790 (Rfree = 0.000) for 3768 atoms. Found 33 (33 requested) and removed 23 (16 requested) atoms. Cycle 12: After refmac, R = 0.2579 (Rfree = 0.000) for 3757 atoms. Found 33 (33 requested) and removed 25 (16 requested) atoms. Cycle 13: After refmac, R = 0.2587 (Rfree = 0.000) for 3748 atoms. Found 33 (33 requested) and removed 25 (16 requested) atoms. Cycle 14: After refmac, R = 0.2567 (Rfree = 0.000) for 3744 atoms. Found 33 (33 requested) and removed 19 (16 requested) atoms. Cycle 15: After refmac, R = 0.2343 (Rfree = 0.000) for 3750 atoms. Found 32 (33 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 2.35 Search for helices and strands: 0 residues in 0 chains, 3932 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3944 seeds are put forward Round 1: 366 peptides, 38 chains. Longest chain 43 peptides. Score 0.565 Round 2: 384 peptides, 32 chains. Longest chain 43 peptides. Score 0.627 Round 3: 385 peptides, 34 chains. Longest chain 45 peptides. Score 0.616 Round 4: 383 peptides, 35 chains. Longest chain 31 peptides. Score 0.607 Round 5: 376 peptides, 43 chains. Longest chain 22 peptides. Score 0.545 Taking the results from Round 2 Chains 35, Residues 352, Estimated correctness of the model 48.1 % 7 chains (143 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6595 restraints for refining 3768 atoms. 4593 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2663 (Rfree = 0.000) for 3768 atoms. Found 33 (33 requested) and removed 28 (16 requested) atoms. Cycle 17: After refmac, R = 0.2544 (Rfree = 0.000) for 3748 atoms. Found 33 (33 requested) and removed 31 (16 requested) atoms. Cycle 18: After refmac, R = 0.2650 (Rfree = 0.000) for 3722 atoms. Found 33 (33 requested) and removed 38 (16 requested) atoms. Cycle 19: After refmac, R = 0.2450 (Rfree = 0.000) for 3704 atoms. Found 30 (33 requested) and removed 28 (16 requested) atoms. Cycle 20: After refmac, R = 0.2299 (Rfree = 0.000) for 3696 atoms. Found 33 (33 requested) and removed 30 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 2.34 Search for helices and strands: 0 residues in 0 chains, 3867 seeds are put forward NCS extension: 39 residues added (0 deleted due to clashes), 3906 seeds are put forward Round 1: 359 peptides, 38 chains. Longest chain 41 peptides. Score 0.555 Round 2: 376 peptides, 33 chains. Longest chain 38 peptides. Score 0.610 Round 3: 371 peptides, 33 chains. Longest chain 46 peptides. Score 0.604 Round 4: 372 peptides, 39 chains. Longest chain 26 peptides. Score 0.566 Round 5: 370 peptides, 39 chains. Longest chain 36 peptides. Score 0.564 Taking the results from Round 2 Chains 37, Residues 343, Estimated correctness of the model 43.7 % 9 chains (137 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6704 restraints for refining 3769 atoms. 4784 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2697 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 31 (16 requested) atoms. Cycle 22: After refmac, R = 0.2536 (Rfree = 0.000) for 3737 atoms. Found 33 (33 requested) and removed 26 (16 requested) atoms. Cycle 23: After refmac, R = 0.2476 (Rfree = 0.000) for 3716 atoms. Found 33 (33 requested) and removed 25 (16 requested) atoms. Cycle 24: After refmac, R = 0.2365 (Rfree = 0.000) for 3719 atoms. Found 28 (33 requested) and removed 22 (16 requested) atoms. Cycle 25: After refmac, R = 0.2395 (Rfree = 0.000) for 3718 atoms. Found 14 (33 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 2.31 Search for helices and strands: 0 residues in 0 chains, 3847 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 3882 seeds are put forward Round 1: 361 peptides, 41 chains. Longest chain 40 peptides. Score 0.537 Round 2: 372 peptides, 36 chains. Longest chain 45 peptides. Score 0.586 Round 3: 370 peptides, 36 chains. Longest chain 28 peptides. Score 0.583 Round 4: 357 peptides, 40 chains. Longest chain 23 peptides. Score 0.538 Round 5: 367 peptides, 39 chains. Longest chain 24 peptides. Score 0.559 Taking the results from Round 2 Chains 40, Residues 336, Estimated correctness of the model 37.2 % 10 chains (147 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6447 restraints for refining 3768 atoms. 4461 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2753 (Rfree = 0.000) for 3768 atoms. Found 33 (33 requested) and removed 34 (16 requested) atoms. Cycle 27: After refmac, R = 0.2589 (Rfree = 0.000) for 3745 atoms. Found 33 (33 requested) and removed 26 (16 requested) atoms. Cycle 28: After refmac, R = 0.2465 (Rfree = 0.000) for 3741 atoms. Found 26 (33 requested) and removed 21 (16 requested) atoms. Cycle 29: After refmac, R = 0.2454 (Rfree = 0.000) for 3728 atoms. Found 24 (33 requested) and removed 24 (16 requested) atoms. Cycle 30: After refmac, R = 0.2575 (Rfree = 0.000) for 3719 atoms. Found 33 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.33 Search for helices and strands: 0 residues in 0 chains, 3881 seeds are put forward NCS extension: 56 residues added (1 deleted due to clashes), 3937 seeds are put forward Round 1: 351 peptides, 35 chains. Longest chain 27 peptides. Score 0.564 Round 2: 379 peptides, 33 chains. Longest chain 51 peptides. Score 0.614 Round 3: 381 peptides, 31 chains. Longest chain 38 peptides. Score 0.629 Round 4: 378 peptides, 30 chains. Longest chain 30 peptides. Score 0.632 Round 5: 374 peptides, 33 chains. Longest chain 47 peptides. Score 0.608 Taking the results from Round 4 Chains 37, Residues 348, Estimated correctness of the model 49.4 % 11 chains (175 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6255 restraints for refining 3769 atoms. 4170 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2690 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 50 (16 requested) atoms. Cycle 32: After refmac, R = 0.2450 (Rfree = 0.000) for 3732 atoms. Found 33 (33 requested) and removed 21 (16 requested) atoms. Cycle 33: After refmac, R = 0.2331 (Rfree = 0.000) for 3720 atoms. Found 33 (33 requested) and removed 25 (16 requested) atoms. Cycle 34: After refmac, R = 0.2328 (Rfree = 0.000) for 3720 atoms. Found 29 (33 requested) and removed 22 (16 requested) atoms. Cycle 35: After refmac, R = 0.2224 (Rfree = 0.000) for 3721 atoms. Found 19 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 2.32 Search for helices and strands: 0 residues in 0 chains, 3893 seeds are put forward NCS extension: 16 residues added (9 deleted due to clashes), 3909 seeds are put forward Round 1: 365 peptides, 37 chains. Longest chain 32 peptides. Score 0.570 Round 2: 368 peptides, 30 chains. Longest chain 61 peptides. Score 0.619 Round 3: 386 peptides, 31 chains. Longest chain 37 peptides. Score 0.635 Round 4: 389 peptides, 34 chains. Longest chain 38 peptides. Score 0.621 Round 5: 364 peptides, 34 chains. Longest chain 50 peptides. Score 0.588 Taking the results from Round 3 Chains 32, Residues 355, Estimated correctness of the model 50.2 % 12 chains (216 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6045 restraints for refining 3769 atoms. 3768 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2791 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 40 (16 requested) atoms. Cycle 37: After refmac, R = 0.2654 (Rfree = 0.000) for 3742 atoms. Found 33 (33 requested) and removed 28 (16 requested) atoms. Cycle 38: After refmac, R = 0.2371 (Rfree = 0.000) for 3722 atoms. Found 33 (33 requested) and removed 29 (16 requested) atoms. Cycle 39: After refmac, R = 0.2346 (Rfree = 0.000) for 3718 atoms. Found 33 (33 requested) and removed 23 (16 requested) atoms. Cycle 40: After refmac, R = 0.2300 (Rfree = 0.000) for 3722 atoms. Found 33 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.33 Search for helices and strands: 0 residues in 0 chains, 3908 seeds are put forward NCS extension: 23 residues added (21 deleted due to clashes), 3931 seeds are put forward Round 1: 366 peptides, 30 chains. Longest chain 51 peptides. Score 0.617 Round 2: 377 peptides, 34 chains. Longest chain 37 peptides. Score 0.605 Round 3: 379 peptides, 30 chains. Longest chain 53 peptides. Score 0.633 Round 4: 378 peptides, 36 chains. Longest chain 19 peptides. Score 0.594 Round 5: 383 peptides, 35 chains. Longest chain 35 peptides. Score 0.607 Taking the results from Round 3 Chains 30, Residues 349, Estimated correctness of the model 49.7 % 10 chains (201 residues) have been docked in sequence ------------------------------------------------------ 16630 reflections ( 99.82 % complete ) and 6106 restraints for refining 3769 atoms. 3880 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2493 (Rfree = 0.000) for 3769 atoms. Found 33 (33 requested) and removed 28 (16 requested) atoms. Cycle 42: After refmac, R = 0.2283 (Rfree = 0.000) for 3765 atoms. Found 33 (33 requested) and removed 24 (16 requested) atoms. Cycle 43: After refmac, R = 0.2224 (Rfree = 0.000) for 3755 atoms. Found 18 (33 requested) and removed 23 (16 requested) atoms. Cycle 44: After refmac, R = 0.2156 (Rfree = 0.000) for 3734 atoms. Found 25 (33 requested) and removed 18 (16 requested) atoms. Cycle 45: After refmac, R = 0.2137 (Rfree = 0.000) for 3732 atoms. Found 23 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 2.35 Search for helices and strands: 0 residues in 0 chains, 3898 seeds are put forward NCS extension: 7 residues added (26 deleted due to clashes), 3905 seeds are put forward Round 1: 361 peptides, 36 chains. Longest chain 37 peptides. Score 0.571 Round 2: 389 peptides, 35 chains. Longest chain 27 peptides. Score 0.615 Round 3: 368 peptides, 34 chains. Longest chain 26 peptides. Score 0.594 Round 4: 379 peptides, 29 chains. Longest chain 34 peptides. Score 0.639 Round 5: 363 peptides, 38 chains. Longest chain 24 peptides. Score 0.560 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 350, Estimated correctness of the model 51.1 % 11 chains (206 residues) have been docked in sequence Sequence coverage is 58 % Consider running further cycles of model building using 2a2m-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 193 A and 200 A Built loop between residues 123 B and 136 B 28 chains (363 residues) following loop building 9 chains (224 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16630 reflections ( 99.82 % complete ) and 5801 restraints for refining 3768 atoms. 3389 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2645 (Rfree = 0.000) for 3768 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2604 (Rfree = 0.000) for 3724 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2485 (Rfree = 0.000) for 3691 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2247 (Rfree = 0.000) for 3663 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 04:50:16 GMT 2018 Job finished. TimeTaking 387.49 Used memory is bytes: 9298736