null Tue 25 Dec 19:27:55 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 2itb-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2itb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2itb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-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/2itb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-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 ============================================================ Tue 25 Dec 19:28:05 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/2itb-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-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 221 and 0 Target number of residues in the AU: 221 Target solvent content: 0.6695 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-4.0-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: 19 Cell parameters: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.65 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: 53.913 4.000 Wilson plot Bfac: 92.15 3315 reflections ( 99.55 % complete ) and 0 restraints for refining 3662 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3605 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3292 (Rfree = 0.000) for 3662 atoms. Found 6 (17 requested) and removed 80 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.97 4.67 Search for helices and strands: 0 residues in 0 chains, 3653 seeds are put forward NCS extension: 0 residues added, 3653 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.200 Round 2: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.240 Round 3: 98 peptides, 20 chains. Longest chain 8 peptides. Score 0.268 Round 4: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.306 Round 5: 96 peptides, 19 chains. Longest chain 9 peptides. Score 0.280 Taking the results from Round 4 Chains 19, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 7468 restraints for refining 2977 atoms. 7159 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3019 (Rfree = 0.000) for 2977 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 2: After refmac, R = 0.2858 (Rfree = 0.000) for 2931 atoms. Found 9 (14 requested) and removed 26 (7 requested) atoms. Cycle 3: After refmac, R = 0.2721 (Rfree = 0.000) for 2904 atoms. Found 1 (13 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2794 (Rfree = 0.000) for 2892 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2769 (Rfree = 0.000) for 2890 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.99 4.70 Search for helices and strands: 0 residues in 0 chains, 2983 seeds are put forward NCS extension: 0 residues added, 2983 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 7 peptides. Score 0.237 Round 2: 129 peptides, 23 chains. Longest chain 18 peptides. Score 0.359 Round 3: 144 peptides, 25 chains. Longest chain 15 peptides. Score 0.388 Round 4: 148 peptides, 24 chains. Longest chain 20 peptides. Score 0.425 Round 5: 158 peptides, 25 chains. Longest chain 20 peptides. Score 0.449 Taking the results from Round 5 Chains 27, Residues 133, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 5970 restraints for refining 2557 atoms. 5427 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2838 (Rfree = 0.000) for 2557 atoms. Found 6 (12 requested) and removed 13 (6 requested) atoms. Cycle 7: After refmac, R = 0.2682 (Rfree = 0.000) for 2534 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.2611 (Rfree = 0.000) for 2518 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2627 (Rfree = 0.000) for 2512 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2570 (Rfree = 0.000) for 2506 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.97 4.67 Search for helices and strands: 0 residues in 0 chains, 2641 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 2667 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 9 peptides. Score 0.285 Round 2: 154 peptides, 28 chains. Longest chain 10 peptides. Score 0.375 Round 3: 151 peptides, 25 chains. Longest chain 12 peptides. Score 0.419 Round 4: 150 peptides, 22 chains. Longest chain 15 peptides. Score 0.470 Round 5: 154 peptides, 22 chains. Longest chain 16 peptides. Score 0.487 Taking the results from Round 5 Chains 22, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6035 restraints for refining 2580 atoms. 5529 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2865 (Rfree = 0.000) for 2580 atoms. Found 8 (12 requested) and removed 12 (6 requested) atoms. Cycle 12: After refmac, R = 0.2657 (Rfree = 0.000) for 2565 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. Cycle 13: After refmac, R = 0.2596 (Rfree = 0.000) for 2546 atoms. Found 2 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2553 (Rfree = 0.000) for 2533 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2487 (Rfree = 0.000) for 2526 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.91 4.60 Search for helices and strands: 0 residues in 0 chains, 2659 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2677 seeds are put forward Round 1: 123 peptides, 23 chains. Longest chain 8 peptides. Score 0.330 Round 2: 143 peptides, 19 chains. Longest chain 18 peptides. Score 0.497 Round 3: 136 peptides, 21 chains. Longest chain 13 peptides. Score 0.430 Round 4: 144 peptides, 22 chains. Longest chain 14 peptides. Score 0.445 Round 5: 148 peptides, 20 chains. Longest chain 19 peptides. Score 0.499 Taking the results from Round 5 Chains 20, Residues 128, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 5983 restraints for refining 2602 atoms. 5470 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2701 (Rfree = 0.000) for 2602 atoms. Found 6 (12 requested) and removed 23 (6 requested) atoms. Cycle 17: After refmac, R = 0.2649 (Rfree = 0.000) for 2580 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.2593 (Rfree = 0.000) for 2573 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.2554 (Rfree = 0.000) for 2568 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2569 (Rfree = 0.000) for 2560 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.97 4.67 Search for helices and strands: 0 residues in 0 chains, 2662 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2676 seeds are put forward Round 1: 143 peptides, 27 chains. Longest chain 12 peptides. Score 0.344 Round 2: 163 peptides, 24 chains. Longest chain 15 peptides. Score 0.487 Round 3: 154 peptides, 23 chains. Longest chain 18 peptides. Score 0.469 Round 4: 151 peptides, 21 chains. Longest chain 16 peptides. Score 0.493 Round 5: 157 peptides, 23 chains. Longest chain 17 peptides. Score 0.481 Taking the results from Round 4 Chains 21, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6278 restraints for refining 2650 atoms. 5779 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2883 (Rfree = 0.000) for 2650 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. Cycle 22: After refmac, R = 0.2752 (Rfree = 0.000) for 2641 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.2754 (Rfree = 0.000) for 2628 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.2727 (Rfree = 0.000) for 2623 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2716 (Rfree = 0.000) for 2611 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.98 4.68 Search for helices and strands: 0 residues in 0 chains, 2739 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 2768 seeds are put forward Round 1: 123 peptides, 26 chains. Longest chain 8 peptides. Score 0.267 Round 2: 139 peptides, 24 chains. Longest chain 10 peptides. Score 0.385 Round 3: 131 peptides, 20 chains. Longest chain 11 peptides. Score 0.427 Round 4: 139 peptides, 20 chains. Longest chain 13 peptides. Score 0.462 Round 5: 147 peptides, 22 chains. Longest chain 13 peptides. Score 0.458 Taking the results from Round 4 Chains 20, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6337 restraints for refining 2675 atoms. 5881 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2908 (Rfree = 0.000) for 2675 atoms. Found 7 (12 requested) and removed 15 (6 requested) atoms. Cycle 27: After refmac, R = 0.2743 (Rfree = 0.000) for 2661 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2777 (Rfree = 0.000) for 2648 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2669 (Rfree = 0.000) for 2642 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2637 (Rfree = 0.000) for 2636 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.96 4.66 Search for helices and strands: 0 residues in 0 chains, 2744 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2760 seeds are put forward Round 1: 86 peptides, 20 chains. Longest chain 7 peptides. Score 0.202 Round 2: 114 peptides, 21 chains. Longest chain 12 peptides. Score 0.328 Round 3: 114 peptides, 21 chains. Longest chain 12 peptides. Score 0.328 Round 4: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.376 Round 5: 115 peptides, 19 chains. Longest chain 14 peptides. Score 0.375 Taking the results from Round 4 Chains 21, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6086 restraints for refining 2542 atoms. 5695 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2812 (Rfree = 0.000) for 2542 atoms. Found 6 (12 requested) and removed 16 (6 requested) atoms. Cycle 32: After refmac, R = 0.2740 (Rfree = 0.000) for 2525 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.2713 (Rfree = 0.000) for 2517 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2685 (Rfree = 0.000) for 2509 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2677 (Rfree = 0.000) for 2503 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.90 4.59 Search for helices and strands: 0 residues in 0 chains, 2603 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2616 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 7 peptides. Score 0.239 Round 2: 125 peptides, 22 chains. Longest chain 14 peptides. Score 0.360 Round 3: 133 peptides, 22 chains. Longest chain 16 peptides. Score 0.397 Round 4: 134 peptides, 23 chains. Longest chain 12 peptides. Score 0.382 Round 5: 142 peptides, 22 chains. Longest chain 16 peptides. Score 0.437 Taking the results from Round 5 Chains 23, Residues 120, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 5800 restraints for refining 2543 atoms. 5299 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2735 (Rfree = 0.000) for 2543 atoms. Found 8 (12 requested) and removed 21 (6 requested) atoms. Cycle 37: After refmac, R = 0.2583 (Rfree = 0.000) for 2518 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2519 (Rfree = 0.000) for 2509 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.2456 (Rfree = 0.000) for 2499 atoms. Found 0 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2443 (Rfree = 0.000) for 2490 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.92 4.61 Search for helices and strands: 0 residues in 0 chains, 2595 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2610 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 7 peptides. Score 0.250 Round 2: 128 peptides, 24 chains. Longest chain 14 peptides. Score 0.333 Round 3: 117 peptides, 21 chains. Longest chain 14 peptides. Score 0.343 Round 4: 120 peptides, 21 chains. Longest chain 13 peptides. Score 0.357 Round 5: 117 peptides, 19 chains. Longest chain 14 peptides. Score 0.384 Taking the results from Round 5 Chains 19, Residues 98, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 5965 restraints for refining 2545 atoms. 5581 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2506 (Rfree = 0.000) for 2545 atoms. Found 4 (12 requested) and removed 14 (6 requested) atoms. Cycle 42: After refmac, R = 0.2419 (Rfree = 0.000) for 2531 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2426 (Rfree = 0.000) for 2527 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2438 (Rfree = 0.000) for 2519 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2391 (Rfree = 0.000) for 2516 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.94 4.64 Search for helices and strands: 0 residues in 0 chains, 2620 seeds are put forward NCS extension: 0 residues added, 2620 seeds are put forward Round 1: 89 peptides, 19 chains. Longest chain 9 peptides. Score 0.242 Round 2: 102 peptides, 17 chains. Longest chain 14 peptides. Score 0.355 Round 3: 111 peptides, 20 chains. Longest chain 7 peptides. Score 0.334 Round 4: 112 peptides, 18 chains. Longest chain 18 peptides. Score 0.382 Round 5: 111 peptides, 20 chains. Longest chain 12 peptides. Score 0.334 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2itb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3315 reflections ( 99.55 % complete ) and 5934 restraints for refining 2504 atoms. 5576 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2692 (Rfree = 0.000) for 2504 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2559 (Rfree = 0.000) for 2495 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2541 (Rfree = 0.000) for 2489 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2524 (Rfree = 0.000) for 2484 atoms. Found 0 (11 requested) and removed 4 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:13:53 GMT 2018 Job finished. TimeTaking 45.96 Used memory is bytes: 7514856