Mon 24 Dec 01:11:14 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 2ooc-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ooc-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ooc-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-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/2ooc-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-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 01:11:20 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/2ooc-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-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 177 and 0 Target number of residues in the AU: 177 Target solvent content: 0.6327 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.53 Input MTZ file: 2ooc-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: 154 Cell parameters: 62.597 62.597 115.277 90.000 90.000 120.000 Input sequence file: 2ooc-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1808 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: 54.211 3.200 Wilson plot Bfac: 67.07 4629 reflections ( 99.81 % complete ) and 0 restraints for refining 2023 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3258 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3347 (Rfree = 0.000) for 2023 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 2090 seeds are put forward NCS extension: 0 residues added, 2090 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 13 peptides. Score 0.337 Round 2: 116 peptides, 19 chains. Longest chain 15 peptides. Score 0.436 Round 3: 123 peptides, 17 chains. Longest chain 17 peptides. Score 0.524 Round 4: 125 peptides, 18 chains. Longest chain 21 peptides. Score 0.511 Round 5: 119 peptides, 16 chains. Longest chain 18 peptides. Score 0.526 Taking the results from Round 5 Chains 17, Residues 103, Estimated correctness of the model 19.6 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3573 restraints for refining 1624 atoms. 3123 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3156 (Rfree = 0.000) for 1624 atoms. Found 10 (14 requested) and removed 20 (7 requested) atoms. Cycle 2: After refmac, R = 0.3057 (Rfree = 0.000) for 1577 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.2934 (Rfree = 0.000) for 1554 atoms. Found 11 (14 requested) and removed 15 (7 requested) atoms. Cycle 4: After refmac, R = 0.2647 (Rfree = 0.000) for 1528 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 5: After refmac, R = 0.2564 (Rfree = 0.000) for 1520 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.18 Search for helices and strands: 0 residues in 0 chains, 1597 seeds are put forward NCS extension: 0 residues added, 1597 seeds are put forward Round 1: 112 peptides, 18 chains. Longest chain 13 peptides. Score 0.438 Round 2: 117 peptides, 20 chains. Longest chain 13 peptides. Score 0.416 Round 3: 114 peptides, 17 chains. Longest chain 18 peptides. Score 0.475 Round 4: 125 peptides, 21 chains. Longest chain 11 peptides. Score 0.438 Round 5: 127 peptides, 17 chains. Longest chain 21 peptides. Score 0.545 Taking the results from Round 5 Chains 19, Residues 110, Estimated correctness of the model 25.4 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3209 restraints for refining 1558 atoms. 2742 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3044 (Rfree = 0.000) for 1558 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 7: After refmac, R = 0.2945 (Rfree = 0.000) for 1524 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.2960 (Rfree = 0.000) for 1505 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.2922 (Rfree = 0.000) for 1497 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.2836 (Rfree = 0.000) for 1489 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.19 Search for helices and strands: 0 residues in 0 chains, 1580 seeds are put forward NCS extension: 0 residues added, 1580 seeds are put forward Round 1: 118 peptides, 19 chains. Longest chain 13 peptides. Score 0.448 Round 2: 127 peptides, 18 chains. Longest chain 14 peptides. Score 0.522 Round 3: 126 peptides, 16 chains. Longest chain 18 peptides. Score 0.562 Round 4: 118 peptides, 15 chains. Longest chain 12 peptides. Score 0.545 Round 5: 123 peptides, 15 chains. Longest chain 17 peptides. Score 0.570 Taking the results from Round 5 Chains 15, Residues 108, Estimated correctness of the model 32.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3362 restraints for refining 1563 atoms. 2900 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3085 (Rfree = 0.000) for 1563 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 12: After refmac, R = 0.2884 (Rfree = 0.000) for 1530 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 13: After refmac, R = 0.2795 (Rfree = 0.000) for 1513 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2837 (Rfree = 0.000) for 1508 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.2582 (Rfree = 0.000) for 1499 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 1580 seeds are put forward NCS extension: 0 residues added, 1580 seeds are put forward Round 1: 109 peptides, 18 chains. Longest chain 15 peptides. Score 0.420 Round 2: 127 peptides, 20 chains. Longest chain 12 peptides. Score 0.474 Round 3: 128 peptides, 18 chains. Longest chain 17 peptides. Score 0.527 Round 4: 125 peptides, 20 chains. Longest chain 11 peptides. Score 0.463 Round 5: 130 peptides, 22 chains. Longest chain 12 peptides. Score 0.442 Taking the results from Round 3 Chains 18, Residues 110, Estimated correctness of the model 19.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3362 restraints for refining 1537 atoms. 2940 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2843 (Rfree = 0.000) for 1537 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2853 (Rfree = 0.000) for 1526 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.2656 (Rfree = 0.000) for 1514 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.2657 (Rfree = 0.000) for 1515 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.2532 (Rfree = 0.000) for 1515 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 1622 seeds are put forward NCS extension: 0 residues added, 1622 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.312 Round 2: 113 peptides, 16 chains. Longest chain 23 peptides. Score 0.494 Round 3: 109 peptides, 16 chains. Longest chain 14 peptides. Score 0.472 Round 4: 108 peptides, 16 chains. Longest chain 11 peptides. Score 0.466 Round 5: 106 peptides, 14 chains. Longest chain 13 peptides. Score 0.505 Taking the results from Round 5 Chains 14, Residues 92, Estimated correctness of the model 12.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3631 restraints for refining 1584 atoms. 3277 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2777 (Rfree = 0.000) for 1584 atoms. Found 11 (14 requested) and removed 19 (7 requested) atoms. Cycle 22: After refmac, R = 0.2731 (Rfree = 0.000) for 1568 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.2618 (Rfree = 0.000) for 1559 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.2571 (Rfree = 0.000) for 1555 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 25: After refmac, R = 0.2649 (Rfree = 0.000) for 1552 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 1666 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 1675 seeds are put forward Round 1: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.353 Round 2: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.406 Round 3: 114 peptides, 18 chains. Longest chain 14 peptides. Score 0.450 Round 4: 106 peptides, 17 chains. Longest chain 11 peptides. Score 0.428 Round 5: 101 peptides, 16 chains. Longest chain 11 peptides. Score 0.425 Taking the results from Round 3 Chains 18, Residues 96, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3531 restraints for refining 1607 atoms. 3136 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2658 (Rfree = 0.000) for 1607 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 27: After refmac, R = 0.2632 (Rfree = 0.000) for 1594 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 28: After refmac, R = 0.2570 (Rfree = 0.000) for 1584 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 29: After refmac, R = 0.2789 (Rfree = 0.000) for 1575 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 30: After refmac, R = 0.2764 (Rfree = 0.000) for 1574 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.17 Search for helices and strands: 0 residues in 0 chains, 1675 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1689 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.286 Round 2: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.364 Round 3: 98 peptides, 18 chains. Longest chain 11 peptides. Score 0.351 Round 4: 93 peptides, 15 chains. Longest chain 13 peptides. Score 0.403 Round 5: 98 peptides, 18 chains. Longest chain 12 peptides. Score 0.351 Taking the results from Round 4 Chains 15, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3644 restraints for refining 1594 atoms. 3347 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2897 (Rfree = 0.000) for 1594 atoms. Found 11 (14 requested) and removed 21 (7 requested) atoms. Cycle 32: After refmac, R = 0.2842 (Rfree = 0.000) for 1577 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Cycle 33: After refmac, R = 0.2714 (Rfree = 0.000) for 1569 atoms. Found 6 (14 requested) and removed 16 (7 requested) atoms. Cycle 34: After refmac, R = 0.2769 (Rfree = 0.000) for 1551 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.2763 (Rfree = 0.000) for 1544 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 1623 seeds are put forward NCS extension: 0 residues added, 1623 seeds are put forward Round 1: 88 peptides, 20 chains. Longest chain 6 peptides. Score 0.226 Round 2: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.353 Round 3: 101 peptides, 18 chains. Longest chain 12 peptides. Score 0.371 Round 4: 106 peptides, 19 chains. Longest chain 12 peptides. Score 0.375 Round 5: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.416 Taking the results from Round 5 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3542 restraints for refining 1552 atoms. 3211 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2732 (Rfree = 0.000) for 1552 atoms. Found 6 (13 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.2785 (Rfree = 0.000) for 1537 atoms. Found 6 (13 requested) and removed 14 (6 requested) atoms. Cycle 38: After refmac, R = 0.2648 (Rfree = 0.000) for 1524 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2700 (Rfree = 0.000) for 1513 atoms. Found 5 (13 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.2393 (Rfree = 0.000) for 1505 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 1584 seeds are put forward NCS extension: 0 residues added, 1584 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.335 Round 2: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.362 Round 3: 100 peptides, 16 chains. Longest chain 11 peptides. Score 0.419 Round 4: 101 peptides, 16 chains. Longest chain 11 peptides. Score 0.425 Round 5: 98 peptides, 16 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 4 Chains 16, Residues 85, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3359 restraints for refining 1544 atoms. 3002 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2864 (Rfree = 0.000) for 1544 atoms. Found 9 (13 requested) and removed 16 (6 requested) atoms. Cycle 42: After refmac, R = 0.3107 (Rfree = 0.000) for 1529 atoms. Found 11 (13 requested) and removed 18 (6 requested) atoms. Cycle 43: After refmac, R = 0.3001 (Rfree = 0.000) for 1513 atoms. Found 8 (13 requested) and removed 11 (6 requested) atoms. Cycle 44: After refmac, R = 0.3010 (Rfree = 0.000) for 1505 atoms. Found 3 (13 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.3058 (Rfree = 0.000) for 1492 atoms. Found 3 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 1558 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1569 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.222 Round 2: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.293 Round 3: 86 peptides, 17 chains. Longest chain 9 peptides. Score 0.300 Round 4: 85 peptides, 17 chains. Longest chain 6 peptides. Score 0.293 Round 5: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.368 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 76, 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 2ooc-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4629 reflections ( 99.81 % complete ) and 3032 restraints for refining 1455 atoms. 2744 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3195 (Rfree = 0.000) for 1455 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3193 (Rfree = 0.000) for 1446 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.3222 (Rfree = 0.000) for 1430 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.3337 (Rfree = 0.000) for 1420 atoms. TimeTaking 28.53