Sun 23 Dec 22:22:56 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 2ooc-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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/2ooc-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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 22:23:05 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/2ooc-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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 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-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: 154 Cell parameters: 62.597 62.597 115.277 90.000 90.000 120.000 Input sequence file: 2ooc-3.2-parrot-hancs.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 1990 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3316 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3223 (Rfree = 0.000) for 1990 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 0 residues added, 2050 seeds are put forward Round 1: 101 peptides, 19 chains. Longest chain 14 peptides. Score 0.343 Round 2: 112 peptides, 16 chains. Longest chain 23 peptides. Score 0.489 Round 3: 124 peptides, 20 chains. Longest chain 13 peptides. Score 0.457 Round 4: 127 peptides, 15 chains. Longest chain 28 peptides. Score 0.589 Round 5: 123 peptides, 16 chains. Longest chain 24 peptides. Score 0.547 Taking the results from Round 4 Chains 17, Residues 112, Estimated correctness of the model 38.1 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4629 reflections ( 99.81 % complete ) and 3296 restraints for refining 1648 atoms. 2717 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2792 (Rfree = 0.000) for 1648 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 2: After refmac, R = 0.2741 (Rfree = 0.000) for 1607 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 3: After refmac, R = 0.2598 (Rfree = 0.000) for 1594 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 4: After refmac, R = 0.2529 (Rfree = 0.000) for 1578 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 5: After refmac, R = 0.2639 (Rfree = 0.000) for 1568 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 1649 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 1689 seeds are put forward Round 1: 117 peptides, 18 chains. Longest chain 16 peptides. Score 0.467 Round 2: 122 peptides, 16 chains. Longest chain 16 peptides. Score 0.542 Round 3: 124 peptides, 18 chains. Longest chain 16 peptides. Score 0.506 Round 4: 121 peptides, 17 chains. Longest chain 16 peptides. Score 0.513 Round 5: 135 peptides, 15 chains. Longest chain 20 peptides. Score 0.625 Taking the results from Round 5 Chains 17, Residues 120, Estimated correctness of the model 47.6 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4629 reflections ( 99.81 % complete ) and 3259 restraints for refining 1635 atoms. 2682 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3330 (Rfree = 0.000) for 1635 atoms. Found 9 (14 requested) and removed 35 (7 requested) atoms. Cycle 7: After refmac, R = 0.3034 (Rfree = 0.000) for 1589 atoms. Found 12 (14 requested) and removed 19 (7 requested) atoms. Cycle 8: After refmac, R = 0.2871 (Rfree = 0.000) for 1567 atoms. Found 2 (14 requested) and removed 16 (7 requested) atoms. Cycle 9: After refmac, R = 0.2704 (Rfree = 0.000) for 1538 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2584 (Rfree = 0.000) for 1527 atoms. Found 3 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 1611 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 1639 seeds are put forward Round 1: 98 peptides, 15 chains. Longest chain 16 peptides. Score 0.433 Round 2: 117 peptides, 17 chains. Longest chain 13 peptides. Score 0.492 Round 3: 112 peptides, 18 chains. Longest chain 11 peptides. Score 0.438 Round 4: 128 peptides, 15 chains. Longest chain 26 peptides. Score 0.594 Round 5: 134 peptides, 18 chains. Longest chain 22 peptides. Score 0.557 Taking the results from Round 4 Chains 16, Residues 113, Estimated correctness of the model 39.4 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 2996 restraints for refining 1565 atoms. 2425 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3422 (Rfree = 0.000) for 1565 atoms. Found 14 (14 requested) and removed 42 (7 requested) atoms. Cycle 12: After refmac, R = 0.3205 (Rfree = 0.000) for 1522 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 13: After refmac, R = 0.3089 (Rfree = 0.000) for 1493 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 14: After refmac, R = 0.3246 (Rfree = 0.000) for 1474 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 15: After refmac, R = 0.3048 (Rfree = 0.000) for 1460 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.49 Search for helices and strands: 0 residues in 0 chains, 1540 seeds are put forward NCS extension: 0 residues added, 1540 seeds are put forward Round 1: 117 peptides, 18 chains. Longest chain 22 peptides. Score 0.467 Round 2: 123 peptides, 20 chains. Longest chain 15 peptides. Score 0.451 Round 3: 121 peptides, 16 chains. Longest chain 28 peptides. Score 0.537 Round 4: 117 peptides, 15 chains. Longest chain 26 peptides. Score 0.540 Round 5: 117 peptides, 17 chains. Longest chain 16 peptides. Score 0.492 Taking the results from Round 4 Chains 15, Residues 102, Estimated correctness of the model 23.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3301 restraints for refining 1513 atoms. 2908 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3343 (Rfree = 0.000) for 1513 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 17: After refmac, R = 0.3221 (Rfree = 0.000) for 1492 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.3096 (Rfree = 0.000) for 1480 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 19: After refmac, R = 0.3047 (Rfree = 0.000) for 1474 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 20: After refmac, R = 0.3176 (Rfree = 0.000) for 1471 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.36 Search for helices and strands: 0 residues in 0 chains, 1579 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1596 seeds are put forward Round 1: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.349 Round 2: 102 peptides, 14 chains. Longest chain 15 peptides. Score 0.483 Round 3: 104 peptides, 16 chains. Longest chain 12 peptides. Score 0.443 Round 4: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.451 Round 5: 110 peptides, 14 chains. Longest chain 14 peptides. Score 0.527 Taking the results from Round 5 Chains 14, Residues 96, Estimated correctness of the model 19.9 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3241 restraints for refining 1595 atoms. 2752 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3165 (Rfree = 0.000) for 1595 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 22: After refmac, R = 0.2943 (Rfree = 0.000) for 1566 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 23: After refmac, R = 0.2990 (Rfree = 0.000) for 1535 atoms. Found 12 (13 requested) and removed 16 (6 requested) atoms. Cycle 24: After refmac, R = 0.3239 (Rfree = 0.000) for 1515 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 25: After refmac, R = 0.2910 (Rfree = 0.000) for 1502 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 1576 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1593 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 11 peptides. Score 0.342 Round 2: 105 peptides, 17 chains. Longest chain 15 peptides. Score 0.422 Round 3: 101 peptides, 16 chains. Longest chain 19 peptides. Score 0.425 Round 4: 100 peptides, 15 chains. Longest chain 17 peptides. Score 0.445 Round 5: 99 peptides, 15 chains. Longest chain 15 peptides. Score 0.439 Taking the results from Round 4 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3481 restraints for refining 1536 atoms. 3156 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3397 (Rfree = 0.000) for 1536 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 27: After refmac, R = 0.3271 (Rfree = 0.000) for 1519 atoms. Found 7 (13 requested) and removed 15 (6 requested) atoms. Cycle 28: After refmac, R = 0.3403 (Rfree = 0.000) for 1498 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 29: After refmac, R = 0.3162 (Rfree = 0.000) for 1478 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.3305 (Rfree = 0.000) for 1471 atoms. Found 11 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 1591 seeds are put forward NCS extension: 0 residues added, 1591 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 8 peptides. Score 0.212 Round 2: 100 peptides, 20 chains. Longest chain 10 peptides. Score 0.309 Round 3: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.323 Round 4: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.371 Round 5: 103 peptides, 20 chains. Longest chain 9 peptides. Score 0.329 Taking the results from Round 4 Chains 18, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3397 restraints for refining 1509 atoms. 3083 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3007 (Rfree = 0.000) for 1509 atoms. Found 11 (13 requested) and removed 18 (6 requested) atoms. Cycle 32: After refmac, R = 0.3018 (Rfree = 0.000) for 1486 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.3112 (Rfree = 0.000) for 1476 atoms. Found 6 (13 requested) and removed 11 (6 requested) atoms. Cycle 34: After refmac, R = 0.3103 (Rfree = 0.000) for 1463 atoms. Found 6 (13 requested) and removed 14 (6 requested) atoms. Cycle 35: After refmac, R = 0.3184 (Rfree = 0.000) for 1452 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 1535 seeds are put forward NCS extension: 0 residues added, 1535 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 7 peptides. Score 0.227 Round 2: 86 peptides, 16 chains. Longest chain 12 peptides. Score 0.329 Round 3: 92 peptides, 15 chains. Longest chain 13 peptides. Score 0.396 Round 4: 89 peptides, 14 chains. Longest chain 13 peptides. Score 0.405 Round 5: 91 peptides, 15 chains. Longest chain 13 peptides. Score 0.390 Taking the results from Round 4 Chains 14, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3207 restraints for refining 1459 atoms. 2921 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3142 (Rfree = 0.000) for 1459 atoms. Found 11 (13 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.3165 (Rfree = 0.000) for 1446 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.3249 (Rfree = 0.000) for 1437 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.3195 (Rfree = 0.000) for 1435 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 40: After refmac, R = 0.3172 (Rfree = 0.000) for 1425 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.67 Search for helices and strands: 0 residues in 0 chains, 1485 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1494 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 5 peptides. Score 0.206 Round 2: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.351 Round 3: 75 peptides, 12 chains. Longest chain 10 peptides. Score 0.372 Round 4: 87 peptides, 14 chains. Longest chain 10 peptides. Score 0.393 Round 5: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.342 Taking the results from Round 4 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4629 reflections ( 99.81 % complete ) and 3047 restraints for refining 1425 atoms. 2769 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3441 (Rfree = 0.000) for 1425 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.3150 (Rfree = 0.000) for 1417 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.3281 (Rfree = 0.000) for 1420 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.3624 (Rfree = 0.000) for 1420 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 45: After refmac, R = 0.3108 (Rfree = 0.000) for 1412 atoms. Found 10 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 1491 seeds are put forward NCS extension: 0 residues added, 1491 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 7 peptides. Score 0.230 Round 2: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.373 Round 3: 93 peptides, 16 chains. Longest chain 9 peptides. Score 0.375 Round 4: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.388 Round 5: 96 peptides, 17 chains. Longest chain 11 peptides. Score 0.366 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 79, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2ooc-3_warpNtrace.pdb as input Building loops using Loopy2018 16 chains (79 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4629 reflections ( 99.81 % complete ) and 3019 restraints for refining 1446 atoms. 2703 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3271 (Rfree = 0.000) for 1446 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3402 (Rfree = 0.000) for 1428 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.3108 (Rfree = 0.000) for 1415 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.3116 (Rfree = 0.000) for 1405 atoms. TimeTaking 31.05