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 2hdo-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-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/2hdo-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-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 22:22:55 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/2hdo-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-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 141 and 0 Target number of residues in the AU: 141 Target solvent content: 0.6311 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 209 Adjusted target solvent content: 0.45 Input MTZ file: 2hdo-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: 169 Cell parameters: 87.040 87.040 47.290 90.000 90.000 120.000 Input sequence file: 2hdo-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1672 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.474 3.200 Wilson plot Bfac: 66.97 3461 reflections ( 99.68 % complete ) and 0 restraints for refining 1863 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3148 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2516 (Rfree = 0.000) for 1863 atoms. Found 13 (16 requested) and removed 180 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 1711 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.244 Round 2: 78 peptides, 15 chains. Longest chain 11 peptides. Score 0.329 Round 3: 88 peptides, 19 chains. Longest chain 7 peptides. Score 0.272 Round 4: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.364 Round 5: 83 peptides, 14 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 5 Chains 14, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3461 reflections ( 99.68 % complete ) and 3448 restraints for refining 1526 atoms. 3186 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2344 (Rfree = 0.000) for 1526 atoms. Found 11 (13 requested) and removed 31 (6 requested) atoms. Cycle 2: After refmac, R = 0.2097 (Rfree = 0.000) for 1498 atoms. Found 7 (13 requested) and removed 15 (6 requested) atoms. Cycle 3: After refmac, R = 0.2014 (Rfree = 0.000) for 1486 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2113 (Rfree = 0.000) for 1480 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 5: After refmac, R = 0.2539 (Rfree = 0.000) for 1476 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.40 Search for helices and strands: 0 residues in 0 chains, 1535 seeds are put forward Round 1: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.356 Round 2: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.416 Round 3: 116 peptides, 18 chains. Longest chain 19 peptides. Score 0.516 Round 4: 113 peptides, 17 chains. Longest chain 13 peptides. Score 0.525 Round 5: 114 peptides, 18 chains. Longest chain 15 peptides. Score 0.502 Taking the results from Round 4 Chains 17, Residues 96, Estimated correctness of the model 19.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3461 reflections ( 99.68 % complete ) and 3240 restraints for refining 1499 atoms. 2846 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2358 (Rfree = 0.000) for 1499 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 7: After refmac, R = 0.2253 (Rfree = 0.000) for 1492 atoms. Found 8 (13 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.2044 (Rfree = 0.000) for 1482 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 9: After refmac, R = 0.2024 (Rfree = 0.000) for 1472 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.2007 (Rfree = 0.000) for 1466 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 1530 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.414 Round 2: 125 peptides, 15 chains. Longest chain 17 peptides. Score 0.646 Round 3: 130 peptides, 16 chains. Longest chain 19 peptides. Score 0.649 Round 4: 142 peptides, 15 chains. Longest chain 22 peptides. Score 0.725 Round 5: 133 peptides, 16 chains. Longest chain 17 peptides. Score 0.664 Taking the results from Round 4 Chains 17, Residues 127, Estimated correctness of the model 70.3 % 4 chains (47 residues) have been docked in sequence Building loops using Loopy2018 17 chains (127 residues) following loop building 4 chains (47 residues) in sequence following loop building ------------------------------------------------------ 3461 reflections ( 99.68 % complete ) and 2771 restraints for refining 1527 atoms. 2101 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2579 (Rfree = 0.000) for 1527 atoms. Found 10 (13 requested) and removed 13 (6 requested) atoms. Cycle 12: After refmac, R = 0.2369 (Rfree = 0.000) for 1510 atoms. Found 5 (13 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2241 (Rfree = 0.000) for 1495 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.2664 (Rfree = 0.000) for 1478 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.2188 (Rfree = 0.000) for 1470 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.44 Search for helices and strands: 0 residues in 0 chains, 1541 seeds are put forward Round 1: 125 peptides, 17 chains. Longest chain 16 peptides. Score 0.598 Round 2: 129 peptides, 14 chains. Longest chain 21 peptides. Score 0.689 Round 3: 136 peptides, 13 chains. Longest chain 32 peptides. Score 0.739 Round 4: 132 peptides, 12 chains. Longest chain 31 peptides. Score 0.742 Round 5: 126 peptides, 12 chains. Longest chain 22 peptides. Score 0.717 Taking the results from Round 4 Chains 16, Residues 120, Estimated correctness of the model 73.6 % 2 chains (23 residues) have been docked in sequence Building loops using Loopy2018 16 chains (120 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ 3461 reflections ( 99.68 % complete ) and 2991 restraints for refining 1475 atoms. 2451 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2416 (Rfree = 0.000) for 1475 atoms. Found 10 (12 requested) and removed 11 (6 requested) atoms. Cycle 17: After refmac, R = 0.2308 (Rfree = 0.000) for 1470 atoms. Found 5 (11 requested) and removed 7 (6 requested) atoms. Cycle 18: After refmac, R = 0.2277 (Rfree = 0.000) for 1467 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2238 (Rfree = 0.000) for 1462 atoms. Found 0 (11 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2255 (Rfree = 0.000) for 1456 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 1534 seeds are put forward Round 1: 122 peptides, 17 chains. Longest chain 17 peptides. Score 0.580 Round 2: 122 peptides, 12 chains. Longest chain 22 peptides. Score 0.699 Round 3: 119 peptides, 15 chains. Longest chain 24 peptides. Score 0.614 Round 4: 109 peptides, 12 chains. Longest chain 20 peptides. Score 0.634 Round 5: 118 peptides, 13 chains. Longest chain 23 peptides. Score 0.658 Taking the results from Round 2 Chains 13, Residues 110, Estimated correctness of the model 65.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3461 reflections ( 99.68 % complete ) and 3313 restraints for refining 1514 atoms. 2847 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2290 (Rfree = 0.000) for 1514 atoms. Found 10 (10 requested) and removed 8 (6 requested) atoms. Cycle 22: After refmac, R = 0.2113 (Rfree = 0.000) for 1512 atoms. Found 3 (10 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.2016 (Rfree = 0.000) for 1508 atoms. Found 6 (10 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.1964 (Rfree = 0.000) for 1502 atoms. Found 4 (10 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1950 (Rfree = 0.000) for 1499 atoms. Found 2 (10 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 1556 seeds are put forward Round 1: 112 peptides, 18 chains. Longest chain 17 peptides. Score 0.489 Round 2: 142 peptides, 20 chains. Longest chain 17 peptides. Score 0.619 Round 3: 141 peptides, 20 chains. Longest chain 17 peptides. Score 0.613 Round 4: 147 peptides, 20 chains. Longest chain 18 peptides. Score 0.645 Round 5: 142 peptides, 18 chains. Longest chain 16 peptides. Score 0.664 Taking the results from Round 5 Chains 19, Residues 124, Estimated correctness of the model 57.2 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3461 reflections ( 99.68 % complete ) and 3226 restraints for refining 1526 atoms. 2697 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2260 (Rfree = 0.000) for 1526 atoms. Found 10 (10 requested) and removed 9 (6 requested) atoms. Cycle 27: After refmac, R = 0.2336 (Rfree = 0.000) for 1522 atoms. Found 10 (10 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.2234 (Rfree = 0.000) for 1518 atoms. Found 10 (10 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.2425 (Rfree = 0.000) for 1518 atoms. Found 10 (10 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.2027 (Rfree = 0.000) for 1515 atoms. Found 5 (10 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.44 Search for helices and strands: 0 residues in 0 chains, 1583 seeds are put forward Round 1: 107 peptides, 18 chains. Longest chain 15 peptides. Score 0.454 Round 2: 124 peptides, 15 chains. Longest chain 19 peptides. Score 0.641 Round 3: 121 peptides, 16 chains. Longest chain 22 peptides. Score 0.600 Round 4: 129 peptides, 17 chains. Longest chain 19 peptides. Score 0.620 Round 5: 123 peptides, 16 chains. Longest chain 17 peptides. Score 0.611 Taking the results from Round 2 Chains 16, Residues 109, Estimated correctness of the model 51.6 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3461 reflections ( 99.68 % complete ) and 3343 restraints for refining 1527 atoms. 2862 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2221 (Rfree = 0.000) for 1527 atoms. Found 7 (10 requested) and removed 10 (6 requested) atoms. Cycle 32: After refmac, R = 0.2304 (Rfree = 0.000) for 1523 atoms. Found 8 (10 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2526 (Rfree = 0.000) for 1518 atoms. Found 10 (10 requested) and removed 9 (6 requested) atoms. Cycle 34: After refmac, R = 0.2434 (Rfree = 0.000) for 1506 atoms. Found 10 (10 requested) and removed 11 (6 requested) atoms. Cycle 35: After refmac, R = 0.2367 (Rfree = 0.000) for 1503 atoms. Found 10 (10 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 1562 seeds are put forward Round 1: 95 peptides, 16 chains. Longest chain 15 peptides. Score 0.429 Round 2: 116 peptides, 17 chains. Longest chain 15 peptides. Score 0.544 Round 3: 112 peptides, 14 chains. Longest chain 18 peptides. Score 0.600 Round 4: 116 peptides, 16 chains. Longest chain 15 peptides. Score 0.571 Round 5: 114 peptides, 15 chains. Longest chain 15 peptides. Score 0.585 Taking the results from Round 3 Chains 14, Residues 98, Estimated correctness of the model 41.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3461 reflections ( 99.68 % complete ) and 3365 restraints for refining 1509 atoms. 2987 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2427 (Rfree = 0.000) for 1509 atoms. Found 9 (10 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.2256 (Rfree = 0.000) for 1501 atoms. Found 5 (10 requested) and removed 12 (6 requested) atoms. Cycle 38: After refmac, R = 0.1965 (Rfree = 0.000) for 1493 atoms. Found 2 (10 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.1839 (Rfree = 0.000) for 1482 atoms. Found 2 (10 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.1846 (Rfree = 0.000) for 1474 atoms. Found 3 (10 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 1533 seeds are put forward Round 1: 92 peptides, 17 chains. Longest chain 14 peptides. Score 0.373 Round 2: 105 peptides, 14 chains. Longest chain 15 peptides. Score 0.558 Round 3: 109 peptides, 14 chains. Longest chain 16 peptides. Score 0.582 Round 4: 105 peptides, 14 chains. Longest chain 16 peptides. Score 0.558 Round 5: 110 peptides, 15 chains. Longest chain 16 peptides. Score 0.561 Taking the results from Round 3 Chains 14, Residues 95, Estimated correctness of the model 36.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3461 reflections ( 99.68 % complete ) and 3302 restraints for refining 1477 atoms. 2936 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2000 (Rfree = 0.000) for 1477 atoms. Found 5 (10 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.1885 (Rfree = 0.000) for 1470 atoms. Found 2 (10 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.1801 (Rfree = 0.000) for 1466 atoms. Found 2 (10 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1797 (Rfree = 0.000) for 1462 atoms. Found 1 (10 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1846 (Rfree = 0.000) for 1456 atoms. Found 0 (10 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 1502 seeds are put forward Round 1: 86 peptides, 15 chains. Longest chain 16 peptides. Score 0.393 Round 2: 102 peptides, 16 chains. Longest chain 14 peptides. Score 0.480 Round 3: 100 peptides, 14 chains. Longest chain 20 peptides. Score 0.526 Round 4: 107 peptides, 16 chains. Longest chain 17 peptides. Score 0.514 Round 5: 114 peptides, 16 chains. Longest chain 17 peptides. Score 0.559 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 98, Estimated correctness of the model 29.5 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2hdo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3461 reflections ( 99.68 % complete ) and 3251 restraints for refining 1492 atoms. 2842 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2306 (Rfree = 0.000) for 1492 atoms. Found 0 (10 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2137 (Rfree = 0.000) for 1485 atoms. Found 0 (10 requested) and removed 1 (6 requested) atoms. Cycle 48: After refmac, R = 0.2108 (Rfree = 0.000) for 1483 atoms. Found 0 (10 requested) and removed 1 (6 requested) atoms. Cycle 49: After refmac, R = 0.2118 (Rfree = 0.000) for 1482 atoms. TimeTaking 30.02