null Sun 23 Dec 22:22:53 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-3.6-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 22:23:03 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-3.6-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 134 and 0 Target number of residues in the AU: 134 Target solvent content: 0.6494 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 77.04 2441 reflections ( 99.59 % complete ) and 0 restraints for refining 1871 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3249 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2682 (Rfree = 0.000) for 1871 atoms. Found 11 (12 requested) and removed 56 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 1851 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 11 peptides. Score 0.310 Round 2: 104 peptides, 18 chains. Longest chain 13 peptides. Score 0.432 Round 3: 119 peptides, 19 chains. Longest chain 13 peptides. Score 0.507 Round 4: 118 peptides, 18 chains. Longest chain 13 peptides. Score 0.529 Round 5: 120 peptides, 15 chains. Longest chain 29 peptides. Score 0.620 Taking the results from Round 5 Chains 15, Residues 105, Estimated correctness of the model 22.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2441 reflections ( 99.59 % complete ) and 3433 restraints for refining 1516 atoms. 3028 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2290 (Rfree = 0.000) for 1516 atoms. Found 5 (9 requested) and removed 15 (4 requested) atoms. Cycle 2: After refmac, R = 0.2163 (Rfree = 0.000) for 1487 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 3: After refmac, R = 0.2032 (Rfree = 0.000) for 1471 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.1782 (Rfree = 0.000) for 1465 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.1883 (Rfree = 0.000) for 1459 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 1539 seeds are put forward Round 1: 101 peptides, 18 chains. Longest chain 11 peptides. Score 0.410 Round 2: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.492 Round 3: 126 peptides, 17 chains. Longest chain 17 peptides. Score 0.603 Round 4: 124 peptides, 18 chains. Longest chain 15 peptides. Score 0.566 Round 5: 126 peptides, 18 chains. Longest chain 13 peptides. Score 0.578 Taking the results from Round 3 Chains 17, Residues 109, Estimated correctness of the model 15.8 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2441 reflections ( 99.59 % complete ) and 3081 restraints for refining 1422 atoms. 2636 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2057 (Rfree = 0.000) for 1422 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 7: After refmac, R = 0.1940 (Rfree = 0.000) for 1397 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 8: After refmac, R = 0.1764 (Rfree = 0.000) for 1385 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.1867 (Rfree = 0.000) for 1381 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.1813 (Rfree = 0.000) for 1379 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 1450 seeds are put forward Round 1: 102 peptides, 17 chains. Longest chain 15 peptides. Score 0.449 Round 2: 110 peptides, 17 chains. Longest chain 16 peptides. Score 0.505 Round 3: 128 peptides, 17 chains. Longest chain 17 peptides. Score 0.615 Round 4: 136 peptides, 17 chains. Longest chain 17 peptides. Score 0.656 Round 5: 125 peptides, 19 chains. Longest chain 15 peptides. Score 0.546 Taking the results from Round 4 Chains 19, Residues 119, Estimated correctness of the model 35.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2441 reflections ( 99.59 % complete ) and 2921 restraints for refining 1420 atoms. 2429 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2056 (Rfree = 0.000) for 1420 atoms. Found 5 (9 requested) and removed 10 (4 requested) atoms. Cycle 12: After refmac, R = 0.1904 (Rfree = 0.000) for 1405 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.1708 (Rfree = 0.000) for 1391 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.1716 (Rfree = 0.000) for 1389 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.1617 (Rfree = 0.000) for 1384 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 1457 seeds are put forward Round 1: 102 peptides, 19 chains. Longest chain 11 peptides. Score 0.385 Round 2: 108 peptides, 16 chains. Longest chain 18 peptides. Score 0.520 Round 3: 119 peptides, 16 chains. Longest chain 16 peptides. Score 0.589 Round 4: 132 peptides, 20 chains. Longest chain 20 peptides. Score 0.562 Round 5: 126 peptides, 19 chains. Longest chain 16 peptides. Score 0.552 Taking the results from Round 3 Chains 16, Residues 103, Estimated correctness of the model 10.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2441 reflections ( 99.59 % complete ) and 3222 restraints for refining 1425 atoms. 2826 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1743 (Rfree = 0.000) for 1425 atoms. Found 2 (9 requested) and removed 10 (4 requested) atoms. Cycle 17: After refmac, R = 0.1812 (Rfree = 0.000) for 1414 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.2494 (Rfree = 0.000) for 1412 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 19: After refmac, R = 0.1878 (Rfree = 0.000) for 1403 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.1581 (Rfree = 0.000) for 1401 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 1453 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 9 peptides. Score 0.246 Round 2: 104 peptides, 18 chains. Longest chain 15 peptides. Score 0.432 Round 3: 108 peptides, 17 chains. Longest chain 15 peptides. Score 0.491 Round 4: 105 peptides, 14 chains. Longest chain 15 peptides. Score 0.558 Round 5: 116 peptides, 17 chains. Longest chain 18 peptides. Score 0.544 Taking the results from Round 4 Chains 16, Residues 91, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 2441 reflections ( 99.59 % complete ) and 3158 restraints for refining 1516 atoms. 2684 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2037 (Rfree = 0.000) for 1516 atoms. Found 4 (9 requested) and removed 14 (4 requested) atoms. Cycle 22: After refmac, R = 0.1792 (Rfree = 0.000) for 1498 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.1711 (Rfree = 0.000) for 1489 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.1633 (Rfree = 0.000) for 1482 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.1657 (Rfree = 0.000) for 1477 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 1552 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.270 Round 2: 86 peptides, 15 chains. Longest chain 17 peptides. Score 0.393 Round 3: 94 peptides, 15 chains. Longest chain 18 peptides. Score 0.454 Round 4: 88 peptides, 13 chains. Longest chain 16 peptides. Score 0.474 Round 5: 96 peptides, 14 chains. Longest chain 14 peptides. Score 0.499 Taking the results from Round 5 Chains 15, Residues 82, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2441 reflections ( 99.59 % complete ) and 3406 restraints for refining 1516 atoms. 3043 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1777 (Rfree = 0.000) for 1516 atoms. Found 8 (9 requested) and removed 43 (4 requested) atoms. Cycle 27: After refmac, R = 0.1774 (Rfree = 0.000) for 1475 atoms. Found 5 (9 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.2105 (Rfree = 0.000) for 1466 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 29: After refmac, R = 0.1723 (Rfree = 0.000) for 1454 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 30: After refmac, R = 0.2260 (Rfree = 0.000) for 1452 atoms. Found 5 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 1503 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 10 peptides. Score 0.252 Round 2: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.339 Round 3: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.361 Round 4: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.322 Round 5: 75 peptides, 14 chains. Longest chain 7 peptides. Score 0.339 Taking the results from Round 3 Chains 15, Residues 67, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2441 reflections ( 99.59 % complete ) and 3443 restraints for refining 1495 atoms. 3163 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1881 (Rfree = 0.000) for 1495 atoms. Found 2 (9 requested) and removed 30 (4 requested) atoms. Cycle 32: After refmac, R = 0.1843 (Rfree = 0.000) for 1459 atoms. Found 2 (9 requested) and removed 14 (4 requested) atoms. Cycle 33: After refmac, R = 0.1675 (Rfree = 0.000) for 1435 atoms. Found 0 (9 requested) and removed 13 (4 requested) atoms. Cycle 34: After refmac, R = 0.1617 (Rfree = 0.000) for 1419 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1555 (Rfree = 0.000) for 1415 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 1456 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.286 Round 2: 74 peptides, 13 chains. Longest chain 12 peptides. Score 0.366 Round 3: 82 peptides, 15 chains. Longest chain 11 peptides. Score 0.361 Round 4: 84 peptides, 12 chains. Longest chain 15 peptides. Score 0.477 Round 5: 80 peptides, 11 chains. Longest chain 15 peptides. Score 0.481 Taking the results from Round 5 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 2441 reflections ( 99.59 % complete ) and 3159 restraints for refining 1475 atoms. 2833 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1922 (Rfree = 0.000) for 1475 atoms. Found 3 (9 requested) and removed 21 (4 requested) atoms. Cycle 37: After refmac, R = 0.1668 (Rfree = 0.000) for 1454 atoms. Found 5 (9 requested) and removed 10 (4 requested) atoms. Cycle 38: After refmac, R = 0.1826 (Rfree = 0.000) for 1447 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.1730 (Rfree = 0.000) for 1443 atoms. Found 3 (9 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.1885 (Rfree = 0.000) for 1434 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 1491 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 8 peptides. Score 0.240 Round 2: 81 peptides, 15 chains. Longest chain 10 peptides. Score 0.353 Round 3: 79 peptides, 15 chains. Longest chain 11 peptides. Score 0.337 Round 4: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.427 Round 5: 80 peptides, 14 chains. Longest chain 9 peptides. Score 0.380 Taking the results from Round 4 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2441 reflections ( 99.59 % complete ) and 3366 restraints for refining 1508 atoms. 3066 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1782 (Rfree = 0.000) for 1508 atoms. Found 7 (9 requested) and removed 13 (4 requested) atoms. Cycle 42: After refmac, R = 0.1719 (Rfree = 0.000) for 1495 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 43: After refmac, R = 0.1669 (Rfree = 0.000) for 1492 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.1718 (Rfree = 0.000) for 1488 atoms. Found 3 (9 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.1765 (Rfree = 0.000) for 1483 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 1541 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 5 peptides. Score 0.197 Round 2: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.327 Round 3: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.261 Round 4: 65 peptides, 12 chains. Longest chain 11 peptides. Score 0.327 Round 5: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.366 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 61, 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 2hdo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2441 reflections ( 99.59 % complete ) and 3566 restraints for refining 1501 atoms. 3335 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1881 (Rfree = 0.000) for 1501 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1803 (Rfree = 0.000) for 1495 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1702 (Rfree = 0.000) for 1490 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1672 (Rfree = 0.000) for 1485 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:08 GMT 2018 Job finished. TimeTaking 29.25 Used memory is bytes: 16652128