Sun 23 Dec 22:22:52 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 2o3l-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-2.0-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/2o3l-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-2.0-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 ============================================================ Sun 23 Dec 22:23:00 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/2o3l-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-2.0-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 191 and 0 Target number of residues in the AU: 191 Target solvent content: 0.5289 Checking the provided sequence file Detected sequence length: 85 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 170 Adjusted target solvent content: 0.58 Input MTZ file: 2o3l-2.0-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: 154 Cell parameters: 61.138 61.138 101.686 90.000 90.000 120.000 Input sequence file: 2o3l-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1360 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 1 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: 52.947 2.000 Wilson plot Bfac: 29.79 15408 reflections ( 99.94 % complete ) and 0 restraints for refining 1521 atoms. Observations/parameters ratio is 2.53 ------------------------------------------------------ Starting model: R = 0.3278 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2705 (Rfree = 0.000) for 1521 atoms. Found 52 (52 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.16 1.94 NCS extension: 0 residues added, 1547 seeds are put forward Round 1: 118 peptides, 15 chains. Longest chain 22 peptides. Score 0.592 Round 2: 127 peptides, 9 chains. Longest chain 39 peptides. Score 0.761 Round 3: 146 peptides, 6 chains. Longest chain 47 peptides. Score 0.861 Round 4: 150 peptides, 5 chains. Longest chain 82 peptides. Score 0.881 Round 5: 151 peptides, 3 chains. Longest chain 78 peptides. Score 0.905 Taking the results from Round 5 Chains 3, Residues 148, Estimated correctness of the model 99.0 % 3 chains (148 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 B and 35 B 2 chains (151 residues) following loop building 2 chains (151 residues) in sequence following loop building ------------------------------------------------------ 15408 reflections ( 99.94 % complete ) and 1396 restraints for refining 1392 atoms. 172 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2507 (Rfree = 0.000) for 1392 atoms. Found 47 (47 requested) and removed 25 (23 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2232 (Rfree = 0.000) for 1406 atoms. Found 47 (47 requested) and removed 17 (24 requested) atoms. Cycle 3: After refmac, R = 0.2087 (Rfree = 0.000) for 1434 atoms. Found 46 (48 requested) and removed 17 (24 requested) atoms. Cycle 4: After refmac, R = 0.2005 (Rfree = 0.000) for 1460 atoms. Found 42 (49 requested) and removed 22 (25 requested) atoms. Cycle 5: After refmac, R = 0.1921 (Rfree = 0.000) for 1473 atoms. Found 48 (48 requested) and removed 13 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.14 1.92 NCS extension: 5 residues added (0 deleted due to clashes), 1514 seeds are put forward Round 1: 153 peptides, 3 chains. Longest chain 79 peptides. Score 0.908 Round 2: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Round 3: 152 peptides, 5 chains. Longest chain 54 peptides. Score 0.885 Round 4: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Round 5: 154 peptides, 3 chains. Longest chain 79 peptides. Score 0.909 Taking the results from Round 4 Chains 2, Residues 154, Estimated correctness of the model 99.3 % 2 chains (154 residues) have been docked in sequence Building loops using Loopy2018 2 chains (154 residues) following loop building 2 chains (154 residues) in sequence following loop building ------------------------------------------------------ 15408 reflections ( 99.94 % complete ) and 1375 restraints for refining 1424 atoms. 126 conditional restraints added. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2116 (Rfree = 0.000) for 1424 atoms. Found 46 (46 requested) and removed 17 (24 requested) atoms. Cycle 7: After refmac, R = 0.1990 (Rfree = 0.000) for 1451 atoms. Found 40 (47 requested) and removed 15 (24 requested) atoms. Cycle 8: After refmac, R = 0.1909 (Rfree = 0.000) for 1474 atoms. Found 37 (48 requested) and removed 17 (25 requested) atoms. Cycle 9: After refmac, R = 0.1853 (Rfree = 0.000) for 1494 atoms. Found 33 (49 requested) and removed 24 (25 requested) atoms. Cycle 10: After refmac, R = 0.1820 (Rfree = 0.000) for 1501 atoms. Found 38 (48 requested) and removed 22 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.13 1.91 NCS extension: 3 residues added (0 deleted due to clashes), 1520 seeds are put forward Round 1: 151 peptides, 4 chains. Longest chain 50 peptides. Score 0.894 Round 2: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Round 3: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Round 4: 155 peptides, 3 chains. Longest chain 79 peptides. Score 0.911 Round 5: 155 peptides, 3 chains. Longest chain 77 peptides. Score 0.911 Taking the results from Round 3 Chains 2, Residues 154, Estimated correctness of the model 99.3 % 2 chains (154 residues) have been docked in sequence Building loops using Loopy2018 2 chains (154 residues) following loop building 2 chains (154 residues) in sequence following loop building ------------------------------------------------------ 15408 reflections ( 99.94 % complete ) and 1379 restraints for refining 1446 atoms. 130 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2065 (Rfree = 0.000) for 1446 atoms. Found 45 (45 requested) and removed 24 (24 requested) atoms. Cycle 12: After refmac, R = 0.1970 (Rfree = 0.000) for 1466 atoms. Found 45 (45 requested) and removed 20 (25 requested) atoms. Cycle 13: After refmac, R = 0.1911 (Rfree = 0.000) for 1489 atoms. Found 46 (46 requested) and removed 23 (25 requested) atoms. Cycle 14: After refmac, R = 0.1893 (Rfree = 0.000) for 1510 atoms. Found 36 (46 requested) and removed 29 (25 requested) atoms. Cycle 15: After refmac, R = 0.1859 (Rfree = 0.000) for 1513 atoms. Found 45 (45 requested) and removed 21 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.14 1.92 NCS extension: 3 residues added (0 deleted due to clashes), 1541 seeds are put forward Round 1: 155 peptides, 3 chains. Longest chain 77 peptides. Score 0.911 Round 2: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Round 3: 154 peptides, 3 chains. Longest chain 79 peptides. Score 0.909 Round 4: 155 peptides, 3 chains. Longest chain 77 peptides. Score 0.911 Round 5: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Taking the results from Round 5 Chains 2, Residues 154, Estimated correctness of the model 99.3 % 2 chains (154 residues) have been docked in sequence Building loops using Loopy2018 2 chains (154 residues) following loop building 2 chains (154 residues) in sequence following loop building ------------------------------------------------------ 15408 reflections ( 99.94 % complete ) and 1386 restraints for refining 1451 atoms. 137 conditional restraints added. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2044 (Rfree = 0.000) for 1451 atoms. Found 43 (43 requested) and removed 21 (24 requested) atoms. Cycle 17: After refmac, R = 0.1964 (Rfree = 0.000) for 1471 atoms. Found 38 (44 requested) and removed 16 (25 requested) atoms. Cycle 18: After refmac, R = 0.1892 (Rfree = 0.000) for 1490 atoms. Found 42 (45 requested) and removed 21 (25 requested) atoms. Cycle 19: After refmac, R = 0.1863 (Rfree = 0.000) for 1509 atoms. Found 30 (45 requested) and removed 22 (25 requested) atoms. Cycle 20: After refmac, R = 0.1817 (Rfree = 0.000) for 1512 atoms. Found 37 (44 requested) and removed 22 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.14 1.92 NCS extension: 3 residues added (0 deleted due to clashes), 1531 seeds are put forward Round 1: 155 peptides, 3 chains. Longest chain 77 peptides. Score 0.911 Round 2: 155 peptides, 3 chains. Longest chain 79 peptides. Score 0.911 Round 3: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Round 4: 155 peptides, 3 chains. Longest chain 79 peptides. Score 0.911 Round 5: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Taking the results from Round 5 Chains 2, Residues 154, Estimated correctness of the model 99.3 % 2 chains (154 residues) have been docked in sequence Building loops using Loopy2018 2 chains (154 residues) following loop building 2 chains (154 residues) in sequence following loop building ------------------------------------------------------ 15408 reflections ( 99.94 % complete ) and 1404 restraints for refining 1449 atoms. 155 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2045 (Rfree = 0.000) for 1449 atoms. Found 41 (41 requested) and removed 24 (24 requested) atoms. Cycle 22: After refmac, R = 0.1942 (Rfree = 0.000) for 1463 atoms. Found 41 (41 requested) and removed 14 (25 requested) atoms. Cycle 23: After refmac, R = 0.1870 (Rfree = 0.000) for 1489 atoms. Found 35 (42 requested) and removed 21 (25 requested) atoms. Cycle 24: After refmac, R = 0.1826 (Rfree = 0.000) for 1500 atoms. Found 38 (41 requested) and removed 20 (25 requested) atoms. Cycle 25: After refmac, R = 0.1816 (Rfree = 0.000) for 1516 atoms. Found 39 (41 requested) and removed 24 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.14 1.92 NCS extension: 3 residues added (0 deleted due to clashes), 1534 seeds are put forward Round 1: 153 peptides, 5 chains. Longest chain 51 peptides. Score 0.887 Round 2: 155 peptides, 3 chains. Longest chain 77 peptides. Score 0.911 Round 3: 155 peptides, 3 chains. Longest chain 79 peptides. Score 0.911 Round 4: 155 peptides, 3 chains. Longest chain 77 peptides. Score 0.911 Round 5: 154 peptides, 4 chains. Longest chain 77 peptides. Score 0.899 Taking the results from Round 4 Chains 3, Residues 152, Estimated correctness of the model 99.2 % 2 chains (143 residues) have been docked in sequence Building loops using Loopy2018 3 chains (152 residues) following loop building 2 chains (143 residues) in sequence following loop building ------------------------------------------------------ 15408 reflections ( 99.94 % complete ) and 1484 restraints for refining 1451 atoms. 282 conditional restraints added. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2062 (Rfree = 0.000) for 1451 atoms. Found 37 (37 requested) and removed 25 (24 requested) atoms. Cycle 27: After refmac, R = 0.1929 (Rfree = 0.000) for 1459 atoms. Found 37 (37 requested) and removed 8 (25 requested) atoms. Cycle 28: After refmac, R = 0.1875 (Rfree = 0.000) for 1486 atoms. Found 36 (37 requested) and removed 14 (25 requested) atoms. Cycle 29: After refmac, R = 0.1816 (Rfree = 0.000) for 1505 atoms. Found 38 (38 requested) and removed 18 (25 requested) atoms. Cycle 30: After refmac, R = 0.1815 (Rfree = 0.000) for 1518 atoms. Found 38 (38 requested) and removed 20 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.14 1.92 NCS extension: 4 residues added (4 deleted due to clashes), 1540 seeds are put forward Round 1: 155 peptides, 3 chains. Longest chain 79 peptides. Score 0.911 Round 2: 155 peptides, 3 chains. Longest chain 77 peptides. Score 0.911 Round 3: 155 peptides, 3 chains. Longest chain 79 peptides. Score 0.911 Round 4: 155 peptides, 3 chains. Longest chain 77 peptides. Score 0.911 Round 5: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Taking the results from Round 5 Chains 2, Residues 154, Estimated correctness of the model 99.3 % 2 chains (154 residues) have been docked in sequence Building loops using Loopy2018 2 chains (154 residues) following loop building 2 chains (154 residues) in sequence following loop building ------------------------------------------------------ 15408 reflections ( 99.94 % complete ) and 1391 restraints for refining 1455 atoms. 142 conditional restraints added. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2033 (Rfree = 0.000) for 1455 atoms. Found 35 (35 requested) and removed 25 (24 requested) atoms. Cycle 32: After refmac, R = 0.1922 (Rfree = 0.000) for 1461 atoms. Found 35 (35 requested) and removed 10 (25 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1845 (Rfree = 0.000) for 1481 atoms. Found 35 (35 requested) and removed 14 (25 requested) atoms. Cycle 34: After refmac, R = 0.1825 (Rfree = 0.000) for 1500 atoms. Found 34 (36 requested) and removed 16 (25 requested) atoms. Cycle 35: After refmac, R = 0.1814 (Rfree = 0.000) for 1518 atoms. Found 36 (36 requested) and removed 25 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.14 1.92 NCS extension: 3 residues added (0 deleted due to clashes), 1532 seeds are put forward Round 1: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Round 2: 155 peptides, 3 chains. Longest chain 79 peptides. Score 0.911 Round 3: 154 peptides, 3 chains. Longest chain 77 peptides. Score 0.909 Round 4: 155 peptides, 3 chains. Longest chain 79 peptides. Score 0.911 Round 5: 154 peptides, 3 chains. Longest chain 77 peptides. Score 0.909 Taking the results from Round 1 Chains 2, Residues 154, Estimated correctness of the model 99.3 % 2 chains (154 residues) have been docked in sequence Building loops using Loopy2018 2 chains (154 residues) following loop building 2 chains (154 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 15408 reflections ( 99.94 % complete ) and 1385 restraints for refining 1458 atoms. 136 conditional restraints added. Observations/parameters ratio is 2.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2008 (Rfree = 0.000) for 1458 atoms. Found 33 (33 requested) and removed 23 (24 requested) atoms. Cycle 37: After refmac, R = 0.1895 (Rfree = 0.000) for 1465 atoms. Found 33 (33 requested) and removed 13 (25 requested) atoms. Cycle 38: After refmac, R = 0.1831 (Rfree = 0.000) for 1485 atoms. Found 33 (33 requested) and removed 15 (25 requested) atoms. Cycle 39: After refmac, R = 0.1830 (Rfree = 0.000) for 1502 atoms. Found 31 (34 requested) and removed 20 (25 requested) atoms. Cycle 40: After refmac, R = 0.1774 (Rfree = 0.000) for 1512 atoms. Found 33 (33 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.13 1.91 NCS extension: 3 residues added (0 deleted due to clashes), 1523 seeds are put forward Round 1: 152 peptides, 4 chains. Longest chain 50 peptides. Score 0.896 Round 2: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Round 3: 152 peptides, 4 chains. Longest chain 67 peptides. Score 0.896 Round 4: 156 peptides, 2 chains. Longest chain 79 peptides. Score 0.922 Round 5: 152 peptides, 4 chains. Longest chain 67 peptides. Score 0.896 Taking the results from Round 4 Chains 2, Residues 154, Estimated correctness of the model 99.3 % 2 chains (154 residues) have been docked in sequence Building loops using Loopy2018 2 chains (154 residues) following loop building 2 chains (154 residues) in sequence following loop building ------------------------------------------------------ 15408 reflections ( 99.94 % complete ) and 1389 restraints for refining 1453 atoms. 140 conditional restraints added. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2005 (Rfree = 0.000) for 1453 atoms. Found 30 (30 requested) and removed 22 (24 requested) atoms. Cycle 42: After refmac, R = 0.1892 (Rfree = 0.000) for 1458 atoms. Found 30 (30 requested) and removed 10 (25 requested) atoms. Cycle 43: After refmac, R = 0.1819 (Rfree = 0.000) for 1477 atoms. Found 30 (30 requested) and removed 10 (25 requested) atoms. Cycle 44: After refmac, R = 0.1787 (Rfree = 0.000) for 1497 atoms. Found 29 (31 requested) and removed 17 (25 requested) atoms. Cycle 45: After refmac, R = 0.1761 (Rfree = 0.000) for 1505 atoms. Found 30 (30 requested) and removed 18 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.13 1.91 NCS extension: 3 residues added (0 deleted due to clashes), 1520 seeds are put forward Round 1: 155 peptides, 2 chains. Longest chain 78 peptides. Score 0.921 Round 2: 154 peptides, 3 chains. Longest chain 78 peptides. Score 0.909 Round 3: 155 peptides, 2 chains. Longest chain 78 peptides. Score 0.921 Round 4: 153 peptides, 4 chains. Longest chain 67 peptides. Score 0.897 Round 5: 154 peptides, 3 chains. Longest chain 78 peptides. Score 0.909 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 153, Estimated correctness of the model 99.3 % 2 chains (153 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (153 residues) following loop building 2 chains (153 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 15408 reflections ( 99.94 % complete ) and 1236 restraints for refining 1213 atoms. Observations/parameters ratio is 3.18 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2464 (Rfree = 0.000) for 1213 atoms. Found 23 (23 requested) and removed 0 (23 requested) atoms. Cycle 47: After refmac, R = 0.2293 (Rfree = 0.000) for 1213 atoms. Found 9 (24 requested) and removed 0 (21 requested) atoms. Cycle 48: After refmac, R = 0.2207 (Rfree = 0.000) for 1213 atoms. Found 11 (24 requested) and removed 1 (21 requested) atoms. Cycle 49: After refmac, R = 0.2144 (Rfree = 0.000) for 1213 atoms. Found 9 (24 requested) and removed 2 (21 requested) atoms. Writing output files ... TimeTaking 32.58