null Tue 25 Dec 19:27:55 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 2obp-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obp-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obp-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-1.7-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/2obp-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-1.7-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 ============================================================ Tue 25 Dec 19:28:05 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/2obp-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-1.7-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 240 and 0 Target number of residues in the AU: 240 Target solvent content: 0.4460 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.56 Input MTZ file: 2obp-1.7-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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.50 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: 29.462 1.702 Wilson plot Bfac: 13.93 26981 reflections ( 99.57 % complete ) and 0 restraints for refining 1719 atoms. Observations/parameters ratio is 3.92 ------------------------------------------------------ Starting model: R = 0.3260 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2818 (Rfree = 0.000) for 1719 atoms. Found 60 (93 requested) and removed 49 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.85 1.71 NCS extension: 0 residues added, 1730 seeds are put forward Round 1: 138 peptides, 11 chains. Longest chain 28 peptides. Score 0.745 Round 2: 148 peptides, 5 chains. Longest chain 57 peptides. Score 0.861 Round 3: 156 peptides, 3 chains. Longest chain 78 peptides. Score 0.899 Round 4: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.900 Round 5: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.900 Taking the results from Round 5 Chains 3, Residues 154, Estimated correctness of the model 99.4 % 3 chains (154 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 76 A 2 chains (157 residues) following loop building 2 chains (157 residues) in sequence following loop building ------------------------------------------------------ 26981 reflections ( 99.57 % complete ) and 1543 restraints for refining 1531 atoms. 373 conditional restraints added. Observations/parameters ratio is 4.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2954 (Rfree = 0.000) for 1531 atoms. Found 48 (83 requested) and removed 42 (41 requested) atoms. Cycle 2: After refmac, R = 0.2800 (Rfree = 0.000) for 1533 atoms. Found 28 (81 requested) and removed 14 (41 requested) atoms. Cycle 3: After refmac, R = 0.2621 (Rfree = 0.000) for 1539 atoms. Found 26 (81 requested) and removed 5 (41 requested) atoms. Cycle 4: After refmac, R = 0.2507 (Rfree = 0.000) for 1548 atoms. Found 20 (82 requested) and removed 7 (42 requested) atoms. Cycle 5: After refmac, R = 0.2434 (Rfree = 0.000) for 1555 atoms. Found 28 (82 requested) and removed 6 (42 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.79 1.65 NCS extension: 44 residues added (35 deleted due to clashes), 1624 seeds are put forward Round 1: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 2: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 3: 157 peptides, 4 chains. Longest chain 63 peptides. Score 0.890 Round 4: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 5: 158 peptides, 4 chains. Longest chain 63 peptides. Score 0.891 Taking the results from Round 4 Chains 3, Residues 155, Estimated correctness of the model 99.4 % 3 chains (155 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 B and 76 B 2 chains (158 residues) following loop building 2 chains (158 residues) in sequence following loop building ------------------------------------------------------ 26981 reflections ( 99.57 % complete ) and 1521 restraints for refining 1531 atoms. 343 conditional restraints added. Observations/parameters ratio is 4.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2535 (Rfree = 0.000) for 1531 atoms. Found 41 (81 requested) and removed 17 (41 requested) atoms. Cycle 7: After refmac, R = 0.2458 (Rfree = 0.000) for 1554 atoms. Found 31 (82 requested) and removed 7 (42 requested) atoms. Cycle 8: After refmac, R = 0.2423 (Rfree = 0.000) for 1574 atoms. Found 17 (83 requested) and removed 9 (42 requested) atoms. Cycle 9: After refmac, R = 0.2366 (Rfree = 0.000) for 1578 atoms. Found 22 (82 requested) and removed 11 (42 requested) atoms. Cycle 10: After refmac, R = 0.2339 (Rfree = 0.000) for 1584 atoms. Found 18 (83 requested) and removed 7 (43 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.78 1.64 NCS extension: 52 residues added (29 deleted due to clashes), 1651 seeds are put forward Round 1: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 2: 159 peptides, 3 chains. Longest chain 82 peptides. Score 0.903 Round 3: 158 peptides, 5 chains. Longest chain 64 peptides. Score 0.881 Round 4: 159 peptides, 3 chains. Longest chain 82 peptides. Score 0.903 Round 5: 158 peptides, 4 chains. Longest chain 64 peptides. Score 0.891 Taking the results from Round 4 Chains 3, Residues 156, Estimated correctness of the model 99.4 % 3 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 B and 76 B 2 chains (159 residues) following loop building 2 chains (159 residues) in sequence following loop building ------------------------------------------------------ 26981 reflections ( 99.57 % complete ) and 1501 restraints for refining 1531 atoms. 319 conditional restraints added. Observations/parameters ratio is 4.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2470 (Rfree = 0.000) for 1531 atoms. Found 36 (80 requested) and removed 18 (41 requested) atoms. Cycle 12: After refmac, R = 0.2401 (Rfree = 0.000) for 1547 atoms. Found 29 (81 requested) and removed 2 (42 requested) atoms. Cycle 13: After refmac, R = 0.2354 (Rfree = 0.000) for 1569 atoms. Found 21 (82 requested) and removed 5 (42 requested) atoms. Cycle 14: After refmac, R = 0.2331 (Rfree = 0.000) for 1577 atoms. Found 28 (82 requested) and removed 4 (42 requested) atoms. Cycle 15: After refmac, R = 0.2311 (Rfree = 0.000) for 1593 atoms. Found 21 (83 requested) and removed 5 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.78 1.64 NCS extension: 51 residues added (31 deleted due to clashes), 1662 seeds are put forward Round 1: 159 peptides, 3 chains. Longest chain 82 peptides. Score 0.903 Round 2: 158 peptides, 4 chains. Longest chain 64 peptides. Score 0.891 Round 3: 158 peptides, 4 chains. Longest chain 59 peptides. Score 0.891 Round 4: 157 peptides, 4 chains. Longest chain 64 peptides. Score 0.890 Round 5: 158 peptides, 3 chains. Longest chain 82 peptides. Score 0.902 Taking the results from Round 1 Chains 3, Residues 156, Estimated correctness of the model 99.4 % 3 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 B and 76 B 2 chains (159 residues) following loop building 2 chains (159 residues) in sequence following loop building ------------------------------------------------------ 26981 reflections ( 99.57 % complete ) and 1501 restraints for refining 1531 atoms. 319 conditional restraints added. Observations/parameters ratio is 4.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2420 (Rfree = 0.000) for 1531 atoms. Found 40 (80 requested) and removed 10 (41 requested) atoms. Cycle 17: After refmac, R = 0.2367 (Rfree = 0.000) for 1555 atoms. Found 24 (81 requested) and removed 2 (42 requested) atoms. Cycle 18: After refmac, R = 0.2338 (Rfree = 0.000) for 1574 atoms. Found 21 (82 requested) and removed 2 (42 requested) atoms. Cycle 19: After refmac, R = 0.2297 (Rfree = 0.000) for 1584 atoms. Found 18 (83 requested) and removed 6 (43 requested) atoms. Cycle 20: After refmac, R = 0.2275 (Rfree = 0.000) for 1589 atoms. Found 26 (83 requested) and removed 3 (43 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.77 1.63 NCS extension: 0 residues added, 1614 seeds are put forward Round 1: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 2: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 3: 158 peptides, 4 chains. Longest chain 64 peptides. Score 0.891 Round 4: 157 peptides, 4 chains. Longest chain 59 peptides. Score 0.890 Round 5: 158 peptides, 5 chains. Longest chain 64 peptides. Score 0.881 Taking the results from Round 2 Chains 3, Residues 155, Estimated correctness of the model 99.4 % 3 chains (155 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 B and 76 B 2 chains (158 residues) following loop building 2 chains (158 residues) in sequence following loop building ------------------------------------------------------ 26981 reflections ( 99.57 % complete ) and 1537 restraints for refining 1544 atoms. 359 conditional restraints added. Observations/parameters ratio is 4.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2397 (Rfree = 0.000) for 1544 atoms. Found 42 (80 requested) and removed 11 (41 requested) atoms. Cycle 22: After refmac, R = 0.2351 (Rfree = 0.000) for 1570 atoms. Found 30 (82 requested) and removed 4 (42 requested) atoms. Cycle 23: After refmac, R = 0.2300 (Rfree = 0.000) for 1591 atoms. Found 24 (83 requested) and removed 7 (43 requested) atoms. Cycle 24: After refmac, R = 0.2267 (Rfree = 0.000) for 1602 atoms. Found 22 (84 requested) and removed 2 (43 requested) atoms. Cycle 25: After refmac, R = 0.2252 (Rfree = 0.000) for 1614 atoms. Found 21 (84 requested) and removed 5 (44 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.77 1.63 NCS extension: 0 residues added, 1630 seeds are put forward Round 1: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 2: 159 peptides, 3 chains. Longest chain 82 peptides. Score 0.903 Round 3: 158 peptides, 4 chains. Longest chain 64 peptides. Score 0.891 Round 4: 159 peptides, 3 chains. Longest chain 82 peptides. Score 0.903 Round 5: 158 peptides, 4 chains. Longest chain 64 peptides. Score 0.891 Taking the results from Round 4 Chains 3, Residues 156, Estimated correctness of the model 99.4 % 3 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 B and 76 B 2 chains (159 residues) following loop building 2 chains (159 residues) in sequence following loop building ------------------------------------------------------ 26981 reflections ( 99.57 % complete ) and 1526 restraints for refining 1537 atoms. 344 conditional restraints added. Observations/parameters ratio is 4.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2388 (Rfree = 0.000) for 1537 atoms. Found 55 (80 requested) and removed 14 (41 requested) atoms. Cycle 27: After refmac, R = 0.2367 (Rfree = 0.000) for 1573 atoms. Found 26 (82 requested) and removed 6 (42 requested) atoms. Cycle 28: After refmac, R = 0.2313 (Rfree = 0.000) for 1591 atoms. Found 16 (83 requested) and removed 4 (43 requested) atoms. Cycle 29: After refmac, R = 0.2299 (Rfree = 0.000) for 1587 atoms. Found 29 (83 requested) and removed 6 (43 requested) atoms. Cycle 30: After refmac, R = 0.2279 (Rfree = 0.000) for 1604 atoms. Found 25 (84 requested) and removed 9 (43 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.78 1.64 NCS extension: 0 residues added, 1622 seeds are put forward Round 1: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 2: 155 peptides, 4 chains. Longest chain 61 peptides. Score 0.886 Round 3: 159 peptides, 3 chains. Longest chain 82 peptides. Score 0.903 Round 4: 154 peptides, 5 chains. Longest chain 61 peptides. Score 0.873 Round 5: 156 peptides, 3 chains. Longest chain 79 peptides. Score 0.899 Taking the results from Round 3 Chains 3, Residues 156, Estimated correctness of the model 99.4 % 3 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 B and 76 B 2 chains (159 residues) following loop building 2 chains (159 residues) in sequence following loop building ------------------------------------------------------ 26981 reflections ( 99.57 % complete ) and 1493 restraints for refining 1533 atoms. 311 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2392 (Rfree = 0.000) for 1533 atoms. Found 45 (80 requested) and removed 12 (41 requested) atoms. Cycle 32: After refmac, R = 0.2369 (Rfree = 0.000) for 1562 atoms. Found 31 (81 requested) and removed 3 (42 requested) atoms. Cycle 33: After refmac, R = 0.2315 (Rfree = 0.000) for 1583 atoms. Found 26 (83 requested) and removed 6 (43 requested) atoms. Cycle 34: After refmac, R = 0.2284 (Rfree = 0.000) for 1598 atoms. Found 23 (83 requested) and removed 8 (43 requested) atoms. Cycle 35: After refmac, R = 0.2270 (Rfree = 0.000) for 1602 atoms. Found 28 (84 requested) and removed 3 (43 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.77 1.63 NCS extension: 0 residues added, 1627 seeds are put forward Round 1: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 2: 157 peptides, 4 chains. Longest chain 63 peptides. Score 0.890 Round 3: 159 peptides, 3 chains. Longest chain 82 peptides. Score 0.903 Round 4: 158 peptides, 4 chains. Longest chain 59 peptides. Score 0.891 Round 5: 158 peptides, 4 chains. Longest chain 64 peptides. Score 0.891 Taking the results from Round 3 Chains 3, Residues 156, Estimated correctness of the model 99.4 % 3 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 B and 76 B 2 chains (159 residues) following loop building 2 chains (159 residues) in sequence following loop building ------------------------------------------------------ 26981 reflections ( 99.57 % complete ) and 1511 restraints for refining 1531 atoms. 329 conditional restraints added. Observations/parameters ratio is 4.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2394 (Rfree = 0.000) for 1531 atoms. Found 48 (80 requested) and removed 8 (41 requested) atoms. Cycle 37: After refmac, R = 0.2354 (Rfree = 0.000) for 1569 atoms. Found 34 (82 requested) and removed 5 (42 requested) atoms. Cycle 38: After refmac, R = 0.2322 (Rfree = 0.000) for 1597 atoms. Found 14 (83 requested) and removed 5 (43 requested) atoms. Cycle 39: After refmac, R = 0.2268 (Rfree = 0.000) for 1599 atoms. Found 21 (84 requested) and removed 2 (43 requested) atoms. Cycle 40: After refmac, R = 0.2267 (Rfree = 0.000) for 1612 atoms. Found 14 (84 requested) and removed 6 (43 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.77 1.63 NCS extension: 0 residues added, 1621 seeds are put forward Round 1: 158 peptides, 3 chains. Longest chain 81 peptides. Score 0.902 Round 2: 157 peptides, 3 chains. Longest chain 81 peptides. Score 0.900 Round 3: 156 peptides, 4 chains. Longest chain 63 peptides. Score 0.888 Round 4: 157 peptides, 4 chains. Longest chain 58 peptides. Score 0.890 Round 5: 156 peptides, 4 chains. Longest chain 63 peptides. Score 0.888 Taking the results from Round 1 Chains 3, Residues 155, Estimated correctness of the model 99.4 % 3 chains (155 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 B and 75 B 2 chains (157 residues) following loop building 2 chains (157 residues) in sequence following loop building ------------------------------------------------------ 26981 reflections ( 99.57 % complete ) and 1524 restraints for refining 1531 atoms. 354 conditional restraints added. Observations/parameters ratio is 4.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2384 (Rfree = 0.000) for 1531 atoms. Found 57 (80 requested) and removed 6 (41 requested) atoms. Cycle 42: After refmac, R = 0.2360 (Rfree = 0.000) for 1579 atoms. Found 26 (82 requested) and removed 8 (42 requested) atoms. Cycle 43: After refmac, R = 0.2317 (Rfree = 0.000) for 1592 atoms. Found 19 (83 requested) and removed 5 (43 requested) atoms. Cycle 44: After refmac, R = 0.2256 (Rfree = 0.000) for 1598 atoms. Found 22 (84 requested) and removed 2 (43 requested) atoms. Cycle 45: After refmac, R = 0.2249 (Rfree = 0.000) for 1616 atoms. Found 14 (84 requested) and removed 11 (43 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.75 1.61 NCS extension: 129 residues added (2 deleted due to clashes), 1748 seeds are put forward Round 1: 159 peptides, 3 chains. Longest chain 81 peptides. Score 0.903 Round 2: 159 peptides, 3 chains. Longest chain 81 peptides. Score 0.903 Round 3: 159 peptides, 3 chains. Longest chain 81 peptides. Score 0.903 Round 4: 158 peptides, 4 chains. Longest chain 63 peptides. Score 0.891 Round 5: 159 peptides, 3 chains. Longest chain 81 peptides. Score 0.903 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 156, Estimated correctness of the model 99.4 % 3 chains (156 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 72 B and 76 B 2 chains (159 residues) following loop building 2 chains (159 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 26981 reflections ( 99.57 % complete ) and 1178 restraints for refining 1164 atoms. Observations/parameters ratio is 5.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2966 (Rfree = 0.000) for 1164 atoms. Found 49 (59 requested) and removed 0 (59 requested) atoms. Cycle 47: After refmac, R = 0.2764 (Rfree = 0.000) for 1164 atoms. Found 15 (61 requested) and removed 0 (32 requested) atoms. Cycle 48: After refmac, R = 0.2622 (Rfree = 0.000) for 1164 atoms. Found 7 (62 requested) and removed 1 (33 requested) atoms. Cycle 49: After refmac, R = 0.2567 (Rfree = 0.000) for 1164 atoms. Found 6 (62 requested) and removed 4 (33 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:28:53 GMT 2018 Job finished. TimeTaking 60.96 Used memory is bytes: 20256352