Sun 23 Dec 22:23:08 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 2a6b-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-3.8-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/2a6b-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-3.8-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 22:23:18 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/2a6b-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-3.8-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 232 and 0 Target number of residues in the AU: 232 Target solvent content: 0.6181 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 234 Adjusted target solvent content: 0.61 Input MTZ file: 2a6b-3.8-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: 90 Cell parameters: 119.176 119.176 46.302 90.000 90.000 90.000 Input sequence file: 2a6b-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.85 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: 29.794 3.800 Wilson plot Bfac: 59.98 3549 reflections ( 98.97 % complete ) and 0 restraints for refining 2078 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3200 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3372 (Rfree = 0.000) for 2078 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 2.90 Search for helices and strands: 0 residues in 0 chains, 2133 seeds are put forward Round 1: 109 peptides, 21 chains. Longest chain 8 peptides. Score 0.313 Round 2: 114 peptides, 17 chains. Longest chain 14 peptides. Score 0.429 Round 3: 122 peptides, 16 chains. Longest chain 14 peptides. Score 0.487 Round 4: 130 peptides, 18 chains. Longest chain 16 peptides. Score 0.482 Round 5: 130 peptides, 17 chains. Longest chain 14 peptides. Score 0.502 Taking the results from Round 5 Chains 17, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3549 reflections ( 98.97 % complete ) and 3815 restraints for refining 1693 atoms. 3380 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3172 (Rfree = 0.000) for 1693 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 2: After refmac, R = 0.3184 (Rfree = 0.000) for 1650 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.2804 (Rfree = 0.000) for 1621 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.3061 (Rfree = 0.000) for 1610 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2773 (Rfree = 0.000) for 1601 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 1684 seeds are put forward Round 1: 122 peptides, 22 chains. Longest chain 13 peptides. Score 0.359 Round 2: 128 peptides, 18 chains. Longest chain 14 peptides. Score 0.473 Round 3: 135 peptides, 16 chains. Longest chain 17 peptides. Score 0.543 Round 4: 125 peptides, 15 chains. Longest chain 17 peptides. Score 0.521 Round 5: 120 peptides, 15 chains. Longest chain 15 peptides. Score 0.499 Taking the results from Round 3 Chains 16, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3549 reflections ( 98.97 % complete ) and 3550 restraints for refining 1625 atoms. 3090 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2688 (Rfree = 0.000) for 1625 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 7: After refmac, R = 0.2363 (Rfree = 0.000) for 1614 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 8: After refmac, R = 0.2201 (Rfree = 0.000) for 1601 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 9: After refmac, R = 0.2177 (Rfree = 0.000) for 1589 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.2042 (Rfree = 0.000) for 1580 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 2.90 Search for helices and strands: 0 residues in 0 chains, 1684 seeds are put forward Round 1: 118 peptides, 21 chains. Longest chain 8 peptides. Score 0.360 Round 2: 112 peptides, 19 chains. Longest chain 13 peptides. Score 0.374 Round 3: 125 peptides, 19 chains. Longest chain 17 peptides. Score 0.438 Round 4: 118 peptides, 15 chains. Longest chain 16 peptides. Score 0.490 Round 5: 119 peptides, 16 chains. Longest chain 17 peptides. Score 0.474 Taking the results from Round 4 Chains 15, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3549 reflections ( 98.97 % complete ) and 3847 restraints for refining 1692 atoms. 3450 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3090 (Rfree = 0.000) for 1692 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 12: After refmac, R = 0.2701 (Rfree = 0.000) for 1678 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 13: After refmac, R = 0.2661 (Rfree = 0.000) for 1652 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2457 (Rfree = 0.000) for 1643 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 15: After refmac, R = 0.2341 (Rfree = 0.000) for 1629 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 1714 seeds are put forward Round 1: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.318 Round 2: 116 peptides, 16 chains. Longest chain 12 peptides. Score 0.460 Round 3: 121 peptides, 17 chains. Longest chain 12 peptides. Score 0.462 Round 4: 122 peptides, 18 chains. Longest chain 15 peptides. Score 0.445 Round 5: 123 peptides, 14 chains. Longest chain 21 peptides. Score 0.532 Taking the results from Round 5 Chains 15, Residues 109, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3549 reflections ( 98.97 % complete ) and 3699 restraints for refining 1691 atoms. 3224 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2715 (Rfree = 0.000) for 1691 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 17: After refmac, R = 0.2487 (Rfree = 0.000) for 1655 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2383 (Rfree = 0.000) for 1642 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 19: After refmac, R = 0.2391 (Rfree = 0.000) for 1622 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.2493 (Rfree = 0.000) for 1610 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 2.90 Search for helices and strands: 0 residues in 0 chains, 1694 seeds are put forward Round 1: 115 peptides, 21 chains. Longest chain 10 peptides. Score 0.345 Round 2: 122 peptides, 18 chains. Longest chain 12 peptides. Score 0.445 Round 3: 126 peptides, 18 chains. Longest chain 13 peptides. Score 0.464 Round 4: 127 peptides, 19 chains. Longest chain 19 peptides. Score 0.448 Round 5: 133 peptides, 19 chains. Longest chain 15 peptides. Score 0.476 Taking the results from Round 5 Chains 19, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3549 reflections ( 98.97 % complete ) and 3776 restraints for refining 1671 atoms. 3339 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2620 (Rfree = 0.000) for 1671 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 22: After refmac, R = 0.2434 (Rfree = 0.000) for 1645 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 23: After refmac, R = 0.2520 (Rfree = 0.000) for 1636 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.2111 (Rfree = 0.000) for 1621 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 25: After refmac, R = 0.2329 (Rfree = 0.000) for 1613 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 2.83 Search for helices and strands: 0 residues in 0 chains, 1702 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 10 peptides. Score 0.355 Round 2: 119 peptides, 17 chains. Longest chain 12 peptides. Score 0.452 Round 3: 132 peptides, 18 chains. Longest chain 12 peptides. Score 0.491 Round 4: 122 peptides, 18 chains. Longest chain 15 peptides. Score 0.445 Round 5: 121 peptides, 16 chains. Longest chain 13 peptides. Score 0.483 Taking the results from Round 3 Chains 18, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3549 reflections ( 98.97 % complete ) and 3749 restraints for refining 1668 atoms. 3311 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2846 (Rfree = 0.000) for 1668 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 27: After refmac, R = 0.2566 (Rfree = 0.000) for 1642 atoms. Found 8 (9 requested) and removed 17 (4 requested) atoms. Cycle 28: After refmac, R = 0.2713 (Rfree = 0.000) for 1621 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 29: After refmac, R = 0.2338 (Rfree = 0.000) for 1599 atoms. Found 5 (8 requested) and removed 14 (4 requested) atoms. Cycle 30: After refmac, R = 0.2318 (Rfree = 0.000) for 1587 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 2.84 Search for helices and strands: 0 residues in 0 chains, 1646 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 7 peptides. Score 0.266 Round 2: 122 peptides, 20 chains. Longest chain 14 peptides. Score 0.403 Round 3: 130 peptides, 19 chains. Longest chain 15 peptides. Score 0.462 Round 4: 130 peptides, 19 chains. Longest chain 13 peptides. Score 0.462 Round 5: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.398 Taking the results from Round 4 Chains 19, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3549 reflections ( 98.97 % complete ) and 3750 restraints for refining 1667 atoms. 3325 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2534 (Rfree = 0.000) for 1667 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 32: After refmac, R = 0.2273 (Rfree = 0.000) for 1645 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 33: After refmac, R = 0.2159 (Rfree = 0.000) for 1627 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 34: After refmac, R = 0.2009 (Rfree = 0.000) for 1615 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.1985 (Rfree = 0.000) for 1613 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 2.84 Search for helices and strands: 0 residues in 0 chains, 1717 seeds are put forward Round 1: 90 peptides, 17 chains. Longest chain 9 peptides. Score 0.303 Round 2: 123 peptides, 23 chains. Longest chain 11 peptides. Score 0.342 Round 3: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.342 Round 4: 125 peptides, 21 chains. Longest chain 11 peptides. Score 0.396 Round 5: 124 peptides, 18 chains. Longest chain 15 peptides. Score 0.455 Taking the results from Round 5 Chains 18, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3549 reflections ( 98.97 % complete ) and 3794 restraints for refining 1693 atoms. 3388 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2451 (Rfree = 0.000) for 1693 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.2465 (Rfree = 0.000) for 1680 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 38: After refmac, R = 0.2341 (Rfree = 0.000) for 1670 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 39: After refmac, R = 0.2331 (Rfree = 0.000) for 1667 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.2244 (Rfree = 0.000) for 1658 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 1744 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 8 peptides. Score 0.229 Round 2: 107 peptides, 19 chains. Longest chain 11 peptides. Score 0.348 Round 3: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.369 Round 4: 120 peptides, 20 chains. Longest chain 12 peptides. Score 0.393 Round 5: 115 peptides, 19 chains. Longest chain 14 peptides. Score 0.390 Taking the results from Round 4 Chains 21, Residues 100, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3549 reflections ( 98.97 % complete ) and 3627 restraints for refining 1670 atoms. 3204 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2888 (Rfree = 0.000) for 1670 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 42: After refmac, R = 0.2417 (Rfree = 0.000) for 1646 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 43: After refmac, R = 0.2264 (Rfree = 0.000) for 1644 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.1949 (Rfree = 0.000) for 1640 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1996 (Rfree = 0.000) for 1636 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 1687 seeds are put forward Round 1: 105 peptides, 20 chains. Longest chain 10 peptides. Score 0.314 Round 2: 115 peptides, 18 chains. Longest chain 16 peptides. Score 0.412 Round 3: 107 peptides, 15 chains. Longest chain 15 peptides. Score 0.438 Round 4: 113 peptides, 17 chains. Longest chain 15 peptides. Score 0.424 Round 5: 107 peptides, 16 chains. Longest chain 15 peptides. Score 0.416 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 92, 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 2a6b-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3549 reflections ( 98.97 % complete ) and 3847 restraints for refining 1677 atoms. 3494 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2577 (Rfree = 0.000) for 1677 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2377 (Rfree = 0.000) for 1667 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2293 (Rfree = 0.000) for 1660 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2050 (Rfree = 0.000) for 1653 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 32.85