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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-3.4-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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-3.4-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 250 and 0 Target number of residues in the AU: 250 Target solvent content: 0.5885 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-3.4-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-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.80 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 3.400 Wilson plot Bfac: 47.62 4915 reflections ( 99.23 % complete ) and 0 restraints for refining 2068 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3102 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2726 (Rfree = 0.000) for 2068 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.98 2.57 Search for helices and strands: 0 residues in 0 chains, 2126 seeds are put forward Round 1: 128 peptides, 23 chains. Longest chain 17 peptides. Score 0.368 Round 2: 145 peptides, 20 chains. Longest chain 13 peptides. Score 0.509 Round 3: 153 peptides, 20 chains. Longest chain 23 peptides. Score 0.542 Round 4: 158 peptides, 19 chains. Longest chain 27 peptides. Score 0.580 Round 5: 160 peptides, 22 chains. Longest chain 14 peptides. Score 0.534 Taking the results from Round 4 Chains 20, Residues 139, Estimated correctness of the model 22.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4915 reflections ( 99.23 % complete ) and 3371 restraints for refining 1702 atoms. 2734 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2412 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 2: After refmac, R = 0.2275 (Rfree = 0.000) for 1680 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2167 (Rfree = 0.000) for 1679 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2130 (Rfree = 0.000) for 1674 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 5: After refmac, R = 0.2077 (Rfree = 0.000) for 1671 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 2.64 Search for helices and strands: 0 residues in 0 chains, 1793 seeds are put forward Round 1: 146 peptides, 23 chains. Longest chain 14 peptides. Score 0.454 Round 2: 157 peptides, 20 chains. Longest chain 20 peptides. Score 0.558 Round 3: 156 peptides, 20 chains. Longest chain 18 peptides. Score 0.554 Round 4: 162 peptides, 21 chains. Longest chain 40 peptides. Score 0.560 Round 5: 144 peptides, 18 chains. Longest chain 17 peptides. Score 0.542 Taking the results from Round 4 Chains 23, Residues 141, Estimated correctness of the model 15.1 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4915 reflections ( 99.23 % complete ) and 3494 restraints for refining 1702 atoms. 2868 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2807 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 7: After refmac, R = 0.2754 (Rfree = 0.000) for 1688 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.2616 (Rfree = 0.000) for 1685 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.2673 (Rfree = 0.000) for 1680 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 10: After refmac, R = 0.2499 (Rfree = 0.000) for 1673 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 2.67 Search for helices and strands: 0 residues in 0 chains, 1764 seeds are put forward Round 1: 152 peptides, 23 chains. Longest chain 12 peptides. Score 0.481 Round 2: 168 peptides, 21 chains. Longest chain 21 peptides. Score 0.583 Round 3: 158 peptides, 19 chains. Longest chain 22 peptides. Score 0.580 Round 4: 160 peptides, 21 chains. Longest chain 16 peptides. Score 0.552 Round 5: 154 peptides, 19 chains. Longest chain 20 peptides. Score 0.564 Taking the results from Round 2 Chains 21, Residues 147, Estimated correctness of the model 23.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4915 reflections ( 99.23 % complete ) and 3738 restraints for refining 1701 atoms. 3171 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2780 (Rfree = 0.000) for 1701 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.2444 (Rfree = 0.000) for 1690 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2392 (Rfree = 0.000) for 1686 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.2258 (Rfree = 0.000) for 1685 atoms. Found 10 (12 requested) and removed 16 (6 requested) atoms. Cycle 15: After refmac, R = 0.2226 (Rfree = 0.000) for 1677 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 2.62 Search for helices and strands: 0 residues in 0 chains, 1770 seeds are put forward Round 1: 140 peptides, 23 chains. Longest chain 14 peptides. Score 0.426 Round 2: 152 peptides, 20 chains. Longest chain 22 peptides. Score 0.538 Round 3: 146 peptides, 21 chains. Longest chain 14 peptides. Score 0.494 Round 4: 150 peptides, 19 chains. Longest chain 20 peptides. Score 0.548 Round 5: 153 peptides, 21 chains. Longest chain 15 peptides. Score 0.524 Taking the results from Round 4 Chains 19, Residues 131, Estimated correctness of the model 10.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4915 reflections ( 99.23 % complete ) and 3785 restraints for refining 1702 atoms. 3280 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2484 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 17: After refmac, R = 0.2256 (Rfree = 0.000) for 1701 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. Cycle 18: After refmac, R = 0.2150 (Rfree = 0.000) for 1697 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2023 (Rfree = 0.000) for 1699 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.1975 (Rfree = 0.000) for 1695 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 2.63 Search for helices and strands: 0 residues in 0 chains, 1785 seeds are put forward Round 1: 135 peptides, 22 chains. Longest chain 12 peptides. Score 0.423 Round 2: 133 peptides, 18 chains. Longest chain 12 peptides. Score 0.496 Round 3: 140 peptides, 17 chains. Longest chain 15 peptides. Score 0.545 Round 4: 135 peptides, 14 chains. Longest chain 21 peptides. Score 0.581 Round 5: 147 peptides, 16 chains. Longest chain 21 peptides. Score 0.591 Taking the results from Round 5 Chains 17, Residues 131, Estimated correctness of the model 25.7 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4915 reflections ( 99.23 % complete ) and 3568 restraints for refining 1702 atoms. 3002 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2783 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 22: After refmac, R = 0.2550 (Rfree = 0.000) for 1690 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.2324 (Rfree = 0.000) for 1685 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 24: After refmac, R = 0.2168 (Rfree = 0.000) for 1678 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.2066 (Rfree = 0.000) for 1674 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 2.60 Search for helices and strands: 0 residues in 0 chains, 1757 seeds are put forward Round 1: 135 peptides, 20 chains. Longest chain 15 peptides. Score 0.464 Round 2: 160 peptides, 22 chains. Longest chain 20 peptides. Score 0.534 Round 3: 140 peptides, 17 chains. Longest chain 16 peptides. Score 0.545 Round 4: 137 peptides, 20 chains. Longest chain 16 peptides. Score 0.473 Round 5: 147 peptides, 21 chains. Longest chain 16 peptides. Score 0.498 Taking the results from Round 3 Chains 17, Residues 123, Estimated correctness of the model 9.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4915 reflections ( 99.23 % complete ) and 3856 restraints for refining 1702 atoms. 3381 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2488 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 27: After refmac, R = 0.2221 (Rfree = 0.000) for 1697 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.2178 (Rfree = 0.000) for 1694 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2078 (Rfree = 0.000) for 1695 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.2084 (Rfree = 0.000) for 1694 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 2.63 Search for helices and strands: 0 residues in 0 chains, 1769 seeds are put forward Round 1: 125 peptides, 20 chains. Longest chain 16 peptides. Score 0.417 Round 2: 146 peptides, 23 chains. Longest chain 16 peptides. Score 0.454 Round 3: 142 peptides, 22 chains. Longest chain 11 peptides. Score 0.456 Round 4: 127 peptides, 20 chains. Longest chain 11 peptides. Score 0.427 Round 5: 124 peptides, 20 chains. Longest chain 11 peptides. Score 0.412 Taking the results from Round 3 Chains 22, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4915 reflections ( 99.23 % complete ) and 3850 restraints for refining 1701 atoms. 3392 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2463 (Rfree = 0.000) for 1701 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.2311 (Rfree = 0.000) for 1698 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.2206 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2123 (Rfree = 0.000) for 1700 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.2059 (Rfree = 0.000) for 1704 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 2.60 Search for helices and strands: 0 residues in 0 chains, 1789 seeds are put forward Round 1: 133 peptides, 21 chains. Longest chain 14 peptides. Score 0.435 Round 2: 138 peptides, 22 chains. Longest chain 13 peptides. Score 0.437 Round 3: 144 peptides, 20 chains. Longest chain 17 peptides. Score 0.504 Round 4: 144 peptides, 18 chains. Longest chain 19 peptides. Score 0.542 Round 5: 151 peptides, 18 chains. Longest chain 17 peptides. Score 0.570 Taking the results from Round 5 Chains 18, Residues 133, Estimated correctness of the model 18.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4915 reflections ( 99.23 % complete ) and 3650 restraints for refining 1702 atoms. 3136 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2648 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 37: After refmac, R = 0.2636 (Rfree = 0.000) for 1691 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.2619 (Rfree = 0.000) for 1686 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.2736 (Rfree = 0.000) for 1684 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 40: After refmac, R = 0.2482 (Rfree = 0.000) for 1678 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.02 2.60 Search for helices and strands: 0 residues in 0 chains, 1766 seeds are put forward Round 1: 127 peptides, 23 chains. Longest chain 15 peptides. Score 0.362 Round 2: 151 peptides, 21 chains. Longest chain 19 peptides. Score 0.515 Round 3: 147 peptides, 20 chains. Longest chain 30 peptides. Score 0.517 Round 4: 158 peptides, 23 chains. Longest chain 27 peptides. Score 0.507 Round 5: 141 peptides, 22 chains. Longest chain 16 peptides. Score 0.451 Taking the results from Round 3 Chains 20, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4915 reflections ( 99.23 % complete ) and 3727 restraints for refining 1702 atoms. 3239 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2562 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2612 (Rfree = 0.000) for 1701 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 43: After refmac, R = 0.2458 (Rfree = 0.000) for 1699 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2383 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.2436 (Rfree = 0.000) for 1699 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 2.65 Search for helices and strands: 0 residues in 0 chains, 1802 seeds are put forward Round 1: 127 peptides, 23 chains. Longest chain 12 peptides. Score 0.362 Round 2: 144 peptides, 23 chains. Longest chain 18 peptides. Score 0.445 Round 3: 149 peptides, 19 chains. Longest chain 23 peptides. Score 0.544 Round 4: 148 peptides, 22 chains. Longest chain 25 peptides. Score 0.483 Round 5: 144 peptides, 19 chains. Longest chain 13 peptides. Score 0.524 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 130, Estimated correctness of the model 9.3 % 1 chains (14 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2a6b-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4915 reflections ( 99.23 % complete ) and 3661 restraints for refining 1702 atoms. 3110 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2563 (Rfree = 0.000) for 1702 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2488 (Rfree = 0.000) for 1688 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2393 (Rfree = 0.000) for 1679 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2330 (Rfree = 0.000) for 1671 atoms. Found 0 (12 requested) and removed 4 (6 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Sun 23 Dec 23:05:35 GMT 2018 Job finished. TimeTaking 42.46