Sun 23 Dec 22:23:02 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 2ess-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ess-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ess-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-4.0-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/2ess-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-4.0-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 22:23:12 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/2ess-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-4.0-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 187 and 0 Target number of residues in the AU: 187 Target solvent content: 0.6743 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 248 Adjusted target solvent content: 0.57 Input MTZ file: 2ess-4.0-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: 152 Cell parameters: 91.150 91.150 64.770 90.000 90.000 120.000 Input sequence file: 2ess-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 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: 29.962 4.001 Wilson plot Bfac: 94.96 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2786 reflections ( 99.68 % complete ) and 0 restraints for refining 2207 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3874 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3494 (Rfree = 0.000) for 2207 atoms. Found 7 (10 requested) and removed 30 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.46 Search for helices and strands: 0 residues in 0 chains, 2206 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.248 Round 2: 106 peptides, 19 chains. Longest chain 8 peptides. Score 0.350 Round 3: 97 peptides, 18 chains. Longest chain 11 peptides. Score 0.324 Round 4: 116 peptides, 20 chains. Longest chain 11 peptides. Score 0.381 Round 5: 116 peptides, 20 chains. Longest chain 9 peptides. Score 0.381 Taking the results from Round 5 Chains 20, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2786 reflections ( 99.68 % complete ) and 4349 restraints for refining 1790 atoms. 3985 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2780 (Rfree = 0.000) for 1790 atoms. Found 5 (8 requested) and removed 15 (4 requested) atoms. Cycle 2: After refmac, R = 0.2958 (Rfree = 0.000) for 1757 atoms. Found 6 (8 requested) and removed 24 (4 requested) atoms. Cycle 3: After refmac, R = 0.2903 (Rfree = 0.000) for 1729 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 4: After refmac, R = 0.2710 (Rfree = 0.000) for 1708 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 5: After refmac, R = 0.2672 (Rfree = 0.000) for 1694 atoms. Found 6 (8 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.81 3.47 Search for helices and strands: 0 residues in 0 chains, 1741 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.283 Round 2: 104 peptides, 16 chains. Longest chain 16 peptides. Score 0.411 Round 3: 113 peptides, 18 chains. Longest chain 11 peptides. Score 0.411 Round 4: 105 peptides, 17 chains. Longest chain 13 peptides. Score 0.392 Round 5: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 5 Chains 18, Residues 95, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2786 reflections ( 99.68 % complete ) and 4210 restraints for refining 1791 atoms. 3815 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2671 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 26 (4 requested) atoms. Cycle 7: After refmac, R = 0.2403 (Rfree = 0.000) for 1766 atoms. Found 4 (8 requested) and removed 11 (4 requested) atoms. Cycle 8: After refmac, R = 0.2372 (Rfree = 0.000) for 1753 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.2337 (Rfree = 0.000) for 1753 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2269 (Rfree = 0.000) for 1745 atoms. Found 0 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.89 3.54 Search for helices and strands: 0 residues in 0 chains, 1773 seeds are put forward Round 1: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.311 Round 2: 104 peptides, 18 chains. Longest chain 10 peptides. Score 0.363 Round 3: 109 peptides, 19 chains. Longest chain 13 peptides. Score 0.367 Round 4: 110 peptides, 17 chains. Longest chain 14 peptides. Score 0.419 Round 5: 110 peptides, 17 chains. Longest chain 16 peptides. Score 0.419 Taking the results from Round 5 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2786 reflections ( 99.68 % complete ) and 4203 restraints for refining 1791 atoms. 3825 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2883 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 12: After refmac, R = 0.2684 (Rfree = 0.000) for 1770 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 13: After refmac, R = 0.2647 (Rfree = 0.000) for 1751 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 14: After refmac, R = 0.2470 (Rfree = 0.000) for 1737 atoms. Found 6 (8 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2519 (Rfree = 0.000) for 1723 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 1759 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.250 Round 2: 85 peptides, 14 chains. Longest chain 16 peptides. Score 0.356 Round 3: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.320 Round 4: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.333 Round 5: 106 peptides, 17 chains. Longest chain 10 peptides. Score 0.398 Taking the results from Round 5 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2786 reflections ( 99.68 % complete ) and 4035 restraints for refining 1761 atoms. 3696 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2442 (Rfree = 0.000) for 1761 atoms. Found 5 (8 requested) and removed 16 (4 requested) atoms. Cycle 17: After refmac, R = 0.2843 (Rfree = 0.000) for 1737 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 18: After refmac, R = 0.2504 (Rfree = 0.000) for 1721 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 19: After refmac, R = 0.2664 (Rfree = 0.000) for 1701 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 20: After refmac, R = 0.2400 (Rfree = 0.000) for 1684 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.51 Search for helices and strands: 0 residues in 0 chains, 1756 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.263 Round 2: 97 peptides, 16 chains. Longest chain 10 peptides. Score 0.373 Round 3: 106 peptides, 17 chains. Longest chain 9 peptides. Score 0.398 Round 4: 98 peptides, 16 chains. Longest chain 9 peptides. Score 0.379 Round 5: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.331 Taking the results from Round 3 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2786 reflections ( 99.68 % complete ) and 3952 restraints for refining 1728 atoms. 3613 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2460 (Rfree = 0.000) for 1728 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 22: After refmac, R = 0.2582 (Rfree = 0.000) for 1708 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 23: After refmac, R = 0.2469 (Rfree = 0.000) for 1698 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 24: After refmac, R = 0.2351 (Rfree = 0.000) for 1692 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 25: After refmac, R = 0.2406 (Rfree = 0.000) for 1686 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.42 Search for helices and strands: 0 residues in 0 chains, 1735 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 6 peptides. Score 0.244 Round 2: 109 peptides, 22 chains. Longest chain 7 peptides. Score 0.295 Round 3: 99 peptides, 19 chains. Longest chain 8 peptides. Score 0.311 Round 4: 110 peptides, 21 chains. Longest chain 9 peptides. Score 0.325 Round 5: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.309 Taking the results from Round 4 Chains 21, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2786 reflections ( 99.68 % complete ) and 3958 restraints for refining 1768 atoms. 3623 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2587 (Rfree = 0.000) for 1768 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.2383 (Rfree = 0.000) for 1749 atoms. Found 4 (8 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.2336 (Rfree = 0.000) for 1731 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.2213 (Rfree = 0.000) for 1723 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 30: After refmac, R = 0.2330 (Rfree = 0.000) for 1715 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 1772 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 6 peptides. Score 0.237 Round 2: 104 peptides, 20 chains. Longest chain 11 peptides. Score 0.315 Round 3: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.314 Round 4: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.337 Round 5: 98 peptides, 18 chains. Longest chain 9 peptides. Score 0.330 Taking the results from Round 4 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2786 reflections ( 99.68 % complete ) and 4169 restraints for refining 1791 atoms. 3874 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2577 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2298 (Rfree = 0.000) for 1780 atoms. Found 5 (8 requested) and removed 13 (4 requested) atoms. Cycle 33: After refmac, R = 0.2417 (Rfree = 0.000) for 1764 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 34: After refmac, R = 0.2224 (Rfree = 0.000) for 1758 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2328 (Rfree = 0.000) for 1749 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.48 Search for helices and strands: 0 residues in 0 chains, 1792 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 6 peptides. Score 0.207 Round 2: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.298 Round 3: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.339 Round 4: 92 peptides, 17 chains. Longest chain 11 peptides. Score 0.320 Round 5: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.345 Taking the results from Round 5 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2786 reflections ( 99.68 % complete ) and 4138 restraints for refining 1791 atoms. 3850 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2440 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 37: After refmac, R = 0.2558 (Rfree = 0.000) for 1780 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.2224 (Rfree = 0.000) for 1773 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 39: After refmac, R = 0.2477 (Rfree = 0.000) for 1765 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 40: After refmac, R = 0.2319 (Rfree = 0.000) for 1759 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.43 Search for helices and strands: 0 residues in 0 chains, 1814 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 8 peptides. Score 0.229 Round 2: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.316 Round 3: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.308 Round 4: 92 peptides, 18 chains. Longest chain 10 peptides. Score 0.295 Round 5: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.326 Taking the results from Round 5 Chains 17, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2786 reflections ( 99.68 % complete ) and 4274 restraints for refining 1791 atoms. 3987 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2376 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2493 (Rfree = 0.000) for 1787 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 43: After refmac, R = 0.2285 (Rfree = 0.000) for 1779 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2292 (Rfree = 0.000) for 1773 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.2366 (Rfree = 0.000) for 1771 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.42 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.203 Round 2: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.267 Round 3: 73 peptides, 14 chains. Longest chain 11 peptides. Score 0.284 Round 4: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.269 Round 5: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.314 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 74, 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 2ess-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2786 reflections ( 99.68 % complete ) and 4082 restraints for refining 1791 atoms. 3803 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2387 (Rfree = 0.000) for 1791 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2343 (Rfree = 0.000) for 1774 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2325 (Rfree = 0.000) for 1763 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2250 (Rfree = 0.000) for 1753 atoms. TimeTaking 33.98