Mon 24 Dec 00:17:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zko-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:17:48 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/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-mrncs/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 173 and 0 Target number of residues in the AU: 173 Target solvent content: 0.6164 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-3.6-parrot-mrncs.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: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2176 target number of atoms Had to go as low as 0.60 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 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: 47.500 3.600 Wilson plot Bfac: 59.59 2852 reflections ( 92.51 % complete ) and 0 restraints for refining 2416 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3522 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3799 (Rfree = 0.000) for 2416 atoms. Found 15 (15 requested) and removed 37 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.72 Search for helices and strands: 0 residues in 0 chains, 2411 seeds are put forward NCS extension: 0 residues added, 2411 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.207 Round 2: 49 peptides, 12 chains. Longest chain 5 peptides. Score 0.176 Round 3: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.229 Round 4: 71 peptides, 16 chains. Longest chain 8 peptides. Score 0.224 Round 5: 77 peptides, 15 chains. Longest chain 11 peptides. Score 0.303 Taking the results from Round 5 Chains 15, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4640 restraints for refining 1972 atoms. 4407 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3230 (Rfree = 0.000) for 1972 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 2: After refmac, R = 0.2877 (Rfree = 0.000) for 1938 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.3219 (Rfree = 0.000) for 1925 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 4: After refmac, R = 0.2874 (Rfree = 0.000) for 1907 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 5: After refmac, R = 0.2979 (Rfree = 0.000) for 1894 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 1925 seeds are put forward NCS extension: 0 residues added, 1925 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 8 peptides. Score 0.239 Round 2: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.277 Round 3: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.352 Round 4: 90 peptides, 17 chains. Longest chain 9 peptides. Score 0.335 Round 5: 99 peptides, 16 chains. Longest chain 10 peptides. Score 0.425 Taking the results from Round 5 Chains 16, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 3888 restraints for refining 1737 atoms. 3572 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3108 (Rfree = 0.000) for 1737 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 7: After refmac, R = 0.2982 (Rfree = 0.000) for 1711 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 8: After refmac, R = 0.3147 (Rfree = 0.000) for 1703 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.2940 (Rfree = 0.000) for 1692 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.2493 (Rfree = 0.000) for 1688 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.72 Search for helices and strands: 0 residues in 0 chains, 1719 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1728 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 2: 86 peptides, 15 chains. Longest chain 9 peptides. Score 0.367 Round 3: 98 peptides, 18 chains. Longest chain 10 peptides. Score 0.361 Round 4: 106 peptides, 17 chains. Longest chain 10 peptides. Score 0.442 Round 5: 103 peptides, 15 chains. Longest chain 15 peptides. Score 0.477 Taking the results from Round 5 Chains 15, Residues 88, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 3706 restraints for refining 1699 atoms. 3352 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2462 (Rfree = 0.000) for 1699 atoms. Found 10 (10 requested) and removed 25 (5 requested) atoms. Cycle 12: After refmac, R = 0.2558 (Rfree = 0.000) for 1674 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 13: After refmac, R = 0.2421 (Rfree = 0.000) for 1661 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 14: After refmac, R = 0.1788 (Rfree = 0.000) for 1660 atoms. Found 1 (10 requested) and removed 9 (5 requested) atoms. Cycle 15: After refmac, R = 0.1652 (Rfree = 0.000) for 1650 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 1692 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1707 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 11 peptides. Score 0.347 Round 2: 106 peptides, 17 chains. Longest chain 16 peptides. Score 0.442 Round 3: 100 peptides, 16 chains. Longest chain 11 peptides. Score 0.431 Round 4: 103 peptides, 15 chains. Longest chain 16 peptides. Score 0.477 Round 5: 109 peptides, 16 chains. Longest chain 16 peptides. Score 0.487 Taking the results from Round 5 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 3805 restraints for refining 1739 atoms. 3449 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2508 (Rfree = 0.000) for 1739 atoms. Found 11 (11 requested) and removed 25 (5 requested) atoms. Cycle 17: After refmac, R = 0.2270 (Rfree = 0.000) for 1722 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.2177 (Rfree = 0.000) for 1719 atoms. Found 6 (11 requested) and removed 13 (5 requested) atoms. Cycle 19: After refmac, R = 0.2007 (Rfree = 0.000) for 1707 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1718 (Rfree = 0.000) for 1707 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.81 Search for helices and strands: 0 residues in 0 chains, 1727 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 1750 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.314 Round 2: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.399 Round 3: 105 peptides, 18 chains. Longest chain 10 peptides. Score 0.408 Round 4: 109 peptides, 17 chains. Longest chain 10 peptides. Score 0.460 Round 5: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 4 Chains 17, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 3828 restraints for refining 1754 atoms. 3477 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2442 (Rfree = 0.000) for 1754 atoms. Found 9 (11 requested) and removed 25 (5 requested) atoms. Cycle 22: After refmac, R = 0.2212 (Rfree = 0.000) for 1728 atoms. Found 8 (11 requested) and removed 15 (5 requested) atoms. Cycle 23: After refmac, R = 0.2199 (Rfree = 0.000) for 1717 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 24: After refmac, R = 0.1976 (Rfree = 0.000) for 1713 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1789 (Rfree = 0.000) for 1710 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.85 Search for helices and strands: 0 residues in 0 chains, 1736 seeds are put forward NCS extension: 0 residues added, 1736 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 8 peptides. Score 0.263 Round 2: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.373 Round 3: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.415 Round 4: 121 peptides, 20 chains. Longest chain 12 peptides. Score 0.454 Round 5: 122 peptides, 20 chains. Longest chain 10 peptides. Score 0.460 Taking the results from Round 5 Chains 20, Residues 102, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4179 restraints for refining 1865 atoms. 3760 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2453 (Rfree = 0.000) for 1865 atoms. Found 6 (11 requested) and removed 31 (5 requested) atoms. Cycle 27: After refmac, R = 0.2546 (Rfree = 0.000) for 1835 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 28: After refmac, R = 0.2190 (Rfree = 0.000) for 1813 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.2205 (Rfree = 0.000) for 1806 atoms. Found 5 (11 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.2131 (Rfree = 0.000) for 1796 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.86 Search for helices and strands: 0 residues in 0 chains, 1814 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1826 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 9 peptides. Score 0.278 Round 2: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.379 Round 3: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.353 Round 4: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.344 Round 5: 87 peptides, 15 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 2 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4160 restraints for refining 1798 atoms. 3872 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2472 (Rfree = 0.000) for 1798 atoms. Found 8 (11 requested) and removed 22 (5 requested) atoms. Cycle 32: After refmac, R = 0.2282 (Rfree = 0.000) for 1778 atoms. Found 9 (11 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.2359 (Rfree = 0.000) for 1774 atoms. Found 3 (11 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.2159 (Rfree = 0.000) for 1765 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. Cycle 35: After refmac, R = 0.2202 (Rfree = 0.000) for 1757 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.87 Search for helices and strands: 0 residues in 0 chains, 1778 seeds are put forward NCS extension: 0 residues added, 1778 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 8 peptides. Score 0.231 Round 2: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.337 Round 3: 87 peptides, 16 chains. Longest chain 8 peptides. Score 0.344 Round 4: 82 peptides, 14 chains. Longest chain 9 peptides. Score 0.370 Round 5: 92 peptides, 15 chains. Longest chain 10 peptides. Score 0.408 Taking the results from Round 5 Chains 15, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4208 restraints for refining 1822 atoms. 3915 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2615 (Rfree = 0.000) for 1822 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. Cycle 37: After refmac, R = 0.2348 (Rfree = 0.000) for 1813 atoms. Found 2 (11 requested) and removed 14 (5 requested) atoms. Cycle 38: After refmac, R = 0.2578 (Rfree = 0.000) for 1798 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 39: After refmac, R = 0.2065 (Rfree = 0.000) for 1788 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.2184 (Rfree = 0.000) for 1782 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 1795 seeds are put forward NCS extension: 0 residues added, 1795 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 8 peptides. Score 0.274 Round 2: 89 peptides, 16 chains. Longest chain 11 peptides. Score 0.358 Round 3: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.372 Round 4: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.364 Round 5: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.379 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 ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4204 restraints for refining 1840 atoms. 3916 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2479 (Rfree = 0.000) for 1840 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 42: After refmac, R = 0.2208 (Rfree = 0.000) for 1831 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 43: After refmac, R = 0.1980 (Rfree = 0.000) for 1820 atoms. Found 4 (11 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2129 (Rfree = 0.000) for 1813 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 45: After refmac, R = 0.2253 (Rfree = 0.000) for 1800 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.80 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward NCS extension: 0 residues added, 1818 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.268 Round 2: 80 peptides, 15 chains. Longest chain 11 peptides. Score 0.325 Round 3: 79 peptides, 14 chains. Longest chain 11 peptides. Score 0.348 Round 4: 74 peptides, 13 chains. Longest chain 11 peptides. Score 0.344 Round 5: 72 peptides, 14 chains. Longest chain 11 peptides. Score 0.297 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 65, 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 1zko-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2852 reflections ( 92.51 % complete ) and 4152 restraints for refining 1817 atoms. 3906 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2220 (Rfree = 0.000) for 1817 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2259 (Rfree = 0.000) for 1807 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2184 (Rfree = 0.000) for 1801 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1858 (Rfree = 0.000) for 1792 atoms. TimeTaking 26.87