Sun 23 Dec 22:22:43 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 1zko-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zko-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zko-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.2-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/1zko-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.2-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 22:22:53 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/1zko-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.2-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 179 and 0 Target number of residues in the AU: 179 Target solvent content: 0.6031 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-3.2-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: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-3.2-parrot-hancs.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 3.200 Wilson plot Bfac: 53.76 4004 reflections ( 92.28 % complete ) and 0 restraints for refining 2430 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3480 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3388 (Rfree = 0.000) for 2430 atoms. Found 19 (21 requested) and removed 39 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.01 3.45 Search for helices and strands: 0 residues in 0 chains, 2436 seeds are put forward NCS extension: 0 residues added, 2436 seeds are put forward Round 1: 102 peptides, 23 chains. Longest chain 7 peptides. Score 0.242 Round 2: 109 peptides, 22 chains. Longest chain 9 peptides. Score 0.321 Round 3: 118 peptides, 25 chains. Longest chain 8 peptides. Score 0.297 Round 4: 123 peptides, 21 chains. Longest chain 14 peptides. Score 0.440 Round 5: 119 peptides, 22 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 4 Chains 23, Residues 102, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4532 restraints for refining 1984 atoms. 4096 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3071 (Rfree = 0.000) for 1984 atoms. Found 11 (17 requested) and removed 20 (8 requested) atoms. Cycle 2: After refmac, R = 0.2942 (Rfree = 0.000) for 1954 atoms. Found 14 (17 requested) and removed 12 (8 requested) atoms. Cycle 3: After refmac, R = 0.2918 (Rfree = 0.000) for 1943 atoms. Found 9 (17 requested) and removed 13 (8 requested) atoms. Cycle 4: After refmac, R = 0.2857 (Rfree = 0.000) for 1938 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2817 (Rfree = 0.000) for 1931 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.57 Search for helices and strands: 0 residues in 0 chains, 1967 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 1975 seeds are put forward Round 1: 104 peptides, 23 chains. Longest chain 7 peptides. Score 0.256 Round 2: 118 peptides, 23 chains. Longest chain 11 peptides. Score 0.354 Round 3: 128 peptides, 23 chains. Longest chain 14 peptides. Score 0.418 Round 4: 127 peptides, 22 chains. Longest chain 11 peptides. Score 0.438 Round 5: 130 peptides, 23 chains. Longest chain 10 peptides. Score 0.431 Taking the results from Round 4 Chains 22, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4450 restraints for refining 1950 atoms. 4052 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2955 (Rfree = 0.000) for 1950 atoms. Found 11 (17 requested) and removed 12 (8 requested) atoms. Cycle 7: After refmac, R = 0.3068 (Rfree = 0.000) for 1938 atoms. Found 10 (17 requested) and removed 16 (8 requested) atoms. Cycle 8: After refmac, R = 0.2928 (Rfree = 0.000) for 1927 atoms. Found 10 (17 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.2759 (Rfree = 0.000) for 1915 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2758 (Rfree = 0.000) for 1904 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 3.47 Search for helices and strands: 0 residues in 0 chains, 1951 seeds are put forward NCS extension: 0 residues added, 1951 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 7 peptides. Score 0.285 Round 2: 117 peptides, 23 chains. Longest chain 9 peptides. Score 0.347 Round 3: 117 peptides, 20 chains. Longest chain 13 peptides. Score 0.429 Round 4: 119 peptides, 20 chains. Longest chain 11 peptides. Score 0.442 Round 5: 132 peptides, 23 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 5 Chains 23, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4460 restraints for refining 1939 atoms. 4047 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2967 (Rfree = 0.000) for 1939 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.3052 (Rfree = 0.000) for 1922 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.2886 (Rfree = 0.000) for 1928 atoms. Found 14 (17 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.2895 (Rfree = 0.000) for 1924 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.2632 (Rfree = 0.000) for 1927 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.02 3.46 Search for helices and strands: 0 residues in 0 chains, 1971 seeds are put forward NCS extension: 0 residues added, 1971 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 7 peptides. Score 0.244 Round 2: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.401 Round 3: 122 peptides, 18 chains. Longest chain 15 peptides. Score 0.511 Round 4: 133 peptides, 20 chains. Longest chain 13 peptides. Score 0.524 Round 5: 144 peptides, 19 chains. Longest chain 15 peptides. Score 0.603 Taking the results from Round 5 Chains 19, Residues 125, Estimated correctness of the model 41.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4122 restraints for refining 1908 atoms. 3641 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2864 (Rfree = 0.000) for 1908 atoms. Found 12 (17 requested) and removed 15 (8 requested) atoms. Cycle 17: After refmac, R = 0.2829 (Rfree = 0.000) for 1903 atoms. Found 13 (17 requested) and removed 14 (8 requested) atoms. Cycle 18: After refmac, R = 0.2555 (Rfree = 0.000) for 1897 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.2517 (Rfree = 0.000) for 1890 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.2507 (Rfree = 0.000) for 1885 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 3.42 Search for helices and strands: 0 residues in 0 chains, 1934 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 1942 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 12 peptides. Score 0.325 Round 2: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.384 Round 3: 94 peptides, 18 chains. Longest chain 8 peptides. Score 0.333 Round 4: 102 peptides, 18 chains. Longest chain 11 peptides. Score 0.388 Round 5: 108 peptides, 20 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 4 Chains 18, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4381 restraints for refining 1890 atoms. 4063 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2904 (Rfree = 0.000) for 1890 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.2770 (Rfree = 0.000) for 1882 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.2842 (Rfree = 0.000) for 1882 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 24: After refmac, R = 0.2835 (Rfree = 0.000) for 1880 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2937 (Rfree = 0.000) for 1875 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.89 3.31 Search for helices and strands: 0 residues in 0 chains, 1937 seeds are put forward NCS extension: 0 residues added, 1937 seeds are put forward Round 1: 86 peptides, 20 chains. Longest chain 7 peptides. Score 0.214 Round 2: 100 peptides, 22 chains. Longest chain 7 peptides. Score 0.257 Round 3: 88 peptides, 17 chains. Longest chain 12 peptides. Score 0.321 Round 4: 89 peptides, 17 chains. Longest chain 10 peptides. Score 0.328 Round 5: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.390 Taking the results from Round 5 Chains 17, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4136 restraints for refining 1830 atoms. 3829 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2998 (Rfree = 0.000) for 1830 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 27: After refmac, R = 0.2702 (Rfree = 0.000) for 1825 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2829 (Rfree = 0.000) for 1824 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.2856 (Rfree = 0.000) for 1825 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.3003 (Rfree = 0.000) for 1827 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 3.43 Search for helices and strands: 0 residues in 0 chains, 1882 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 1889 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.208 Round 2: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.292 Round 3: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.308 Round 4: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.325 Round 5: 82 peptides, 13 chains. Longest chain 9 peptides. Score 0.400 Taking the results from Round 5 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4096 restraints for refining 1811 atoms. 3833 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2778 (Rfree = 0.000) for 1811 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.2892 (Rfree = 0.000) for 1812 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.2853 (Rfree = 0.000) for 1811 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.2682 (Rfree = 0.000) for 1817 atoms. Found 15 (16 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.2462 (Rfree = 0.000) for 1822 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.98 3.41 Search for helices and strands: 0 residues in 0 chains, 1859 seeds are put forward NCS extension: 0 residues added, 1859 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.209 Round 2: 88 peptides, 17 chains. Longest chain 11 peptides. Score 0.321 Round 3: 81 peptides, 16 chains. Longest chain 10 peptides. Score 0.301 Round 4: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.278 Round 5: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.341 Taking the results from Round 5 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 3985 restraints for refining 1772 atoms. 3743 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2823 (Rfree = 0.000) for 1772 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 37: After refmac, R = 0.2740 (Rfree = 0.000) for 1769 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 38: After refmac, R = 0.2272 (Rfree = 0.000) for 1772 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. Cycle 39: After refmac, R = 0.2551 (Rfree = 0.000) for 1765 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.2320 (Rfree = 0.000) for 1765 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.96 3.39 Search for helices and strands: 0 residues in 0 chains, 1815 seeds are put forward NCS extension: 0 residues added, 1815 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 7 peptides. Score 0.224 Round 2: 68 peptides, 15 chains. Longest chain 7 peptides. Score 0.233 Round 3: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.272 Round 4: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.282 Round 5: 65 peptides, 11 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 5 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 3790 restraints for refining 1722 atoms. 3585 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2561 (Rfree = 0.000) for 1722 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 42: After refmac, R = 0.2581 (Rfree = 0.000) for 1723 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.2380 (Rfree = 0.000) for 1726 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.2265 (Rfree = 0.000) for 1732 atoms. Found 12 (15 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.2066 (Rfree = 0.000) for 1734 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.94 3.37 Search for helices and strands: 0 residues in 0 chains, 1771 seeds are put forward NCS extension: 0 residues added, 1771 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 6 peptides. Score 0.218 Round 2: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.307 Round 3: 70 peptides, 14 chains. Longest chain 12 peptides. Score 0.282 Round 4: 66 peptides, 13 chains. Longest chain 10 peptides. Score 0.284 Round 5: 76 peptides, 15 chains. Longest chain 13 peptides. Score 0.295 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 56, 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. 4004 reflections ( 92.28 % complete ) and 3666 restraints for refining 1674 atoms. 3455 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2256 (Rfree = 0.000) for 1674 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2175 (Rfree = 0.000) for 1664 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2148 (Rfree = 0.000) for 1656 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2018 (Rfree = 0.000) for 1648 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. TimeTaking 31.87