Sun 23 Dec 22:22:52 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 2hq7-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-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/2hq7-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-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 22:23:02 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/2hq7-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-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 194 and 0 Target number of residues in the AU: 194 Target solvent content: 0.6293 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-3.4-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2336 target number of atoms Had to go as low as 0.75 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: 89.671 3.400 Wilson plot Bfac: 66.03 4012 reflections ( 99.41 % complete ) and 0 restraints for refining 2610 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3102 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2618 (Rfree = 0.000) for 2610 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 2679 seeds are put forward NCS extension: 0 residues added, 2679 seeds are put forward Round 1: 161 peptides, 28 chains. Longest chain 13 peptides. Score 0.455 Round 2: 171 peptides, 23 chains. Longest chain 18 peptides. Score 0.602 Round 3: 190 peptides, 23 chains. Longest chain 18 peptides. Score 0.674 Round 4: 202 peptides, 22 chains. Longest chain 21 peptides. Score 0.727 Round 5: 205 peptides, 20 chains. Longest chain 24 peptides. Score 0.762 Taking the results from Round 5 Chains 20, Residues 185, Estimated correctness of the model 72.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4545 restraints for refining 2124 atoms. 3825 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2123 (Rfree = 0.000) for 2124 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 2: After refmac, R = 0.2039 (Rfree = 0.000) for 2088 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. Cycle 3: After refmac, R = 0.1958 (Rfree = 0.000) for 2074 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 4: After refmac, R = 0.1822 (Rfree = 0.000) for 2062 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 5: After refmac, R = 0.1749 (Rfree = 0.000) for 2052 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 2123 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 2155 seeds are put forward Round 1: 178 peptides, 23 chains. Longest chain 16 peptides. Score 0.630 Round 2: 186 peptides, 20 chains. Longest chain 30 peptides. Score 0.707 Round 3: 205 peptides, 20 chains. Longest chain 24 peptides. Score 0.762 Round 4: 202 peptides, 18 chains. Longest chain 31 peptides. Score 0.778 Round 5: 197 peptides, 20 chains. Longest chain 17 peptides. Score 0.740 Taking the results from Round 4 Chains 20, Residues 184, Estimated correctness of the model 75.7 % 3 chains (54 residues) have been docked in sequence Building loops using Loopy2018 20 chains (184 residues) following loop building 3 chains (54 residues) in sequence following loop building ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4052 restraints for refining 2124 atoms. 3117 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2256 (Rfree = 0.000) for 2124 atoms. Found 14 (14 requested) and removed 19 (8 requested) atoms. Cycle 7: After refmac, R = 0.1992 (Rfree = 0.000) for 2106 atoms. Found 5 (13 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.1879 (Rfree = 0.000) for 2091 atoms. Found 6 (13 requested) and removed 9 (7 requested) atoms. Cycle 9: After refmac, R = 0.1809 (Rfree = 0.000) for 2081 atoms. Found 3 (13 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.1712 (Rfree = 0.000) for 2077 atoms. Found 6 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 2128 seeds are put forward NCS extension: 44 residues added (11 deleted due to clashes), 2172 seeds are put forward Round 1: 178 peptides, 23 chains. Longest chain 15 peptides. Score 0.630 Round 2: 192 peptides, 24 chains. Longest chain 26 peptides. Score 0.665 Round 3: 209 peptides, 22 chains. Longest chain 26 peptides. Score 0.747 Round 4: 194 peptides, 23 chains. Longest chain 21 peptides. Score 0.688 Round 5: 191 peptides, 17 chains. Longest chain 27 peptides. Score 0.763 Taking the results from Round 5 Chains 17, Residues 174, Estimated correctness of the model 72.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4682 restraints for refining 2123 atoms. 4003 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2006 (Rfree = 0.000) for 2123 atoms. Found 10 (13 requested) and removed 11 (8 requested) atoms. Cycle 12: After refmac, R = 0.1890 (Rfree = 0.000) for 2119 atoms. Found 7 (12 requested) and removed 8 (8 requested) atoms. Cycle 13: After refmac, R = 0.1798 (Rfree = 0.000) for 2112 atoms. Found 5 (11 requested) and removed 7 (7 requested) atoms. Cycle 14: After refmac, R = 0.1804 (Rfree = 0.000) for 2109 atoms. Found 4 (11 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1811 (Rfree = 0.000) for 2103 atoms. Found 5 (11 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 2165 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2193 seeds are put forward Round 1: 161 peptides, 20 chains. Longest chain 31 peptides. Score 0.616 Round 2: 189 peptides, 19 chains. Longest chain 23 peptides. Score 0.730 Round 3: 186 peptides, 18 chains. Longest chain 22 peptides. Score 0.735 Round 4: 173 peptides, 17 chains. Longest chain 32 peptides. Score 0.710 Round 5: 176 peptides, 20 chains. Longest chain 28 peptides. Score 0.673 Taking the results from Round 3 Chains 18, Residues 168, Estimated correctness of the model 66.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4696 restraints for refining 2124 atoms. 4042 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2063 (Rfree = 0.000) for 2124 atoms. Found 10 (11 requested) and removed 9 (8 requested) atoms. Cycle 17: After refmac, R = 0.1872 (Rfree = 0.000) for 2120 atoms. Found 5 (11 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.1849 (Rfree = 0.000) for 2113 atoms. Found 7 (10 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.1763 (Rfree = 0.000) for 2111 atoms. Found 4 (10 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1744 (Rfree = 0.000) for 2106 atoms. Found 1 (9 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2165 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 2184 seeds are put forward Round 1: 156 peptides, 20 chains. Longest chain 18 peptides. Score 0.595 Round 2: 183 peptides, 20 chains. Longest chain 25 peptides. Score 0.697 Round 3: 175 peptides, 17 chains. Longest chain 22 peptides. Score 0.716 Round 4: 181 peptides, 18 chains. Longest chain 25 peptides. Score 0.720 Round 5: 176 peptides, 16 chains. Longest chain 28 peptides. Score 0.734 Taking the results from Round 5 Chains 17, Residues 160, Estimated correctness of the model 66.2 % 2 chains (45 residues) have been docked in sequence Building loops using Loopy2018 17 chains (160 residues) following loop building 2 chains (45 residues) in sequence following loop building ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4200 restraints for refining 2124 atoms. 3389 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2052 (Rfree = 0.000) for 2124 atoms. Found 7 (10 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.1841 (Rfree = 0.000) for 2112 atoms. Found 4 (9 requested) and removed 10 (7 requested) atoms. Cycle 23: After refmac, R = 0.1745 (Rfree = 0.000) for 2105 atoms. Found 3 (8 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.1717 (Rfree = 0.000) for 2098 atoms. Found 3 (8 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1687 (Rfree = 0.000) for 2094 atoms. Found 0 (8 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 2160 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2190 seeds are put forward Round 1: 163 peptides, 23 chains. Longest chain 14 peptides. Score 0.568 Round 2: 176 peptides, 21 chains. Longest chain 20 peptides. Score 0.657 Round 3: 170 peptides, 24 chains. Longest chain 15 peptides. Score 0.579 Round 4: 176 peptides, 20 chains. Longest chain 27 peptides. Score 0.673 Round 5: 176 peptides, 21 chains. Longest chain 21 peptides. Score 0.657 Taking the results from Round 4 Chains 22, Residues 156, Estimated correctness of the model 50.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4619 restraints for refining 2124 atoms. 3982 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2021 (Rfree = 0.000) for 2124 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 27: After refmac, R = 0.1941 (Rfree = 0.000) for 2120 atoms. Found 1 (8 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.1875 (Rfree = 0.000) for 2111 atoms. Found 6 (7 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1817 (Rfree = 0.000) for 2110 atoms. Found 1 (7 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1771 (Rfree = 0.000) for 2103 atoms. Found 2 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 2156 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2173 seeds are put forward Round 1: 136 peptides, 21 chains. Longest chain 12 peptides. Score 0.481 Round 2: 163 peptides, 21 chains. Longest chain 15 peptides. Score 0.606 Round 3: 153 peptides, 21 chains. Longest chain 16 peptides. Score 0.563 Round 4: 153 peptides, 18 chains. Longest chain 25 peptides. Score 0.620 Round 5: 162 peptides, 21 chains. Longest chain 28 peptides. Score 0.602 Taking the results from Round 4 Chains 19, Residues 135, Estimated correctness of the model 35.1 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4585 restraints for refining 2123 atoms. 3946 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2031 (Rfree = 0.000) for 2123 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.1870 (Rfree = 0.000) for 2112 atoms. Found 4 (8 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.1800 (Rfree = 0.000) for 2106 atoms. Found 3 (7 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1706 (Rfree = 0.000) for 2101 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1644 (Rfree = 0.000) for 2094 atoms. Found 6 (7 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2145 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 2165 seeds are put forward Round 1: 134 peptides, 21 chains. Longest chain 16 peptides. Score 0.471 Round 2: 135 peptides, 17 chains. Longest chain 25 peptides. Score 0.562 Round 3: 134 peptides, 17 chains. Longest chain 15 peptides. Score 0.558 Round 4: 146 peptides, 19 chains. Longest chain 27 peptides. Score 0.571 Round 5: 140 peptides, 18 chains. Longest chain 14 peptides. Score 0.565 Taking the results from Round 4 Chains 19, Residues 127, Estimated correctness of the model 18.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4867 restraints for refining 2124 atoms. 4378 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1911 (Rfree = 0.000) for 2124 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.1785 (Rfree = 0.000) for 2124 atoms. Found 2 (8 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1780 (Rfree = 0.000) for 2118 atoms. Found 2 (7 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1721 (Rfree = 0.000) for 2113 atoms. Found 3 (7 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1677 (Rfree = 0.000) for 2108 atoms. Found 1 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2172 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2196 seeds are put forward Round 1: 116 peptides, 18 chains. Longest chain 13 peptides. Score 0.445 Round 2: 132 peptides, 16 chains. Longest chain 19 peptides. Score 0.570 Round 3: 133 peptides, 15 chains. Longest chain 19 peptides. Score 0.594 Round 4: 131 peptides, 17 chains. Longest chain 19 peptides. Score 0.544 Round 5: 132 peptides, 18 chains. Longest chain 15 peptides. Score 0.527 Taking the results from Round 3 Chains 15, Residues 118, Estimated correctness of the model 26.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4951 restraints for refining 2124 atoms. 4494 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1950 (Rfree = 0.000) for 2124 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.1877 (Rfree = 0.000) for 2122 atoms. Found 3 (8 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1748 (Rfree = 0.000) for 2114 atoms. Found 3 (7 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1716 (Rfree = 0.000) for 2108 atoms. Found 1 (7 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1703 (Rfree = 0.000) for 2101 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 2139 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2160 seeds are put forward Round 1: 115 peptides, 18 chains. Longest chain 15 peptides. Score 0.440 Round 2: 136 peptides, 19 chains. Longest chain 13 peptides. Score 0.525 Round 3: 141 peptides, 21 chains. Longest chain 15 peptides. Score 0.506 Round 4: 147 peptides, 20 chains. Longest chain 22 peptides. Score 0.556 Round 5: 132 peptides, 20 chains. Longest chain 14 peptides. Score 0.483 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 127, Estimated correctness of the model 13.7 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2hq7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 4012 reflections ( 99.41 % complete ) and 4831 restraints for refining 2123 atoms. 4311 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1927 (Rfree = 0.000) for 2123 atoms. Found 0 (8 requested) and removed 6 (8 requested) atoms. Cycle 47: After refmac, R = 0.1859 (Rfree = 0.000) for 2113 atoms. Found 0 (7 requested) and removed 2 (7 requested) atoms. Cycle 48: After refmac, R = 0.1932 (Rfree = 0.000) for 2110 atoms. Found 0 (7 requested) and removed 0 (7 requested) atoms. Cycle 49: After refmac, R = 0.1842 (Rfree = 0.000) for 2110 atoms. TimeTaking 43.55