Mon 24 Dec 07:54:58 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hq7-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-noncs ############### 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 07:55:02 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/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-noncs/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 199 and 0 Target number of residues in the AU: 199 Target solvent content: 0.6197 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: 2hq7-3.2-parrot-noncs.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: 2hq7-3.2-parrot-noncs.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 3.200 Wilson plot Bfac: 61.20 4803 reflections ( 99.48 % complete ) and 0 restraints for refining 2589 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3149 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2760 (Rfree = 0.000) for 2589 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 2638 seeds are put forward NCS extension: 0 residues added, 2638 seeds are put forward Round 1: 142 peptides, 25 chains. Longest chain 12 peptides. Score 0.422 Round 2: 173 peptides, 23 chains. Longest chain 14 peptides. Score 0.610 Round 3: 184 peptides, 23 chains. Longest chain 15 peptides. Score 0.653 Round 4: 201 peptides, 19 chains. Longest chain 29 peptides. Score 0.764 Round 5: 195 peptides, 20 chains. Longest chain 17 peptides. Score 0.734 Taking the results from Round 4 Chains 19, Residues 182, Estimated correctness of the model 77.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4636 restraints for refining 2132 atoms. 3927 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2348 (Rfree = 0.000) for 2132 atoms. Found 17 (19 requested) and removed 18 (9 requested) atoms. Cycle 2: After refmac, R = 0.2181 (Rfree = 0.000) for 2103 atoms. Found 9 (19 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.2115 (Rfree = 0.000) for 2094 atoms. Found 12 (17 requested) and removed 9 (9 requested) atoms. Cycle 4: After refmac, R = 0.2051 (Rfree = 0.000) for 2093 atoms. Found 3 (17 requested) and removed 9 (9 requested) atoms. Cycle 5: After refmac, R = 0.2014 (Rfree = 0.000) for 2085 atoms. Found 7 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.45 Search for helices and strands: 0 residues in 0 chains, 2170 seeds are put forward NCS extension: 42 residues added (3 deleted due to clashes), 2212 seeds are put forward Round 1: 173 peptides, 25 chains. Longest chain 14 peptides. Score 0.573 Round 2: 203 peptides, 23 chains. Longest chain 31 peptides. Score 0.716 Round 3: 198 peptides, 20 chains. Longest chain 26 peptides. Score 0.743 Round 4: 207 peptides, 20 chains. Longest chain 24 peptides. Score 0.767 Round 5: 204 peptides, 22 chains. Longest chain 23 peptides. Score 0.733 Taking the results from Round 4 Chains 20, Residues 187, Estimated correctness of the model 78.1 % 2 chains (26 residues) have been docked in sequence Building loops using Loopy2018 20 chains (187 residues) following loop building 2 chains (26 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4414 restraints for refining 2133 atoms. 3596 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2412 (Rfree = 0.000) for 2133 atoms. Found 17 (17 requested) and removed 15 (9 requested) atoms. Cycle 7: After refmac, R = 0.2219 (Rfree = 0.000) for 2126 atoms. Found 13 (17 requested) and removed 11 (9 requested) atoms. Cycle 8: After refmac, R = 0.2157 (Rfree = 0.000) for 2122 atoms. Found 9 (16 requested) and removed 12 (9 requested) atoms. Cycle 9: After refmac, R = 0.1936 (Rfree = 0.000) for 2112 atoms. Found 5 (16 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.1896 (Rfree = 0.000) for 2107 atoms. Found 4 (15 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.45 Search for helices and strands: 0 residues in 0 chains, 2159 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 2171 seeds are put forward Round 1: 171 peptides, 20 chains. Longest chain 24 peptides. Score 0.655 Round 2: 205 peptides, 20 chains. Longest chain 26 peptides. Score 0.762 Round 3: 198 peptides, 18 chains. Longest chain 28 peptides. Score 0.768 Round 4: 200 peptides, 21 chains. Longest chain 28 peptides. Score 0.735 Round 5: 201 peptides, 20 chains. Longest chain 26 peptides. Score 0.751 Taking the results from Round 3 Chains 20, Residues 180, Estimated correctness of the model 78.2 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4537 restraints for refining 2118 atoms. 3784 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2253 (Rfree = 0.000) for 2118 atoms. Found 15 (15 requested) and removed 20 (9 requested) atoms. Cycle 12: After refmac, R = 0.2041 (Rfree = 0.000) for 2108 atoms. Found 12 (14 requested) and removed 9 (9 requested) atoms. Cycle 13: After refmac, R = 0.2245 (Rfree = 0.000) for 2105 atoms. Found 14 (14 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.1924 (Rfree = 0.000) for 2101 atoms. Found 6 (13 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.1774 (Rfree = 0.000) for 2093 atoms. Found 4 (13 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward NCS extension: 15 residues added (12 deleted due to clashes), 2168 seeds are put forward Round 1: 171 peptides, 20 chains. Longest chain 27 peptides. Score 0.655 Round 2: 199 peptides, 23 chains. Longest chain 27 peptides. Score 0.704 Round 3: 187 peptides, 20 chains. Longest chain 27 peptides. Score 0.710 Round 4: 188 peptides, 21 chains. Longest chain 27 peptides. Score 0.698 Round 5: 181 peptides, 21 chains. Longest chain 27 peptides. Score 0.674 Taking the results from Round 3 Chains 21, Residues 167, Estimated correctness of the model 67.3 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4478 restraints for refining 2133 atoms. 3741 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2055 (Rfree = 0.000) for 2133 atoms. Found 13 (13 requested) and removed 17 (9 requested) atoms. Cycle 17: After refmac, R = 0.1863 (Rfree = 0.000) for 2125 atoms. Found 5 (13 requested) and removed 17 (9 requested) atoms. Cycle 18: After refmac, R = 0.1807 (Rfree = 0.000) for 2112 atoms. Found 8 (12 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.1731 (Rfree = 0.000) for 2108 atoms. Found 4 (12 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.1736 (Rfree = 0.000) for 2100 atoms. Found 4 (11 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2169 seeds are put forward NCS extension: 43 residues added (5 deleted due to clashes), 2212 seeds are put forward Round 1: 156 peptides, 20 chains. Longest chain 24 peptides. Score 0.595 Round 2: 173 peptides, 18 chains. Longest chain 27 peptides. Score 0.695 Round 3: 179 peptides, 19 chains. Longest chain 26 peptides. Score 0.699 Round 4: 182 peptides, 17 chains. Longest chain 27 peptides. Score 0.738 Round 5: 179 peptides, 16 chains. Longest chain 27 peptides. Score 0.743 Taking the results from Round 5 Chains 16, Residues 163, Estimated correctness of the model 73.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4607 restraints for refining 2121 atoms. 3971 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1971 (Rfree = 0.000) for 2121 atoms. Found 11 (11 requested) and removed 13 (9 requested) atoms. Cycle 22: After refmac, R = 0.1852 (Rfree = 0.000) for 2119 atoms. Found 8 (11 requested) and removed 10 (9 requested) atoms. Cycle 23: After refmac, R = 0.1843 (Rfree = 0.000) for 2116 atoms. Found 5 (10 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.1684 (Rfree = 0.000) for 2112 atoms. Found 4 (10 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.1666 (Rfree = 0.000) for 2106 atoms. Found 2 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2163 seeds are put forward NCS extension: 41 residues added (10 deleted due to clashes), 2204 seeds are put forward Round 1: 157 peptides, 22 chains. Longest chain 17 peptides. Score 0.561 Round 2: 173 peptides, 19 chains. Longest chain 27 peptides. Score 0.679 Round 3: 179 peptides, 18 chains. Longest chain 30 peptides. Score 0.714 Round 4: 179 peptides, 18 chains. Longest chain 31 peptides. Score 0.714 Round 5: 180 peptides, 19 chains. Longest chain 32 peptides. Score 0.702 Taking the results from Round 4 Chains 18, Residues 161, Estimated correctness of the model 68.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4626 restraints for refining 2133 atoms. 4000 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1957 (Rfree = 0.000) for 2133 atoms. Found 9 (9 requested) and removed 11 (9 requested) atoms. Cycle 27: After refmac, R = 0.1835 (Rfree = 0.000) for 2130 atoms. Found 7 (9 requested) and removed 10 (9 requested) atoms. Cycle 28: After refmac, R = 0.1819 (Rfree = 0.000) for 2126 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.1829 (Rfree = 0.000) for 2120 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.1782 (Rfree = 0.000) for 2113 atoms. Found 4 (9 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 2197 seeds are put forward NCS extension: 47 residues added (6 deleted due to clashes), 2244 seeds are put forward Round 1: 152 peptides, 19 chains. Longest chain 18 peptides. Score 0.597 Round 2: 176 peptides, 16 chains. Longest chain 27 peptides. Score 0.734 Round 3: 166 peptides, 17 chains. Longest chain 18 peptides. Score 0.687 Round 4: 168 peptides, 19 chains. Longest chain 18 peptides. Score 0.661 Round 5: 159 peptides, 18 chains. Longest chain 26 peptides. Score 0.644 Taking the results from Round 2 Chains 19, Residues 160, Estimated correctness of the model 72.1 % 2 chains (33 residues) have been docked in sequence Building loops using Loopy2018 19 chains (160 residues) following loop building 2 chains (33 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4357 restraints for refining 2133 atoms. 3609 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2046 (Rfree = 0.000) for 2133 atoms. Found 9 (9 requested) and removed 20 (9 requested) atoms. Cycle 32: After refmac, R = 0.1905 (Rfree = 0.000) for 2119 atoms. Found 5 (9 requested) and removed 12 (9 requested) atoms. Cycle 33: After refmac, R = 0.1857 (Rfree = 0.000) for 2110 atoms. Found 8 (9 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.1794 (Rfree = 0.000) for 2109 atoms. Found 3 (9 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.1782 (Rfree = 0.000) for 2101 atoms. Found 5 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.40 Search for helices and strands: 0 residues in 0 chains, 2172 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2187 seeds are put forward Round 1: 146 peptides, 17 chains. Longest chain 20 peptides. Score 0.611 Round 2: 165 peptides, 18 chains. Longest chain 26 peptides. Score 0.667 Round 3: 180 peptides, 20 chains. Longest chain 26 peptides. Score 0.687 Round 4: 182 peptides, 20 chains. Longest chain 26 peptides. Score 0.694 Round 5: 161 peptides, 20 chains. Longest chain 21 peptides. Score 0.616 Taking the results from Round 4 Chains 22, Residues 162, Estimated correctness of the model 63.9 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4501 restraints for refining 2118 atoms. 3845 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1937 (Rfree = 0.000) for 2118 atoms. Found 9 (9 requested) and removed 14 (9 requested) atoms. Cycle 37: After refmac, R = 0.1826 (Rfree = 0.000) for 2113 atoms. Found 6 (9 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.1767 (Rfree = 0.000) for 2108 atoms. Found 2 (9 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1759 (Rfree = 0.000) for 2101 atoms. Found 2 (9 requested) and removed 10 (9 requested) atoms. Cycle 40: After refmac, R = 0.1739 (Rfree = 0.000) for 2093 atoms. Found 6 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2136 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 2178 seeds are put forward Round 1: 152 peptides, 21 chains. Longest chain 17 peptides. Score 0.558 Round 2: 155 peptides, 16 chains. Longest chain 27 peptides. Score 0.664 Round 3: 145 peptides, 14 chains. Longest chain 18 peptides. Score 0.662 Round 4: 148 peptides, 17 chains. Longest chain 27 peptides. Score 0.619 Round 5: 162 peptides, 17 chains. Longest chain 16 peptides. Score 0.672 Taking the results from Round 5 Chains 17, Residues 145, Estimated correctness of the model 59.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4674 restraints for refining 2130 atoms. 4111 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1992 (Rfree = 0.000) for 2130 atoms. Found 9 (9 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.1902 (Rfree = 0.000) for 2127 atoms. Found 9 (9 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.1851 (Rfree = 0.000) for 2126 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.1803 (Rfree = 0.000) for 2120 atoms. Found 4 (9 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2045 (Rfree = 0.000) for 2113 atoms. Found 9 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 2175 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2193 seeds are put forward Round 1: 146 peptides, 20 chains. Longest chain 13 peptides. Score 0.551 Round 2: 162 peptides, 18 chains. Longest chain 27 peptides. Score 0.656 Round 3: 156 peptides, 21 chains. Longest chain 17 peptides. Score 0.576 Round 4: 161 peptides, 15 chains. Longest chain 23 peptides. Score 0.702 Round 5: 155 peptides, 18 chains. Longest chain 25 peptides. Score 0.628 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 146, Estimated correctness of the model 65.6 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hq7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4803 reflections ( 99.48 % complete ) and 4733 restraints for refining 2133 atoms. 4164 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1917 (Rfree = 0.000) for 2133 atoms. Found 0 (9 requested) and removed 1 (9 requested) atoms. Cycle 47: After refmac, R = 0.1832 (Rfree = 0.000) for 2132 atoms. Found 0 (9 requested) and removed 2 (9 requested) atoms. Cycle 48: After refmac, R = 0.1858 (Rfree = 0.000) for 2130 atoms. Found 0 (9 requested) and removed 3 (9 requested) atoms. Cycle 49: After refmac, R = 0.1845 (Rfree = 0.000) for 2127 atoms. TimeTaking 27.72