Mon 24 Dec 08:02:39 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 2hq7-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.6-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/2hq7-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.6-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 08:02:44 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/2hq7-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.6-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 188 and 0 Target number of residues in the AU: 188 Target solvent content: 0.6408 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: 2hq7-3.6-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: 2hq7-3.6-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 3.600 Wilson plot Bfac: 72.21 3381 reflections ( 99.30 % complete ) and 0 restraints for refining 2614 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3268 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2806 (Rfree = 0.000) for 2614 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.78 Search for helices and strands: 0 residues in 0 chains, 2659 seeds are put forward NCS extension: 0 residues added, 2659 seeds are put forward Round 1: 106 peptides, 20 chains. Longest chain 9 peptides. Score 0.338 Round 2: 147 peptides, 20 chains. Longest chain 14 peptides. Score 0.556 Round 3: 156 peptides, 19 chains. Longest chain 17 peptides. Score 0.614 Round 4: 176 peptides, 22 chains. Longest chain 16 peptides. Score 0.640 Round 5: 182 peptides, 18 chains. Longest chain 19 peptides. Score 0.723 Taking the results from Round 5 Chains 19, Residues 164, Estimated correctness of the model 56.4 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4511 restraints for refining 2117 atoms. 3805 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2286 (Rfree = 0.000) for 2117 atoms. Found 10 (13 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.2116 (Rfree = 0.000) for 2083 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2066 (Rfree = 0.000) for 2069 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.1998 (Rfree = 0.000) for 2062 atoms. Found 2 (12 requested) and removed 11 (6 requested) atoms. Cycle 5: After refmac, R = 0.1995 (Rfree = 0.000) for 2048 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.74 Search for helices and strands: 0 residues in 0 chains, 2121 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2141 seeds are put forward Round 1: 145 peptides, 27 chains. Longest chain 11 peptides. Score 0.392 Round 2: 165 peptides, 22 chains. Longest chain 19 peptides. Score 0.596 Round 3: 180 peptides, 23 chains. Longest chain 22 peptides. Score 0.638 Round 4: 184 peptides, 20 chains. Longest chain 31 peptides. Score 0.700 Round 5: 182 peptides, 20 chains. Longest chain 21 peptides. Score 0.694 Taking the results from Round 4 Chains 20, Residues 164, Estimated correctness of the model 49.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4587 restraints for refining 2094 atoms. 3951 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2053 (Rfree = 0.000) for 2094 atoms. Found 9 (12 requested) and removed 15 (6 requested) atoms. Cycle 7: After refmac, R = 0.1872 (Rfree = 0.000) for 2080 atoms. Found 3 (12 requested) and removed 14 (6 requested) atoms. Cycle 8: After refmac, R = 0.1856 (Rfree = 0.000) for 2063 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.1796 (Rfree = 0.000) for 2056 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.1755 (Rfree = 0.000) for 2048 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.71 Search for helices and strands: 0 residues in 0 chains, 2126 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 2161 seeds are put forward Round 1: 157 peptides, 25 chains. Longest chain 14 peptides. Score 0.499 Round 2: 157 peptides, 22 chains. Longest chain 12 peptides. Score 0.561 Round 3: 170 peptides, 26 chains. Longest chain 17 peptides. Score 0.540 Round 4: 176 peptides, 21 chains. Longest chain 21 peptides. Score 0.657 Round 5: 168 peptides, 21 chains. Longest chain 16 peptides. Score 0.626 Taking the results from Round 4 Chains 21, Residues 155, Estimated correctness of the model 35.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4877 restraints for refining 2117 atoms. 4278 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1909 (Rfree = 0.000) for 2117 atoms. Found 4 (12 requested) and removed 15 (6 requested) atoms. Cycle 12: After refmac, R = 0.1780 (Rfree = 0.000) for 2098 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.1765 (Rfree = 0.000) for 2092 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.1723 (Rfree = 0.000) for 2084 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.1724 (Rfree = 0.000) for 2079 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.72 Search for helices and strands: 0 residues in 0 chains, 2139 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2152 seeds are put forward Round 1: 138 peptides, 25 chains. Longest chain 10 peptides. Score 0.400 Round 2: 162 peptides, 23 chains. Longest chain 15 peptides. Score 0.563 Round 3: 154 peptides, 21 chains. Longest chain 17 peptides. Score 0.567 Round 4: 155 peptides, 19 chains. Longest chain 17 peptides. Score 0.610 Round 5: 157 peptides, 20 chains. Longest chain 18 peptides. Score 0.600 Taking the results from Round 4 Chains 19, Residues 136, Estimated correctness of the model 18.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 5010 restraints for refining 2117 atoms. 4485 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1987 (Rfree = 0.000) for 2117 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 17: After refmac, R = 0.2057 (Rfree = 0.000) for 2111 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.1964 (Rfree = 0.000) for 2109 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.1669 (Rfree = 0.000) for 2103 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1617 (Rfree = 0.000) for 2097 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.71 Search for helices and strands: 0 residues in 0 chains, 2151 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2171 seeds are put forward Round 1: 127 peptides, 21 chains. Longest chain 13 peptides. Score 0.434 Round 2: 152 peptides, 22 chains. Longest chain 13 peptides. Score 0.538 Round 3: 160 peptides, 25 chains. Longest chain 12 peptides. Score 0.514 Round 4: 154 peptides, 20 chains. Longest chain 17 peptides. Score 0.587 Round 5: 156 peptides, 20 chains. Longest chain 24 peptides. Score 0.595 Taking the results from Round 5 Chains 20, Residues 136, Estimated correctness of the model 12.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4895 restraints for refining 2117 atoms. 4371 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1946 (Rfree = 0.000) for 2117 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 22: After refmac, R = 0.1850 (Rfree = 0.000) for 2112 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.1784 (Rfree = 0.000) for 2112 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.1729 (Rfree = 0.000) for 2109 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1675 (Rfree = 0.000) for 2108 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.74 Search for helices and strands: 0 residues in 0 chains, 2167 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2188 seeds are put forward Round 1: 112 peptides, 22 chains. Longest chain 10 peptides. Score 0.323 Round 2: 128 peptides, 21 chains. Longest chain 11 peptides. Score 0.439 Round 3: 142 peptides, 21 chains. Longest chain 14 peptides. Score 0.511 Round 4: 145 peptides, 21 chains. Longest chain 14 peptides. Score 0.526 Round 5: 134 peptides, 18 chains. Longest chain 13 peptides. Score 0.537 Taking the results from Round 5 Chains 18, Residues 116, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4859 restraints for refining 2117 atoms. 4357 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1855 (Rfree = 0.000) for 2117 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 27: After refmac, R = 0.1755 (Rfree = 0.000) for 2115 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.1847 (Rfree = 0.000) for 2103 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.1789 (Rfree = 0.000) for 2093 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1748 (Rfree = 0.000) for 2084 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.75 Search for helices and strands: 0 residues in 0 chains, 2157 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2173 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 11 peptides. Score 0.353 Round 2: 138 peptides, 21 chains. Longest chain 14 peptides. Score 0.491 Round 3: 138 peptides, 23 chains. Longest chain 12 peptides. Score 0.446 Round 4: 125 peptides, 18 chains. Longest chain 12 peptides. Score 0.492 Round 5: 145 peptides, 20 chains. Longest chain 12 peptides. Score 0.546 Taking the results from Round 5 Chains 20, Residues 125, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4821 restraints for refining 2117 atoms. 4305 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1915 (Rfree = 0.000) for 2117 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 32: After refmac, R = 0.1846 (Rfree = 0.000) for 2107 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.1856 (Rfree = 0.000) for 2101 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.1778 (Rfree = 0.000) for 2094 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1672 (Rfree = 0.000) for 2086 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.79 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2165 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.320 Round 2: 116 peptides, 19 chains. Longest chain 14 peptides. Score 0.421 Round 3: 121 peptides, 18 chains. Longest chain 18 peptides. Score 0.472 Round 4: 129 peptides, 18 chains. Longest chain 14 peptides. Score 0.512 Round 5: 115 peptides, 15 chains. Longest chain 18 peptides. Score 0.510 Taking the results from Round 4 Chains 18, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4936 restraints for refining 2090 atoms. 4510 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1936 (Rfree = 0.000) for 2090 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.1990 (Rfree = 0.000) for 2083 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.1891 (Rfree = 0.000) for 2082 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.1586 (Rfree = 0.000) for 2085 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.1694 (Rfree = 0.000) for 2078 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.75 Search for helices and strands: 0 residues in 0 chains, 2133 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2151 seeds are put forward Round 1: 97 peptides, 17 chains. Longest chain 12 peptides. Score 0.361 Round 2: 117 peptides, 18 chains. Longest chain 16 peptides. Score 0.450 Round 3: 115 peptides, 16 chains. Longest chain 23 peptides. Score 0.487 Round 4: 117 peptides, 19 chains. Longest chain 20 peptides. Score 0.426 Round 5: 125 peptides, 16 chains. Longest chain 21 peptides. Score 0.537 Taking the results from Round 5 Chains 16, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 5081 restraints for refining 2117 atoms. 4661 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1952 (Rfree = 0.000) for 2117 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 42: After refmac, R = 0.1966 (Rfree = 0.000) for 2104 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.1842 (Rfree = 0.000) for 2103 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1869 (Rfree = 0.000) for 2105 atoms. Found 10 (12 requested) and removed 11 (6 requested) atoms. Cycle 45: After refmac, R = 0.1764 (Rfree = 0.000) for 2100 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.72 Search for helices and strands: 0 residues in 0 chains, 2164 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2194 seeds are put forward Round 1: 95 peptides, 15 chains. Longest chain 17 peptides. Score 0.401 Round 2: 104 peptides, 15 chains. Longest chain 20 peptides. Score 0.452 Round 3: 110 peptides, 19 chains. Longest chain 17 peptides. Score 0.387 Round 4: 115 peptides, 17 chains. Longest chain 17 peptides. Score 0.463 Round 5: 104 peptides, 14 chains. Longest chain 20 peptides. Score 0.477 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 90, 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 2hq7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3381 reflections ( 99.30 % complete ) and 4986 restraints for refining 2065 atoms. 4640 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1863 (Rfree = 0.000) for 2065 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1887 (Rfree = 0.000) for 2056 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1858 (Rfree = 0.000) for 2045 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1595 (Rfree = 0.000) for 2038 atoms. TimeTaking 29.4