Starting phenix.real_space_refine on Tue Oct 27 19:40:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m9b_23722/10_2026/7m9b_23722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m9b_23722/10_2026/7m9b_23722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m9b_23722/10_2026/7m9b_23722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m9b_23722/10_2026/7m9b_23722.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m9b_23722/10_2026/7m9b_23722.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m9b_23722/10_2026/7m9b_23722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m9b_23722/10_2026/7m9b_23722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m9b_23722/10_2026/7m9b_23722.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 96 5.16 5 C 16294 2.51 5 N 4756 2.21 5 O 4919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26139 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2054 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2058 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2062 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "M" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "N" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.94, per 1000 atoms: 0.23 Number of scatterers: 26139 At special positions: 0 Unit cell: (144.97, 144.97, 171.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 74 15.00 O 4919 8.00 N 4756 7.00 C 16294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 884.7 milliseconds 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5784 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 12 sheets defined 63.6% alpha, 6.4% beta 24 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.504A pdb=" N LEU A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 65 through 75 removed outlier: 3.537A pdb=" N ASP A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.528A pdb=" N LYS A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 removed outlier: 4.237A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.514A pdb=" N ASP A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.893A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 259 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.564A pdb=" N ALA A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.569A pdb=" N TYR B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 150 through 151 No H-bonds generated for 'chain 'B' and resid 150 through 151' Processing helix chain 'B' and resid 152 through 164 removed outlier: 4.131A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 removed outlier: 3.803A pdb=" N ASP B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.877A pdb=" N LEU B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 188' Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.532A pdb=" N PHE B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 4.779A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 Processing helix chain 'B' and resid 264 through 275 removed outlier: 3.960A pdb=" N LEU B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 36 through 53 Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.741A pdb=" N HIS C 77 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.616A pdb=" N LEU C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 136 Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 150 through 164 removed outlier: 3.980A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.979A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.562A pdb=" N LEU C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 190' Processing helix chain 'C' and resid 200 through 215 Processing helix chain 'C' and resid 226 through 238 Processing helix chain 'C' and resid 240 through 259 removed outlier: 4.035A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 247 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 275 Processing helix chain 'D' and resid 20 through 30 removed outlier: 3.615A pdb=" N GLU D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 53 Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.517A pdb=" N HIS D 77 " --> pdb=" O TYR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.580A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 200 through 215 Processing helix chain 'D' and resid 226 through 238 removed outlier: 3.728A pdb=" N ARG D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 77 removed outlier: 3.710A pdb=" N HIS E 77 " --> pdb=" O TYR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 121 through 136 removed outlier: 3.866A pdb=" N CYS E 136 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 149 Processing helix chain 'E' and resid 153 through 164 removed outlier: 3.529A pdb=" N VAL E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.740A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 200 through 215 Processing helix chain 'E' and resid 226 through 238 removed outlier: 4.453A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 258 Processing helix chain 'E' and resid 264 through 275 Processing helix chain 'F' and resid 20 through 29 removed outlier: 3.933A pdb=" N LEU F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 53 removed outlier: 3.555A pdb=" N ASP F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.690A pdb=" N HIS F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.509A pdb=" N ASP F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS F 136 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 164 removed outlier: 3.865A pdb=" N ALA F 155 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 182 removed outlier: 3.740A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 201 through 215 Processing helix chain 'F' and resid 226 through 238 Processing helix chain 'F' and resid 240 through 257 Processing helix chain 'F' and resid 264 through 275 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 77 removed outlier: 3.551A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS G 77 " --> pdb=" O TYR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.536A pdb=" N CYS G 136 " --> pdb=" O VAL G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 174 through 183 removed outlier: 3.956A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 179 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP G 183 " --> pdb=" O VAL G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 200 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.904A pdb=" N ARG G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 275 removed outlier: 3.907A pdb=" N GLN G 269 " --> pdb=" O LYS G 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU G 270 " --> pdb=" O ALA G 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 271 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS G 273 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 30 removed outlier: 3.515A pdb=" N GLU H 24 " --> pdb=" O TRP H 20 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 53 removed outlier: 3.822A pdb=" N GLY H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS H 49 " --> pdb=" O TRP H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.685A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS H 77 " --> pdb=" O TYR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 121 through 136 removed outlier: 3.520A pdb=" N CYS H 136 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 165 removed outlier: 3.553A pdb=" N GLY H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 183 removed outlier: 3.673A pdb=" N ALA H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP H 183 " --> pdb=" O VAL H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 Processing helix chain 'H' and resid 200 through 215 Processing helix chain 'H' and resid 226 through 238 removed outlier: 3.755A pdb=" N ARG H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 259 removed outlier: 4.187A pdb=" N LEU H 256 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER H 257 " --> pdb=" O ILE H 253 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 275 removed outlier: 3.553A pdb=" N VAL H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS H 273 " --> pdb=" O GLN H 269 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 30 Processing helix chain 'I' and resid 36 through 53 Processing helix chain 'I' and resid 65 through 77 removed outlier: 4.098A pdb=" N HIS I 77 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 113 Processing helix chain 'I' and resid 121 through 136 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 173 through 181 removed outlier: 3.761A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 Processing helix chain 'I' and resid 200 through 215 removed outlier: 3.656A pdb=" N GLN I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 238 removed outlier: 3.504A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER I 235 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA I 236 " --> pdb=" O ILE I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 258 Processing helix chain 'I' and resid 264 through 275 Processing helix chain 'J' and resid 20 through 30 Processing helix chain 'J' and resid 36 through 53 Processing helix chain 'J' and resid 65 through 77 Processing helix chain 'J' and resid 101 through 113 removed outlier: 3.536A pdb=" N LEU J 113 " --> pdb=" O ILE J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 136 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 150 through 164 removed outlier: 3.867A pdb=" N PHE J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 181 removed outlier: 4.177A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 Processing helix chain 'J' and resid 200 through 215 Processing helix chain 'J' and resid 226 through 238 removed outlier: 3.556A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 258 Processing helix chain 'J' and resid 264 through 273 removed outlier: 3.653A pdb=" N ALA J 272 " --> pdb=" O LEU J 268 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS J 273 " --> pdb=" O GLN J 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 29 Processing helix chain 'K' and resid 36 through 53 Processing helix chain 'K' and resid 65 through 77 removed outlier: 3.709A pdb=" N ARG K 74 " --> pdb=" O CYS K 70 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS K 77 " --> pdb=" O TYR K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.585A pdb=" N LEU K 113 " --> pdb=" O ILE K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 136 Processing helix chain 'K' and resid 145 through 149 Processing helix chain 'K' and resid 152 through 164 removed outlier: 4.444A pdb=" N ASP K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 181 removed outlier: 3.683A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 190 Processing helix chain 'K' and resid 200 through 216 Processing helix chain 'K' and resid 226 through 238 Processing helix chain 'K' and resid 240 through 258 removed outlier: 4.372A pdb=" N GLU K 246 " --> pdb=" O GLY K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 275 removed outlier: 3.640A pdb=" N TYR K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 30 Processing helix chain 'L' and resid 36 through 53 Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.613A pdb=" N ARG L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS L 77 " --> pdb=" O TYR L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 113 Processing helix chain 'L' and resid 121 through 136 Processing helix chain 'L' and resid 145 through 149 Processing helix chain 'L' and resid 150 through 164 Processing helix chain 'L' and resid 175 through 181 Processing helix chain 'L' and resid 183 through 190 Processing helix chain 'L' and resid 201 through 215 Processing helix chain 'L' and resid 226 through 238 removed outlier: 4.377A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 233 " --> pdb=" O MET L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 258 Processing helix chain 'L' and resid 264 through 275 removed outlier: 3.646A pdb=" N VAL L 271 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS L 273 " --> pdb=" O GLN L 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.311A pdb=" N VAL A 92 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.437A pdb=" N VAL B 92 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS B 56 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLY B 172 " --> pdb=" O CYS B 56 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL B 58 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.672A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASP C 144 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE C 94 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 141 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL C 171 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 143 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 170 " --> pdb=" O CYS C 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.315A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP D 144 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE D 94 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 141 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL D 171 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE D 143 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N CYS D 56 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N GLY D 172 " --> pdb=" O CYS D 56 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL D 58 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.457A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASP E 144 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE E 94 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.433A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU F 141 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL F 171 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE F 143 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.497A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU G 141 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL G 171 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE G 143 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.687A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASP H 144 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE H 94 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.454A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N CYS I 56 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLY I 172 " --> pdb=" O CYS I 56 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL I 58 " --> pdb=" O GLY I 172 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU I 194 " --> pdb=" O ARG I 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.424A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.609A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU K 141 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL K 171 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE K 143 " --> pdb=" O VAL K 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 91 through 94 removed outlier: 6.286A pdb=" N VAL L 92 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU L 141 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL L 171 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE L 143 " --> pdb=" O VAL L 171 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N CYS L 56 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N GLY L 172 " --> pdb=" O CYS L 56 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL L 58 " --> pdb=" O GLY L 172 " (cutoff:3.500A) 1307 hydrogen bonds defined for protein. 3861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7514 1.34 - 1.45: 3809 1.45 - 1.57: 15061 1.57 - 1.69: 136 1.69 - 1.81: 144 Bond restraints: 26664 Sorted by residual: bond pdb=" N PRO K 90 " pdb=" CD PRO K 90 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.38e+01 bond pdb=" C3' DA M 21 " pdb=" C2' DA M 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT N 3 " pdb=" C2' DT N 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT N 9 " pdb=" C2' DT N 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT N 25 " pdb=" C2' DT N 25 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 26659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 36070 5.41 - 10.82: 50 10.82 - 16.23: 4 16.23 - 21.64: 3 21.64 - 27.05: 2 Bond angle restraints: 36129 Sorted by residual: angle pdb=" N ASP C 174 " pdb=" CA ASP C 174 " pdb=" C ASP C 174 " ideal model delta sigma weight residual 114.75 98.33 16.42 1.26e+00 6.30e-01 1.70e+02 angle pdb=" N ARG C 85 " pdb=" CA ARG C 85 " pdb=" C ARG C 85 " ideal model delta sigma weight residual 109.81 136.86 -27.05 2.21e+00 2.05e-01 1.50e+02 angle pdb=" N THR C 173 " pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 110.56 132.84 -22.28 1.94e+00 2.66e-01 1.32e+02 angle pdb=" N LYS C 217 " pdb=" CA LYS C 217 " pdb=" C LYS C 217 " ideal model delta sigma weight residual 109.96 92.98 16.98 1.49e+00 4.50e-01 1.30e+02 angle pdb=" N ARG C 85 " pdb=" CA ARG C 85 " pdb=" CB ARG C 85 " ideal model delta sigma weight residual 110.37 92.03 18.34 1.78e+00 3.16e-01 1.06e+02 ... (remaining 36124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 15975 35.10 - 70.19: 432 70.19 - 105.29: 13 105.29 - 140.39: 8 140.39 - 175.48: 6 Dihedral angle restraints: 16434 sinusoidal: 7494 harmonic: 8940 Sorted by residual: dihedral pdb=" O2A ADP L 301 " pdb=" O3A ADP L 301 " pdb=" PA ADP L 301 " pdb=" PB ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 115.49 -175.48 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP J 301 " pdb=" O3A ADP J 301 " pdb=" PA ADP J 301 " pdb=" PB ADP J 301 " ideal model delta sinusoidal sigma weight residual 300.00 128.31 171.69 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP K 301 " pdb=" O3A ADP K 301 " pdb=" PB ADP K 301 " pdb=" PA ADP K 301 " ideal model delta sinusoidal sigma weight residual -60.00 101.87 -161.88 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 16431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 4056 0.159 - 0.318: 13 0.318 - 0.477: 1 0.477 - 0.636: 1 0.636 - 0.795: 1 Chirality restraints: 4072 Sorted by residual: chirality pdb=" CA THR C 173 " pdb=" N THR C 173 " pdb=" C THR C 173 " pdb=" CB THR C 173 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" CA ARG C 85 " pdb=" N ARG C 85 " pdb=" C ARG C 85 " pdb=" CB ARG C 85 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" CA GLN C 81 " pdb=" N GLN C 81 " pdb=" C GLN C 81 " pdb=" CB GLN C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 4069 not shown) Planarity restraints: 4356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 85 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.94e+00 pdb=" N PRO C 86 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 85 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO D 86 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 85 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO H 86 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 86 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 86 " 0.024 5.00e-02 4.00e+02 ... (remaining 4353 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 10 2.09 - 2.79: 5352 2.79 - 3.49: 35095 3.49 - 4.20: 57985 4.20 - 4.90: 102386 Nonbonded interactions: 200828 Sorted by model distance: nonbonded pdb=" OE2 GLU A 212 " pdb=" OG SER A 222 " model vdw 1.382 3.040 nonbonded pdb=" OE1 GLU C 212 " pdb=" CB LEU C 224 " model vdw 1.822 3.440 nonbonded pdb=" OE1 GLU E 152 " pdb=" NZ LYS F 99 " model vdw 1.927 3.120 nonbonded pdb=" OD2 ASP F 124 " pdb=" NZ LYS G 119 " model vdw 1.945 3.120 nonbonded pdb=" OE2 GLU E 188 " pdb=" OG SER F 62 " model vdw 2.025 3.040 ... (remaining 200823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'B' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'C' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'D' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'E' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'F' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 216 or (resid 217 and (name N or name CA or name C or name O or name \ CB )) or resid 218 through 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 275)) selection = (chain 'G' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'H' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 211 or ( \ resid 212 and (name N or name CA or name C or name O or name CB )) or resid 213 \ through 275)) selection = (chain 'I' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'J' and (resid 19 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 216 o \ r (resid 217 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 18 through 224 or (resid 225 and (name N or name CA or name C or name O or name \ CB )) or resid 226 through 275)) selection = (chain 'K' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 216 or (resid 217 and (name N or name CA or name C or name O or name \ CB )) or resid 218 through 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 275)) selection = (chain 'L' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 24.940 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26665 Z= 0.212 Angle : 0.678 27.054 36129 Z= 0.428 Chirality : 0.045 0.795 4072 Planarity : 0.004 0.066 4356 Dihedral : 14.972 175.485 10650 Min Nonbonded Distance : 1.382 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3060 helix: 0.25 (0.11), residues: 1810 sheet: 0.73 (0.36), residues: 204 loop : -0.05 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.011 0.001 TYR J 93 PHE 0.008 0.001 PHE H 204 TRP 0.015 0.001 TRP K 20 HIS 0.005 0.001 HIS K 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.21 (26664) covalent geometry : angle 0.67769 / 0.43 (36129) hydrogen bonds : bond 0.15820 / 10.29 ( 1355) hydrogen bonds : angle 6.09345 / 4.44 ( 3957) Misc. bond : bond 0.00171 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1420 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.7690 (mt) cc_final: 0.6640 (tp) REVERT: A 129 THR cc_start: 0.8523 (m) cc_final: 0.8193 (t) REVERT: A 229 MET cc_start: 0.3554 (mtp) cc_final: 0.3196 (mpp) REVERT: B 107 LYS cc_start: 0.9036 (mtpt) cc_final: 0.8627 (mtmm) REVERT: C 46 LEU cc_start: 0.8938 (mt) cc_final: 0.8706 (mt) REVERT: C 173 THR cc_start: 0.7704 (p) cc_final: 0.7097 (t) REVERT: C 196 PHE cc_start: 0.7620 (t80) cc_final: 0.6875 (t80) REVERT: D 141 LEU cc_start: 0.9466 (tp) cc_final: 0.9242 (tt) REVERT: D 159 ASP cc_start: 0.7892 (m-30) cc_final: 0.7622 (m-30) REVERT: E 156 ASP cc_start: 0.7928 (m-30) cc_final: 0.7525 (m-30) REVERT: E 163 ASP cc_start: 0.7713 (m-30) cc_final: 0.6599 (m-30) REVERT: G 71 ASP cc_start: 0.6116 (m-30) cc_final: 0.5631 (m-30) REVERT: H 93 TYR cc_start: 0.7811 (t80) cc_final: 0.7326 (t80) REVERT: H 127 ASP cc_start: 0.7890 (m-30) cc_final: 0.7654 (m-30) REVERT: H 159 ASP cc_start: 0.7100 (m-30) cc_final: 0.6812 (m-30) REVERT: I 99 LYS cc_start: 0.7410 (mttt) cc_final: 0.7005 (mttm) REVERT: I 170 LEU cc_start: 0.9291 (mt) cc_final: 0.9060 (mt) REVERT: I 198 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7895 (mtmt) REVERT: I 232 ILE cc_start: 0.8159 (mt) cc_final: 0.7869 (tt) REVERT: J 93 TYR cc_start: 0.7404 (t80) cc_final: 0.7097 (t80) REVERT: J 123 SER cc_start: 0.8816 (p) cc_final: 0.8563 (p) REVERT: J 144 ASP cc_start: 0.8272 (t0) cc_final: 0.7841 (t0) REVERT: J 245 ASP cc_start: 0.7971 (t0) cc_final: 0.7749 (t0) REVERT: K 46 LEU cc_start: 0.8224 (mt) cc_final: 0.7816 (mt) REVERT: L 190 PHE cc_start: 0.6452 (m-80) cc_final: 0.6221 (m-80) outliers start: 3 outliers final: 2 residues processed: 1421 average time/residue: 0.1891 time to fit residues: 408.1543 Evaluate side-chains 722 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 720 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain I residue 77 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0010 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN D 185 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN I 185 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN J 38 GLN J 77 HIS L 185 GLN L 193 HIS L 269 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.094444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.065996 restraints weight = 91954.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068273 restraints weight = 48130.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069771 restraints weight = 31348.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070718 restraints weight = 23415.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071403 restraints weight = 19243.443| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26665 Z= 0.196 Angle : 0.863 11.575 36129 Z= 0.438 Chirality : 0.048 0.272 4072 Planarity : 0.006 0.063 4356 Dihedral : 16.086 179.038 4199 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.84 % Rotamer: Outliers : 3.73 % Allowed : 18.05 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3060 helix: 0.76 (0.12), residues: 1845 sheet: 1.12 (0.36), residues: 204 loop : 0.22 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 27 TYR 0.029 0.002 TYR A 75 PHE 0.022 0.002 PHE L 154 TRP 0.028 0.002 TRP L 20 HIS 0.017 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (26664) covalent geometry : angle 0.86262 / 0.44 (36129) hydrogen bonds : bond 0.06690 / 4.51 ( 1355) hydrogen bonds : angle 5.19777 / 3.76 ( 3957) Misc. bond : bond 0.00120 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 797 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.8546 (tpp) cc_final: 0.8173 (mmm) REVERT: B 93 TYR cc_start: 0.8718 (t80) cc_final: 0.8251 (t80) REVERT: B 145 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 159 ASP cc_start: 0.9319 (t70) cc_final: 0.8582 (t0) REVERT: B 182 ARG cc_start: 0.9416 (mtp85) cc_final: 0.9105 (ptp-110) REVERT: C 46 LEU cc_start: 0.9665 (mt) cc_final: 0.9405 (mp) REVERT: C 80 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7791 (tp-100) REVERT: C 185 GLN cc_start: 0.7987 (mp10) cc_final: 0.7454 (mp10) REVERT: C 199 LEU cc_start: 0.8429 (tp) cc_final: 0.7982 (tp) REVERT: C 223 ASN cc_start: 0.8552 (t0) cc_final: 0.8315 (t0) REVERT: D 111 GLU cc_start: 0.8503 (pp20) cc_final: 0.8285 (pp20) REVERT: D 138 VAL cc_start: 0.9301 (t) cc_final: 0.9050 (p) REVERT: D 145 GLU cc_start: 0.8693 (pt0) cc_final: 0.8259 (pt0) REVERT: D 159 ASP cc_start: 0.9264 (m-30) cc_final: 0.8806 (m-30) REVERT: D 210 MET cc_start: 0.9176 (ttt) cc_final: 0.8813 (ttp) REVERT: D 214 MET cc_start: 0.8758 (mmm) cc_final: 0.8515 (mmm) REVERT: D 246 GLU cc_start: 0.9313 (tt0) cc_final: 0.8884 (pp20) REVERT: E 46 LEU cc_start: 0.9707 (mt) cc_final: 0.9489 (mt) REVERT: E 75 TYR cc_start: 0.8671 (t80) cc_final: 0.8398 (t80) REVERT: E 80 GLN cc_start: 0.8626 (pm20) cc_final: 0.8207 (pm20) REVERT: E 132 VAL cc_start: 0.9684 (t) cc_final: 0.9424 (p) REVERT: E 159 ASP cc_start: 0.9271 (t0) cc_final: 0.8938 (t0) REVERT: E 163 ASP cc_start: 0.8627 (m-30) cc_final: 0.8365 (m-30) REVERT: E 250 GLU cc_start: 0.9322 (tp30) cc_final: 0.8932 (tp30) REVERT: E 274 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7378 (mt-10) REVERT: F 99 LYS cc_start: 0.9434 (ttmm) cc_final: 0.8960 (tppt) REVERT: F 145 GLU cc_start: 0.8730 (tp30) cc_final: 0.8515 (tp30) REVERT: F 204 PHE cc_start: 0.9473 (t80) cc_final: 0.9062 (t80) REVERT: F 214 MET cc_start: 0.8754 (ttm) cc_final: 0.8367 (ttt) REVERT: F 232 ILE cc_start: 0.9447 (mt) cc_final: 0.8871 (tp) REVERT: G 143 ILE cc_start: 0.8651 (mm) cc_final: 0.8328 (tp) REVERT: G 162 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8456 (mp0) REVERT: G 183 ASP cc_start: 0.8250 (t0) cc_final: 0.7980 (t0) REVERT: G 190 PHE cc_start: 0.7826 (m-80) cc_final: 0.7404 (m-10) REVERT: H 127 ASP cc_start: 0.8995 (m-30) cc_final: 0.8714 (m-30) REVERT: H 148 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.8883 (ptp-170) REVERT: H 156 ASP cc_start: 0.9231 (m-30) cc_final: 0.9025 (m-30) REVERT: H 159 ASP cc_start: 0.8354 (m-30) cc_final: 0.7889 (m-30) REVERT: H 183 ASP cc_start: 0.8330 (t70) cc_final: 0.7906 (t70) REVERT: H 229 MET cc_start: 0.9132 (ptm) cc_final: 0.8899 (ptp) REVERT: I 140 MET cc_start: 0.8960 (ttp) cc_final: 0.8742 (ttm) REVERT: I 170 LEU cc_start: 0.9654 (mt) cc_final: 0.9396 (mt) REVERT: I 185 GLN cc_start: 0.9196 (mt0) cc_final: 0.8765 (mp10) REVERT: J 75 TYR cc_start: 0.8712 (m-80) cc_final: 0.8393 (m-10) REVERT: J 185 GLN cc_start: 0.8894 (mt0) cc_final: 0.8429 (mp10) REVERT: J 229 MET cc_start: 0.9026 (mmm) cc_final: 0.8536 (mmm) REVERT: K 42 LEU cc_start: 0.9686 (tp) cc_final: 0.9448 (tp) REVERT: K 46 LEU cc_start: 0.9594 (mt) cc_final: 0.9375 (mt) REVERT: K 199 LEU cc_start: 0.8692 (mm) cc_final: 0.8210 (tp) REVERT: K 210 MET cc_start: 0.8893 (tpt) cc_final: 0.8142 (tpp) REVERT: K 214 MET cc_start: 0.9389 (mmm) cc_final: 0.8912 (mmp) REVERT: K 250 GLU cc_start: 0.9232 (tt0) cc_final: 0.8758 (tm-30) REVERT: L 75 TYR cc_start: 0.8737 (m-10) cc_final: 0.8409 (m-80) REVERT: L 97 HIS cc_start: 0.7726 (m-70) cc_final: 0.7493 (m-70) REVERT: L 168 VAL cc_start: 0.9610 (m) cc_final: 0.9377 (p) REVERT: L 250 GLU cc_start: 0.8765 (pt0) cc_final: 0.8182 (pt0) REVERT: L 254 ARG cc_start: 0.9499 (ptp-110) cc_final: 0.9101 (ptp-170) outliers start: 100 outliers final: 54 residues processed: 856 average time/residue: 0.1714 time to fit residues: 230.6241 Evaluate side-chains 706 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 651 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 20 TRP Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 269 GLN Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [259, 92, 269, 4, 224, 157, 190, 71, 117, 155, 110] chunk 259 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN D 22 GLN D 185 GLN D 269 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 ASN L 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.092145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063633 restraints weight = 93082.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065852 restraints weight = 48969.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067294 restraints weight = 32053.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068206 restraints weight = 24023.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068861 restraints weight = 19847.548| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26665 Z= 0.194 Angle : 0.783 11.068 36129 Z= 0.398 Chirality : 0.046 0.290 4072 Planarity : 0.005 0.054 4356 Dihedral : 16.026 175.507 4199 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 3.88 % Allowed : 19.84 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3060 helix: 0.91 (0.12), residues: 1878 sheet: 1.32 (0.28), residues: 314 loop : 0.16 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 158 TYR 0.022 0.002 TYR J 275 PHE 0.026 0.002 PHE G 106 TRP 0.018 0.002 TRP K 20 HIS 0.020 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (26664) covalent geometry : angle 0.78286 / 0.40 (36129) hydrogen bonds : bond 0.05924 / 4.00 ( 1355) hydrogen bonds : angle 5.02300 / 3.64 ( 3957) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 680 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.8479 (tpp) cc_final: 0.8233 (mmm) REVERT: A 229 MET cc_start: 0.0458 (mmt) cc_final: 0.0221 (mmt) REVERT: B 145 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7945 (mp0) REVERT: B 159 ASP cc_start: 0.9090 (t70) cc_final: 0.8846 (t0) REVERT: B 182 ARG cc_start: 0.9472 (mtp85) cc_final: 0.9109 (ptp-110) REVERT: B 211 TRP cc_start: 0.9200 (m100) cc_final: 0.8323 (m100) REVERT: C 46 LEU cc_start: 0.9686 (mt) cc_final: 0.9418 (mp) REVERT: C 80 GLN cc_start: 0.8450 (tp-100) cc_final: 0.7902 (tp-100) REVERT: C 98 GLN cc_start: 0.8946 (tp40) cc_final: 0.8711 (mm-40) REVERT: C 185 GLN cc_start: 0.8200 (mp10) cc_final: 0.7727 (mp10) REVERT: C 199 LEU cc_start: 0.8363 (tp) cc_final: 0.7906 (tp) REVERT: C 223 ASN cc_start: 0.8982 (t0) cc_final: 0.8480 (t0) REVERT: D 159 ASP cc_start: 0.9264 (m-30) cc_final: 0.8775 (m-30) REVERT: D 246 GLU cc_start: 0.9286 (tt0) cc_final: 0.8836 (pp20) REVERT: E 46 LEU cc_start: 0.9754 (mt) cc_final: 0.9551 (mt) REVERT: E 75 TYR cc_start: 0.8716 (t80) cc_final: 0.8441 (t80) REVERT: E 80 GLN cc_start: 0.8710 (pm20) cc_final: 0.8147 (pm20) REVERT: E 132 VAL cc_start: 0.9747 (t) cc_final: 0.9494 (p) REVERT: E 159 ASP cc_start: 0.9299 (t0) cc_final: 0.8939 (t0) REVERT: E 163 ASP cc_start: 0.8678 (m-30) cc_final: 0.8424 (m-30) REVERT: E 274 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7560 (mt-10) REVERT: F 37 GLN cc_start: 0.9125 (pp30) cc_final: 0.8922 (pp30) REVERT: F 81 GLN cc_start: 0.8681 (tp40) cc_final: 0.8454 (mm110) REVERT: F 125 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: F 145 GLU cc_start: 0.8929 (tp30) cc_final: 0.8654 (tp30) REVERT: F 204 PHE cc_start: 0.9471 (t80) cc_final: 0.9147 (t80) REVERT: G 53 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8319 (mmm-85) REVERT: G 140 MET cc_start: 0.8894 (ttp) cc_final: 0.7940 (mtp) REVERT: G 150 LYS cc_start: 0.8601 (tttt) cc_final: 0.8393 (mtmm) REVERT: G 183 ASP cc_start: 0.8321 (t0) cc_final: 0.7980 (t0) REVERT: G 185 GLN cc_start: 0.9102 (tt0) cc_final: 0.8796 (tm-30) REVERT: G 196 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7989 (t80) REVERT: G 211 TRP cc_start: 0.9013 (t60) cc_final: 0.8809 (t60) REVERT: G 214 MET cc_start: 0.8649 (mmt) cc_final: 0.7965 (mpp) REVERT: H 127 ASP cc_start: 0.9005 (m-30) cc_final: 0.8706 (m-30) REVERT: H 148 ARG cc_start: 0.9434 (OUTLIER) cc_final: 0.8853 (ptp-170) REVERT: H 159 ASP cc_start: 0.8453 (m-30) cc_final: 0.8020 (m-30) REVERT: H 169 VAL cc_start: 0.9801 (t) cc_final: 0.9593 (p) REVERT: H 183 ASP cc_start: 0.8279 (t70) cc_final: 0.7655 (t70) REVERT: I 47 ASP cc_start: 0.8585 (m-30) cc_final: 0.8215 (m-30) REVERT: I 140 MET cc_start: 0.9018 (ttp) cc_final: 0.8813 (ttm) REVERT: I 170 LEU cc_start: 0.9691 (mt) cc_final: 0.9375 (mt) REVERT: I 229 MET cc_start: 0.9415 (mmm) cc_final: 0.9137 (mmm) REVERT: I 250 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8221 (tm-30) REVERT: J 75 TYR cc_start: 0.8757 (m-80) cc_final: 0.8433 (m-10) REVERT: J 111 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8702 (mt-10) REVERT: J 176 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8405 (tt) REVERT: J 180 ILE cc_start: 0.9259 (mt) cc_final: 0.8991 (mp) REVERT: J 185 GLN cc_start: 0.8955 (mt0) cc_final: 0.8602 (mp10) REVERT: J 229 MET cc_start: 0.8968 (mmm) cc_final: 0.8363 (mmm) REVERT: J 274 GLU cc_start: 0.9139 (pt0) cc_final: 0.8576 (pm20) REVERT: K 199 LEU cc_start: 0.8770 (mm) cc_final: 0.8082 (tp) REVERT: K 204 PHE cc_start: 0.9153 (t80) cc_final: 0.8803 (t80) REVERT: K 210 MET cc_start: 0.8985 (tpt) cc_final: 0.8570 (tpt) REVERT: K 250 GLU cc_start: 0.9223 (tt0) cc_final: 0.8693 (tm-30) REVERT: L 75 TYR cc_start: 0.8645 (m-10) cc_final: 0.8337 (m-80) REVERT: L 98 GLN cc_start: 0.8563 (mp10) cc_final: 0.8179 (mm-40) REVERT: L 168 VAL cc_start: 0.9636 (m) cc_final: 0.9431 (p) REVERT: L 223 ASN cc_start: 0.9590 (t0) cc_final: 0.9154 (p0) REVERT: L 254 ARG cc_start: 0.9525 (ptp-110) cc_final: 0.9136 (ptp-170) outliers start: 104 outliers final: 78 residues processed: 742 average time/residue: 0.1641 time to fit residues: 194.5952 Evaluate side-chains 705 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 622 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 20 TRP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 253 ILE Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [141, 186, 134, 47, 227, 195, 14, 161, 228, 32, 197] chunk 141 optimal weight: 3.9990 chunk 186 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 195 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN I 213 GLN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.092471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.064232 restraints weight = 92755.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066444 restraints weight = 48635.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.067900 restraints weight = 31754.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.068820 restraints weight = 23703.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.069471 restraints weight = 19549.672| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26665 Z= 0.155 Angle : 0.773 13.170 36129 Z= 0.387 Chirality : 0.045 0.345 4072 Planarity : 0.004 0.059 4356 Dihedral : 15.910 175.444 4197 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 4.29 % Allowed : 19.88 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3060 helix: 1.02 (0.12), residues: 1812 sheet: 1.50 (0.36), residues: 204 loop : 0.32 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 148 TYR 0.025 0.001 TYR I 275 PHE 0.021 0.002 PHE J 204 TRP 0.024 0.002 TRP K 20 HIS 0.020 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (26664) covalent geometry : angle 0.77251 / 0.39 (36129) hydrogen bonds : bond 0.05355 / 3.64 ( 1355) hydrogen bonds : angle 4.83563 / 3.49 ( 3957) Misc. bond : bond 0.00094 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 676 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9638 (tp) cc_final: 0.9243 (pp) REVERT: A 185 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8670 (mp10) REVERT: B 144 ASP cc_start: 0.8141 (t70) cc_final: 0.7770 (t0) REVERT: B 145 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7384 (mt-10) REVERT: B 159 ASP cc_start: 0.9128 (t70) cc_final: 0.8887 (t0) REVERT: B 163 ASP cc_start: 0.8951 (m-30) cc_final: 0.8732 (m-30) REVERT: B 211 TRP cc_start: 0.9200 (m100) cc_final: 0.8383 (m100) REVERT: C 38 GLN cc_start: 0.8961 (tp40) cc_final: 0.8393 (tp40) REVERT: C 46 LEU cc_start: 0.9689 (mt) cc_final: 0.9403 (mp) REVERT: C 80 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8004 (tp-100) REVERT: C 139 GLU cc_start: 0.8628 (mp0) cc_final: 0.8353 (mp0) REVERT: C 184 GLU cc_start: 0.8495 (pm20) cc_final: 0.8235 (pm20) REVERT: C 185 GLN cc_start: 0.8237 (mp10) cc_final: 0.7046 (mp10) REVERT: C 199 LEU cc_start: 0.8441 (tp) cc_final: 0.7948 (tp) REVERT: C 223 ASN cc_start: 0.9022 (t0) cc_final: 0.8638 (t0) REVERT: C 260 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8987 (tp) REVERT: C 269 GLN cc_start: 0.9002 (pp30) cc_final: 0.8640 (pp30) REVERT: D 175 ARG cc_start: 0.9221 (mmm-85) cc_final: 0.8864 (mmm-85) REVERT: D 246 GLU cc_start: 0.9247 (tt0) cc_final: 0.9016 (tt0) REVERT: E 42 LEU cc_start: 0.9757 (tp) cc_final: 0.9546 (tt) REVERT: E 75 TYR cc_start: 0.8774 (t80) cc_final: 0.8499 (t80) REVERT: E 80 GLN cc_start: 0.8765 (pm20) cc_final: 0.8138 (pm20) REVERT: E 132 VAL cc_start: 0.9767 (t) cc_final: 0.9498 (p) REVERT: E 149 LEU cc_start: 0.9413 (mm) cc_final: 0.9109 (mm) REVERT: E 159 ASP cc_start: 0.9251 (t70) cc_final: 0.8825 (t0) REVERT: E 163 ASP cc_start: 0.8690 (m-30) cc_final: 0.8384 (m-30) REVERT: E 210 MET cc_start: 0.9453 (ptp) cc_final: 0.9071 (ptp) REVERT: E 229 MET cc_start: 0.8942 (mmt) cc_final: 0.8134 (mmp) REVERT: E 270 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8581 (pt0) REVERT: F 37 GLN cc_start: 0.9105 (pp30) cc_final: 0.8792 (pp30) REVERT: F 145 GLU cc_start: 0.8924 (tp30) cc_final: 0.8606 (tp30) REVERT: F 204 PHE cc_start: 0.9507 (t80) cc_final: 0.9136 (t80) REVERT: F 214 MET cc_start: 0.8956 (ttm) cc_final: 0.8513 (ttt) REVERT: G 75 TYR cc_start: 0.8439 (m-10) cc_final: 0.8114 (m-10) REVERT: G 140 MET cc_start: 0.8914 (ttp) cc_final: 0.8201 (mtp) REVERT: G 163 ASP cc_start: 0.8986 (t70) cc_final: 0.8579 (p0) REVERT: G 164 LEU cc_start: 0.8610 (mt) cc_final: 0.8199 (mp) REVERT: G 183 ASP cc_start: 0.8323 (t0) cc_final: 0.7929 (t0) REVERT: G 185 GLN cc_start: 0.9051 (tt0) cc_final: 0.8654 (tp40) REVERT: G 196 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7641 (t80) REVERT: H 127 ASP cc_start: 0.9000 (m-30) cc_final: 0.8687 (m-30) REVERT: H 148 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.8850 (ptp90) REVERT: H 163 ASP cc_start: 0.8467 (m-30) cc_final: 0.8216 (m-30) REVERT: H 183 ASP cc_start: 0.8269 (t70) cc_final: 0.7814 (t70) REVERT: I 140 MET cc_start: 0.8973 (ttp) cc_final: 0.8733 (ttm) REVERT: I 185 GLN cc_start: 0.9324 (mp10) cc_final: 0.9034 (mp10) REVERT: I 210 MET cc_start: 0.8955 (ppp) cc_final: 0.8405 (ppp) REVERT: I 229 MET cc_start: 0.9489 (mmm) cc_final: 0.9231 (mmm) REVERT: I 250 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8208 (tm-30) REVERT: J 75 TYR cc_start: 0.8691 (m-80) cc_final: 0.8369 (m-10) REVERT: J 111 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8671 (mt-10) REVERT: J 176 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8627 (tt) REVERT: J 180 ILE cc_start: 0.9207 (mt) cc_final: 0.8954 (mp) REVERT: J 185 GLN cc_start: 0.8993 (mt0) cc_final: 0.8642 (mp10) REVERT: J 229 MET cc_start: 0.8965 (mmm) cc_final: 0.8289 (mmm) REVERT: J 246 GLU cc_start: 0.8982 (tp30) cc_final: 0.8771 (tp30) REVERT: J 274 GLU cc_start: 0.9146 (pt0) cc_final: 0.8619 (pm20) REVERT: K 38 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8543 (tt0) REVERT: K 63 ARG cc_start: 0.9516 (mmm160) cc_final: 0.9135 (mmm-85) REVERT: K 199 LEU cc_start: 0.8896 (mm) cc_final: 0.8371 (tp) REVERT: K 204 PHE cc_start: 0.9155 (t80) cc_final: 0.8792 (t80) REVERT: K 210 MET cc_start: 0.8938 (tpt) cc_final: 0.7669 (tpp) REVERT: K 214 MET cc_start: 0.9399 (mmp) cc_final: 0.8479 (mtp) REVERT: K 250 GLU cc_start: 0.9242 (tt0) cc_final: 0.8602 (tm-30) REVERT: L 37 GLN cc_start: 0.9506 (mp10) cc_final: 0.9178 (pm20) REVERT: L 42 LEU cc_start: 0.9590 (tp) cc_final: 0.9354 (mp) REVERT: L 75 TYR cc_start: 0.8655 (m-10) cc_final: 0.8320 (m-80) REVERT: L 98 GLN cc_start: 0.8380 (mp10) cc_final: 0.7819 (mm-40) REVERT: L 223 ASN cc_start: 0.9632 (t0) cc_final: 0.9135 (p0) REVERT: L 254 ARG cc_start: 0.9514 (ptp-110) cc_final: 0.9285 (ptp-110) outliers start: 115 outliers final: 73 residues processed: 740 average time/residue: 0.1611 time to fit residues: 191.0560 Evaluate side-chains 668 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 589 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 20 TRP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [150, 269, 217, 219, 145, 181, 53, 195, 295, 125, 210] chunk 150 optimal weight: 40.0000 chunk 269 optimal weight: 0.9980 chunk 217 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 145 optimal weight: 0.0370 chunk 181 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 295 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 210 optimal weight: 0.5980 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN E 213 GLN H 185 GLN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.091918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.063593 restraints weight = 93238.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.065760 restraints weight = 49385.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067157 restraints weight = 32553.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068077 restraints weight = 24520.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068690 restraints weight = 20318.687| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26665 Z= 0.151 Angle : 0.753 11.576 36129 Z= 0.376 Chirality : 0.045 0.398 4072 Planarity : 0.004 0.059 4356 Dihedral : 15.799 178.477 4197 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.16 % Favored : 97.71 % Rotamer: Outliers : 3.95 % Allowed : 21.60 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 3060 helix: 1.08 (0.12), residues: 1846 sheet: 1.44 (0.29), residues: 314 loop : 0.07 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 158 TYR 0.029 0.002 TYR L 240 PHE 0.017 0.002 PHE F 190 TRP 0.028 0.002 TRP K 211 HIS 0.016 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (26664) covalent geometry : angle 0.75253 / 0.38 (36129) hydrogen bonds : bond 0.05046 / 3.43 ( 1355) hydrogen bonds : angle 4.79651 / 3.46 ( 3957) Misc. bond : bond 0.00098 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 640 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 CYS cc_start: 0.8910 (p) cc_final: 0.8394 (t) REVERT: A 140 MET cc_start: 0.8981 (tpp) cc_final: 0.8706 (tpp) REVERT: A 141 LEU cc_start: 0.9640 (tp) cc_final: 0.9290 (pp) REVERT: A 185 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8719 (mp10) REVERT: B 145 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7777 (mp0) REVERT: B 159 ASP cc_start: 0.9138 (t70) cc_final: 0.8820 (t0) REVERT: B 163 ASP cc_start: 0.8959 (m-30) cc_final: 0.8649 (m-30) REVERT: B 211 TRP cc_start: 0.9181 (m100) cc_final: 0.8631 (m100) REVERT: C 38 GLN cc_start: 0.8922 (tp40) cc_final: 0.8409 (tp40) REVERT: C 46 LEU cc_start: 0.9706 (mt) cc_final: 0.9435 (mp) REVERT: C 80 GLN cc_start: 0.8556 (tp-100) cc_final: 0.7988 (tp-100) REVERT: C 139 GLU cc_start: 0.8648 (mp0) cc_final: 0.8329 (mp0) REVERT: C 173 THR cc_start: 0.8004 (p) cc_final: 0.7340 (t) REVERT: C 185 GLN cc_start: 0.8238 (mp10) cc_final: 0.7148 (mp10) REVERT: C 199 LEU cc_start: 0.8285 (tp) cc_final: 0.7797 (tp) REVERT: C 223 ASN cc_start: 0.9163 (t0) cc_final: 0.8818 (t0) REVERT: C 260 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8997 (tp) REVERT: C 269 GLN cc_start: 0.8936 (pp30) cc_final: 0.8568 (pp30) REVERT: D 175 ARG cc_start: 0.9169 (mmm-85) cc_final: 0.8938 (mmm-85) REVERT: D 210 MET cc_start: 0.9259 (ttt) cc_final: 0.8996 (ttp) REVERT: E 75 TYR cc_start: 0.8771 (t80) cc_final: 0.8495 (t80) REVERT: E 80 GLN cc_start: 0.8836 (pm20) cc_final: 0.8286 (pm20) REVERT: E 132 VAL cc_start: 0.9773 (t) cc_final: 0.9514 (p) REVERT: E 159 ASP cc_start: 0.9177 (t70) cc_final: 0.8779 (t0) REVERT: E 163 ASP cc_start: 0.8660 (m-30) cc_final: 0.8354 (m-30) REVERT: E 229 MET cc_start: 0.8910 (mmt) cc_final: 0.8138 (mmp) REVERT: E 270 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8616 (pt0) REVERT: E 274 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7344 (pt0) REVERT: F 37 GLN cc_start: 0.9141 (pp30) cc_final: 0.8840 (pp30) REVERT: F 145 GLU cc_start: 0.9007 (tp30) cc_final: 0.8590 (tp30) REVERT: F 204 PHE cc_start: 0.9517 (t80) cc_final: 0.9060 (t80) REVERT: F 211 TRP cc_start: 0.9414 (t-100) cc_final: 0.9201 (t-100) REVERT: G 53 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8425 (mmm-85) REVERT: G 75 TYR cc_start: 0.8488 (m-10) cc_final: 0.8217 (m-10) REVERT: G 107 LYS cc_start: 0.9439 (ptpt) cc_final: 0.9138 (pttm) REVERT: G 140 MET cc_start: 0.8826 (ttp) cc_final: 0.8254 (ttp) REVERT: G 163 ASP cc_start: 0.8961 (t70) cc_final: 0.8541 (p0) REVERT: G 164 LEU cc_start: 0.8589 (mt) cc_final: 0.8072 (mp) REVERT: G 183 ASP cc_start: 0.8266 (t0) cc_final: 0.8021 (t70) REVERT: G 196 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7466 (t80) REVERT: G 210 MET cc_start: 0.7620 (ttt) cc_final: 0.7053 (ttt) REVERT: G 214 MET cc_start: 0.8729 (mmt) cc_final: 0.8058 (mpp) REVERT: H 81 GLN cc_start: 0.8906 (pm20) cc_final: 0.8393 (tp40) REVERT: H 127 ASP cc_start: 0.8946 (m-30) cc_final: 0.8623 (m-30) REVERT: H 144 ASP cc_start: 0.7794 (t0) cc_final: 0.7532 (t0) REVERT: H 148 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.8749 (ptp90) REVERT: H 163 ASP cc_start: 0.8541 (m-30) cc_final: 0.8296 (m-30) REVERT: H 183 ASP cc_start: 0.8300 (t70) cc_final: 0.7937 (t70) REVERT: H 185 GLN cc_start: 0.9353 (mm110) cc_final: 0.9126 (mm110) REVERT: H 246 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8889 (pp20) REVERT: H 247 ILE cc_start: 0.9790 (mm) cc_final: 0.9317 (mm) REVERT: I 140 MET cc_start: 0.8883 (ttp) cc_final: 0.8647 (ttm) REVERT: I 154 PHE cc_start: 0.9314 (m-80) cc_final: 0.8964 (m-80) REVERT: I 210 MET cc_start: 0.8938 (ppp) cc_final: 0.8339 (ppp) REVERT: I 214 MET cc_start: 0.9362 (tpp) cc_final: 0.9152 (mmm) REVERT: I 229 MET cc_start: 0.9491 (mmm) cc_final: 0.9126 (mmm) REVERT: I 240 TYR cc_start: 0.7685 (m-10) cc_final: 0.7480 (m-10) REVERT: I 250 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7936 (tm-30) REVERT: J 75 TYR cc_start: 0.8700 (m-80) cc_final: 0.8401 (m-10) REVERT: J 111 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8638 (mt-10) REVERT: J 176 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8612 (tt) REVERT: J 180 ILE cc_start: 0.9234 (mt) cc_final: 0.9016 (mp) REVERT: J 185 GLN cc_start: 0.8979 (mt0) cc_final: 0.8648 (mp10) REVERT: J 229 MET cc_start: 0.8925 (mmm) cc_final: 0.8229 (mmm) REVERT: J 246 GLU cc_start: 0.9051 (tp30) cc_final: 0.8754 (tp30) REVERT: J 274 GLU cc_start: 0.9125 (pt0) cc_final: 0.8647 (pm20) REVERT: K 37 GLN cc_start: 0.8679 (pm20) cc_final: 0.8299 (pp30) REVERT: K 210 MET cc_start: 0.8973 (tpt) cc_final: 0.7697 (tpp) REVERT: K 214 MET cc_start: 0.9381 (mmp) cc_final: 0.8474 (mtp) REVERT: K 250 GLU cc_start: 0.9266 (tt0) cc_final: 0.8585 (tm-30) REVERT: L 37 GLN cc_start: 0.9483 (mp10) cc_final: 0.9205 (pm20) REVERT: L 42 LEU cc_start: 0.9586 (tp) cc_final: 0.9366 (mp) REVERT: L 75 TYR cc_start: 0.8626 (m-10) cc_final: 0.8277 (m-80) REVERT: L 223 ASN cc_start: 0.9626 (t0) cc_final: 0.9179 (p0) REVERT: L 229 MET cc_start: 0.9044 (mpp) cc_final: 0.8842 (pmm) outliers start: 106 outliers final: 73 residues processed: 693 average time/residue: 0.1632 time to fit residues: 181.5802 Evaluate side-chains 659 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 581 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 20 TRP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [18, 267, 17, 295, 108, 78, 107, 296, 214, 48, 119] chunk 18 optimal weight: 6.9990 chunk 267 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.090420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.062320 restraints weight = 93957.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.064471 restraints weight = 49649.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065862 restraints weight = 32562.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066760 restraints weight = 24452.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067370 restraints weight = 20224.606| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26665 Z= 0.175 Angle : 0.757 13.191 36129 Z= 0.377 Chirality : 0.044 0.210 4072 Planarity : 0.004 0.057 4356 Dihedral : 15.698 179.489 4197 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.71 % Rotamer: Outliers : 4.21 % Allowed : 22.98 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3060 helix: 1.10 (0.12), residues: 1836 sheet: 1.49 (0.29), residues: 314 loop : 0.14 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 158 TYR 0.022 0.001 TYR G 93 PHE 0.017 0.002 PHE K 204 TRP 0.029 0.002 TRP K 211 HIS 0.013 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (26664) covalent geometry : angle 0.75729 / 0.38 (36129) hydrogen bonds : bond 0.04944 / 3.35 ( 1355) hydrogen bonds : angle 4.84064 / 3.48 ( 3957) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 609 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 CYS cc_start: 0.8851 (p) cc_final: 0.8487 (t) REVERT: A 140 MET cc_start: 0.8853 (tpp) cc_final: 0.8579 (tpp) REVERT: A 141 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9276 (pp) REVERT: A 185 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8480 (mp10) REVERT: A 240 TYR cc_start: 0.9256 (m-80) cc_final: 0.8819 (t80) REVERT: B 144 ASP cc_start: 0.8192 (t70) cc_final: 0.7023 (t0) REVERT: B 145 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7020 (mp0) REVERT: B 159 ASP cc_start: 0.9160 (t70) cc_final: 0.8806 (t0) REVERT: B 163 ASP cc_start: 0.9034 (m-30) cc_final: 0.8725 (m-30) REVERT: B 175 ARG cc_start: 0.9428 (ttp-110) cc_final: 0.9224 (ttm110) REVERT: B 183 ASP cc_start: 0.8818 (t0) cc_final: 0.8297 (t0) REVERT: B 184 GLU cc_start: 0.8809 (pm20) cc_final: 0.8151 (pm20) REVERT: B 211 TRP cc_start: 0.9228 (m100) cc_final: 0.8576 (m100) REVERT: C 38 GLN cc_start: 0.8857 (tp40) cc_final: 0.8259 (tp40) REVERT: C 46 LEU cc_start: 0.9700 (mt) cc_final: 0.9438 (mp) REVERT: C 80 GLN cc_start: 0.8531 (tp-100) cc_final: 0.7978 (tp-100) REVERT: C 98 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8723 (mm-40) REVERT: C 139 GLU cc_start: 0.8659 (mp0) cc_final: 0.8318 (mp0) REVERT: C 173 THR cc_start: 0.8016 (p) cc_final: 0.7361 (t) REVERT: C 184 GLU cc_start: 0.8151 (pm20) cc_final: 0.7914 (pm20) REVERT: C 199 LEU cc_start: 0.8383 (tp) cc_final: 0.7808 (tp) REVERT: C 223 ASN cc_start: 0.9212 (t0) cc_final: 0.8890 (t0) REVERT: C 260 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9021 (tp) REVERT: C 269 GLN cc_start: 0.9038 (pp30) cc_final: 0.8698 (pp30) REVERT: D 175 ARG cc_start: 0.9206 (mmm-85) cc_final: 0.8978 (mmm-85) REVERT: D 194 LEU cc_start: 0.9351 (tt) cc_final: 0.9145 (tt) REVERT: D 196 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8777 (m-80) REVERT: D 246 GLU cc_start: 0.9250 (tt0) cc_final: 0.8800 (pp20) REVERT: E 75 TYR cc_start: 0.8809 (t80) cc_final: 0.8548 (t80) REVERT: E 80 GLN cc_start: 0.8928 (pm20) cc_final: 0.8378 (pm20) REVERT: E 98 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8212 (mm-40) REVERT: E 132 VAL cc_start: 0.9794 (t) cc_final: 0.9559 (p) REVERT: E 149 LEU cc_start: 0.9500 (mm) cc_final: 0.9277 (mm) REVERT: E 159 ASP cc_start: 0.9176 (t70) cc_final: 0.8760 (t0) REVERT: E 163 ASP cc_start: 0.8664 (m-30) cc_final: 0.8428 (m-30) REVERT: E 270 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8639 (pt0) REVERT: F 37 GLN cc_start: 0.9194 (pp30) cc_final: 0.8922 (pp30) REVERT: F 116 ARG cc_start: 0.8476 (mmp80) cc_final: 0.8214 (mmp80) REVERT: F 145 GLU cc_start: 0.9102 (tp30) cc_final: 0.8675 (tp30) REVERT: F 204 PHE cc_start: 0.9572 (t80) cc_final: 0.9093 (t80) REVERT: F 211 TRP cc_start: 0.9418 (t-100) cc_final: 0.9109 (t-100) REVERT: F 214 MET cc_start: 0.9031 (ttm) cc_final: 0.8798 (ttm) REVERT: G 53 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8423 (mmm-85) REVERT: G 75 TYR cc_start: 0.8569 (m-10) cc_final: 0.8271 (m-10) REVERT: G 107 LYS cc_start: 0.9465 (ptpt) cc_final: 0.9164 (pttm) REVERT: G 140 MET cc_start: 0.8723 (ttp) cc_final: 0.8155 (ttp) REVERT: G 163 ASP cc_start: 0.8954 (t70) cc_final: 0.8565 (p0) REVERT: G 164 LEU cc_start: 0.8681 (mt) cc_final: 0.8419 (mp) REVERT: G 183 ASP cc_start: 0.8506 (t0) cc_final: 0.8225 (t70) REVERT: H 127 ASP cc_start: 0.8984 (m-30) cc_final: 0.8660 (m-30) REVERT: H 144 ASP cc_start: 0.7900 (t0) cc_final: 0.7648 (t0) REVERT: H 148 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8848 (ptp90) REVERT: H 163 ASP cc_start: 0.8648 (m-30) cc_final: 0.8368 (m-30) REVERT: H 183 ASP cc_start: 0.8329 (t70) cc_final: 0.7926 (t70) REVERT: H 229 MET cc_start: 0.9030 (ptt) cc_final: 0.8756 (ppp) REVERT: I 140 MET cc_start: 0.8977 (ttp) cc_final: 0.8728 (ttm) REVERT: I 210 MET cc_start: 0.9049 (ppp) cc_final: 0.8362 (ppp) REVERT: I 229 MET cc_start: 0.9518 (mmm) cc_final: 0.9152 (mmm) REVERT: I 250 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7989 (tm-30) REVERT: J 75 TYR cc_start: 0.8688 (m-80) cc_final: 0.8396 (m-10) REVERT: J 111 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8720 (mt-10) REVERT: J 176 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8659 (tt) REVERT: J 180 ILE cc_start: 0.9204 (mt) cc_final: 0.8978 (mt) REVERT: J 185 GLN cc_start: 0.8998 (mt0) cc_final: 0.8681 (mp10) REVERT: J 229 MET cc_start: 0.8936 (mmm) cc_final: 0.8252 (mmm) REVERT: J 246 GLU cc_start: 0.9135 (tp30) cc_final: 0.8725 (tp30) REVERT: K 116 ARG cc_start: 0.8882 (ttm-80) cc_final: 0.8658 (ttm110) REVERT: K 187 LEU cc_start: 0.9323 (tt) cc_final: 0.8775 (mt) REVERT: K 210 MET cc_start: 0.8971 (tpt) cc_final: 0.7688 (tpp) REVERT: K 214 MET cc_start: 0.9416 (mmp) cc_final: 0.8555 (mtp) REVERT: K 229 MET cc_start: 0.9442 (mmp) cc_final: 0.9236 (mmm) REVERT: K 250 GLU cc_start: 0.9260 (tt0) cc_final: 0.8577 (tm-30) REVERT: L 38 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8776 (tt0) REVERT: L 42 LEU cc_start: 0.9596 (tp) cc_final: 0.9374 (mp) REVERT: L 75 TYR cc_start: 0.8616 (m-10) cc_final: 0.8308 (m-80) REVERT: L 98 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7738 (mp10) REVERT: L 210 MET cc_start: 0.9587 (ptm) cc_final: 0.9164 (ppp) REVERT: L 223 ASN cc_start: 0.9634 (t0) cc_final: 0.9177 (p0) REVERT: L 229 MET cc_start: 0.9101 (mpp) cc_final: 0.8713 (ptp) REVERT: L 240 TYR cc_start: 0.8510 (m-80) cc_final: 0.7749 (t80) outliers start: 113 outliers final: 79 residues processed: 675 average time/residue: 0.1579 time to fit residues: 172.5906 Evaluate side-chains 647 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 561 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 269 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 140 MET Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [291, 18, 37, 187, 66, 245, 102, 129, 281, 5, 208] chunk 291 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 245 optimal weight: 0.0030 chunk 102 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 208 optimal weight: 0.0770 overall best weight: 1.1750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.090812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062753 restraints weight = 93715.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.064888 restraints weight = 49516.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.066285 restraints weight = 32614.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.067216 restraints weight = 24442.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067819 restraints weight = 20101.798| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26665 Z= 0.149 Angle : 0.768 13.418 36129 Z= 0.380 Chirality : 0.044 0.383 4072 Planarity : 0.004 0.101 4356 Dihedral : 15.559 177.896 4197 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.96 % Favored : 97.81 % Rotamer: Outliers : 3.84 % Allowed : 23.57 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 3060 helix: 1.12 (0.12), residues: 1836 sheet: 1.44 (0.29), residues: 314 loop : 0.16 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 254 TYR 0.016 0.001 TYR I 275 PHE 0.016 0.002 PHE K 190 TRP 0.030 0.002 TRP K 211 HIS 0.012 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (26664) covalent geometry : angle 0.76776 / 0.38 (36129) hydrogen bonds : bond 0.04823 / 3.28 ( 1355) hydrogen bonds : angle 4.79959 / 3.45 ( 3957) Misc. bond : bond 0.00084 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 601 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 CYS cc_start: 0.8823 (p) cc_final: 0.8401 (t) REVERT: A 185 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8634 (mp10) REVERT: A 240 TYR cc_start: 0.9389 (m-80) cc_final: 0.9013 (t80) REVERT: B 107 LYS cc_start: 0.9576 (ttmm) cc_final: 0.9173 (ptpp) REVERT: B 144 ASP cc_start: 0.8243 (t70) cc_final: 0.7847 (t0) REVERT: B 145 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7155 (mt-10) REVERT: B 159 ASP cc_start: 0.9148 (t70) cc_final: 0.8777 (t0) REVERT: B 163 ASP cc_start: 0.8978 (m-30) cc_final: 0.8643 (m-30) REVERT: B 211 TRP cc_start: 0.9214 (m100) cc_final: 0.8536 (m100) REVERT: C 38 GLN cc_start: 0.8911 (tp40) cc_final: 0.8437 (tp40) REVERT: C 46 LEU cc_start: 0.9694 (mt) cc_final: 0.9427 (mp) REVERT: C 80 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8078 (tp-100) REVERT: C 139 GLU cc_start: 0.8708 (mp0) cc_final: 0.8327 (mp0) REVERT: C 173 THR cc_start: 0.7919 (p) cc_final: 0.7399 (t) REVERT: C 184 GLU cc_start: 0.8000 (pm20) cc_final: 0.7752 (pm20) REVERT: C 199 LEU cc_start: 0.8336 (tp) cc_final: 0.7974 (tp) REVERT: C 214 MET cc_start: 0.9552 (tpp) cc_final: 0.9164 (mmm) REVERT: C 223 ASN cc_start: 0.9227 (t0) cc_final: 0.8915 (t0) REVERT: C 260 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9010 (tp) REVERT: C 269 GLN cc_start: 0.9111 (pp30) cc_final: 0.8899 (pp30) REVERT: D 152 GLU cc_start: 0.8529 (mp0) cc_final: 0.8236 (mp0) REVERT: D 175 ARG cc_start: 0.9200 (mmm-85) cc_final: 0.8991 (mmm-85) REVERT: D 196 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8792 (m-80) REVERT: D 246 GLU cc_start: 0.9256 (tt0) cc_final: 0.8813 (pp20) REVERT: E 75 TYR cc_start: 0.8739 (t80) cc_final: 0.8463 (t80) REVERT: E 80 GLN cc_start: 0.8834 (pm20) cc_final: 0.8286 (pm20) REVERT: E 98 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8123 (mm-40) REVERT: E 132 VAL cc_start: 0.9804 (t) cc_final: 0.9562 (p) REVERT: E 159 ASP cc_start: 0.9151 (t70) cc_final: 0.8754 (t0) REVERT: E 163 ASP cc_start: 0.8670 (m-30) cc_final: 0.8450 (m-30) REVERT: E 185 GLN cc_start: 0.9366 (mm-40) cc_final: 0.8933 (mp10) REVERT: E 229 MET cc_start: 0.8853 (mmt) cc_final: 0.8484 (mmp) REVERT: E 270 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8546 (pt0) REVERT: F 37 GLN cc_start: 0.9149 (pp30) cc_final: 0.8913 (pp30) REVERT: F 116 ARG cc_start: 0.8475 (mmp80) cc_final: 0.8264 (mmp80) REVERT: F 140 MET cc_start: 0.9050 (ppp) cc_final: 0.8679 (ppp) REVERT: F 145 GLU cc_start: 0.9133 (tp30) cc_final: 0.8612 (tp30) REVERT: F 156 ASP cc_start: 0.9122 (m-30) cc_final: 0.8892 (t70) REVERT: F 196 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: F 204 PHE cc_start: 0.9577 (t80) cc_final: 0.9077 (t80) REVERT: G 53 ARG cc_start: 0.8726 (mmm-85) cc_final: 0.8443 (mmm-85) REVERT: G 75 TYR cc_start: 0.8482 (m-10) cc_final: 0.8189 (m-10) REVERT: G 107 LYS cc_start: 0.9469 (ptpt) cc_final: 0.9154 (pttm) REVERT: G 140 MET cc_start: 0.8675 (ttp) cc_final: 0.8119 (ttp) REVERT: G 163 ASP cc_start: 0.8964 (t70) cc_final: 0.8607 (p0) REVERT: G 164 LEU cc_start: 0.8745 (mt) cc_final: 0.8445 (mp) REVERT: G 183 ASP cc_start: 0.8651 (t0) cc_final: 0.8151 (t70) REVERT: G 196 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7620 (t80) REVERT: G 210 MET cc_start: 0.7572 (ttt) cc_final: 0.6939 (ttt) REVERT: G 214 MET cc_start: 0.8806 (mmt) cc_final: 0.8056 (mpp) REVERT: H 127 ASP cc_start: 0.8980 (m-30) cc_final: 0.8648 (m-30) REVERT: H 144 ASP cc_start: 0.8038 (t0) cc_final: 0.7675 (t0) REVERT: H 148 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.9030 (ptp-170) REVERT: H 163 ASP cc_start: 0.8687 (m-30) cc_final: 0.8351 (m-30) REVERT: H 183 ASP cc_start: 0.8342 (t70) cc_final: 0.7908 (t0) REVERT: H 185 GLN cc_start: 0.9381 (mm-40) cc_final: 0.9178 (mm110) REVERT: H 229 MET cc_start: 0.9069 (ptt) cc_final: 0.8800 (ppp) REVERT: I 140 MET cc_start: 0.8956 (ttp) cc_final: 0.8690 (ttm) REVERT: I 210 MET cc_start: 0.9123 (ppp) cc_final: 0.8509 (ppp) REVERT: I 211 TRP cc_start: 0.9046 (t-100) cc_final: 0.8736 (t-100) REVERT: I 229 MET cc_start: 0.9561 (mmm) cc_final: 0.9179 (mmm) REVERT: I 250 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8043 (tm-30) REVERT: J 75 TYR cc_start: 0.8705 (m-80) cc_final: 0.8398 (m-10) REVERT: J 162 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8505 (mm-30) REVERT: J 176 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8614 (tt) REVERT: J 180 ILE cc_start: 0.9207 (mt) cc_final: 0.8988 (mt) REVERT: J 185 GLN cc_start: 0.9005 (mt0) cc_final: 0.8735 (mp10) REVERT: J 229 MET cc_start: 0.8875 (mmm) cc_final: 0.8188 (mmm) REVERT: J 246 GLU cc_start: 0.9144 (tp30) cc_final: 0.8831 (tp30) REVERT: J 250 GLU cc_start: 0.8957 (tp30) cc_final: 0.8672 (tp30) REVERT: J 275 TYR cc_start: 0.5829 (m-10) cc_final: 0.5598 (m-80) REVERT: K 187 LEU cc_start: 0.9306 (tt) cc_final: 0.8805 (mt) REVERT: K 199 LEU cc_start: 0.8913 (mm) cc_final: 0.8416 (tp) REVERT: K 204 PHE cc_start: 0.9439 (t80) cc_final: 0.8946 (t80) REVERT: K 210 MET cc_start: 0.8991 (tpt) cc_final: 0.8771 (tpp) REVERT: K 214 MET cc_start: 0.9418 (mmp) cc_final: 0.8883 (ttt) REVERT: K 229 MET cc_start: 0.9454 (mmp) cc_final: 0.9227 (mmm) REVERT: K 250 GLU cc_start: 0.9345 (tt0) cc_final: 0.8738 (tt0) REVERT: K 275 TYR cc_start: 0.6903 (m-80) cc_final: 0.6552 (m-10) REVERT: L 38 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8728 (tt0) REVERT: L 56 CYS cc_start: 0.8491 (p) cc_final: 0.8106 (m) REVERT: L 76 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8112 (ptt180) REVERT: L 95 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8626 (ptm160) REVERT: L 98 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7657 (mp10) REVERT: L 149 LEU cc_start: 0.8814 (tp) cc_final: 0.8423 (tp) REVERT: L 185 GLN cc_start: 0.9432 (tp-100) cc_final: 0.9053 (tm-30) REVERT: L 210 MET cc_start: 0.9597 (ptm) cc_final: 0.9267 (ppp) REVERT: L 223 ASN cc_start: 0.9653 (t0) cc_final: 0.9181 (p0) REVERT: L 229 MET cc_start: 0.9176 (mpp) cc_final: 0.8777 (ptp) REVERT: L 240 TYR cc_start: 0.8487 (m-80) cc_final: 0.7787 (t80) outliers start: 103 outliers final: 71 residues processed: 665 average time/residue: 0.1549 time to fit residues: 166.8026 Evaluate side-chains 652 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 572 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 269 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [285, 74, 135, 274, 56, 3, 174, 233, 157, 129, 85] chunk 285 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 274 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN D 22 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.090879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.062663 restraints weight = 94522.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064802 restraints weight = 50223.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.066199 restraints weight = 33110.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067127 restraints weight = 24919.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067727 restraints weight = 20548.159| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26665 Z= 0.140 Angle : 0.777 14.142 36129 Z= 0.382 Chirality : 0.044 0.319 4072 Planarity : 0.004 0.111 4356 Dihedral : 15.454 177.605 4197 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.06 % Favored : 97.71 % Rotamer: Outliers : 3.32 % Allowed : 24.28 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.15), residues: 3060 helix: 1.09 (0.12), residues: 1836 sheet: 1.35 (0.29), residues: 314 loop : 0.16 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 254 TYR 0.022 0.001 TYR G 93 PHE 0.021 0.002 PHE L 196 TRP 0.032 0.002 TRP K 211 HIS 0.009 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (26664) covalent geometry : angle 0.77746 / 0.38 (36129) hydrogen bonds : bond 0.04698 / 3.21 ( 1355) hydrogen bonds : angle 4.77837 / 3.43 ( 3957) Misc. bond : bond 0.00150 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 596 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 CYS cc_start: 0.8742 (p) cc_final: 0.8430 (t) REVERT: A 185 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8842 (mm-40) REVERT: A 240 TYR cc_start: 0.9387 (m-80) cc_final: 0.9059 (t80) REVERT: B 107 LYS cc_start: 0.9564 (ttmm) cc_final: 0.9166 (ptpp) REVERT: B 144 ASP cc_start: 0.8207 (t70) cc_final: 0.7832 (t0) REVERT: B 145 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7179 (mt-10) REVERT: B 159 ASP cc_start: 0.9126 (t70) cc_final: 0.8682 (t0) REVERT: B 163 ASP cc_start: 0.8975 (m-30) cc_final: 0.8605 (m-30) REVERT: B 211 TRP cc_start: 0.9236 (m100) cc_final: 0.8549 (m100) REVERT: C 38 GLN cc_start: 0.9016 (tp40) cc_final: 0.8218 (tp40) REVERT: C 46 LEU cc_start: 0.9718 (mt) cc_final: 0.9445 (mp) REVERT: C 80 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8096 (tp-100) REVERT: C 98 GLN cc_start: 0.8975 (mm110) cc_final: 0.8624 (mm110) REVERT: C 139 GLU cc_start: 0.8707 (mp0) cc_final: 0.8324 (mp0) REVERT: C 173 THR cc_start: 0.8022 (p) cc_final: 0.7460 (t) REVERT: C 184 GLU cc_start: 0.8046 (pm20) cc_final: 0.7812 (pm20) REVERT: C 199 LEU cc_start: 0.8538 (tp) cc_final: 0.8112 (tp) REVERT: C 223 ASN cc_start: 0.9221 (t0) cc_final: 0.8892 (t0) REVERT: C 260 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8995 (tp) REVERT: D 118 THR cc_start: 0.9109 (m) cc_final: 0.8823 (p) REVERT: D 152 GLU cc_start: 0.8521 (mp0) cc_final: 0.8237 (mp0) REVERT: D 196 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: D 246 GLU cc_start: 0.9245 (tt0) cc_final: 0.8779 (pp20) REVERT: E 75 TYR cc_start: 0.8719 (t80) cc_final: 0.8438 (t80) REVERT: E 80 GLN cc_start: 0.8820 (pm20) cc_final: 0.8279 (pm20) REVERT: E 98 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7956 (mm-40) REVERT: E 132 VAL cc_start: 0.9809 (t) cc_final: 0.9571 (p) REVERT: E 159 ASP cc_start: 0.9093 (t70) cc_final: 0.8683 (t0) REVERT: E 163 ASP cc_start: 0.8599 (m-30) cc_final: 0.8382 (m-30) REVERT: E 185 GLN cc_start: 0.9364 (mm-40) cc_final: 0.8924 (mp10) REVERT: E 253 ILE cc_start: 0.9806 (tt) cc_final: 0.9516 (pt) REVERT: E 270 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8591 (pt0) REVERT: F 37 GLN cc_start: 0.9151 (pp30) cc_final: 0.8891 (pp30) REVERT: F 116 ARG cc_start: 0.8450 (mmp80) cc_final: 0.8247 (mmp80) REVERT: F 140 MET cc_start: 0.9021 (ppp) cc_final: 0.8701 (ppp) REVERT: F 145 GLU cc_start: 0.9141 (tp30) cc_final: 0.8591 (tp30) REVERT: F 185 GLN cc_start: 0.9311 (tp-100) cc_final: 0.8926 (tp-100) REVERT: F 196 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: F 204 PHE cc_start: 0.9599 (t80) cc_final: 0.9106 (t80) REVERT: F 211 TRP cc_start: 0.9202 (t-100) cc_final: 0.8777 (t60) REVERT: F 214 MET cc_start: 0.8925 (ttm) cc_final: 0.8637 (ttm) REVERT: G 53 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8493 (mmm-85) REVERT: G 75 TYR cc_start: 0.8513 (m-10) cc_final: 0.8172 (m-10) REVERT: G 107 LYS cc_start: 0.9469 (ptpt) cc_final: 0.9144 (pttm) REVERT: G 140 MET cc_start: 0.8740 (ttp) cc_final: 0.8174 (ttp) REVERT: G 183 ASP cc_start: 0.8697 (t0) cc_final: 0.8268 (t70) REVERT: G 194 LEU cc_start: 0.8808 (mt) cc_final: 0.8203 (mp) REVERT: G 196 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7313 (t80) REVERT: G 210 MET cc_start: 0.7659 (ttt) cc_final: 0.6967 (ttp) REVERT: G 214 MET cc_start: 0.8949 (mmt) cc_final: 0.8323 (mpp) REVERT: H 127 ASP cc_start: 0.8932 (m-30) cc_final: 0.8596 (m-30) REVERT: H 144 ASP cc_start: 0.7904 (t0) cc_final: 0.7682 (t0) REVERT: H 148 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8753 (ptp90) REVERT: H 163 ASP cc_start: 0.8670 (m-30) cc_final: 0.8292 (m-30) REVERT: H 183 ASP cc_start: 0.8375 (t70) cc_final: 0.8036 (t70) REVERT: H 185 GLN cc_start: 0.9363 (mm-40) cc_final: 0.9131 (mm110) REVERT: H 214 MET cc_start: 0.8895 (mtm) cc_final: 0.8677 (ptp) REVERT: H 229 MET cc_start: 0.8985 (ptt) cc_final: 0.8765 (ppp) REVERT: I 54 LYS cc_start: 0.9076 (tttt) cc_final: 0.8843 (ttpt) REVERT: I 140 MET cc_start: 0.8919 (ttp) cc_final: 0.8664 (ttm) REVERT: I 210 MET cc_start: 0.9122 (ppp) cc_final: 0.8486 (ppp) REVERT: I 229 MET cc_start: 0.9577 (mmm) cc_final: 0.9186 (mmm) REVERT: I 250 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8103 (tm-30) REVERT: J 75 TYR cc_start: 0.8687 (m-80) cc_final: 0.8404 (m-10) REVERT: J 162 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8418 (mm-30) REVERT: J 163 ASP cc_start: 0.9245 (t70) cc_final: 0.8819 (p0) REVERT: J 176 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8645 (tt) REVERT: J 180 ILE cc_start: 0.9190 (mt) cc_final: 0.8970 (mt) REVERT: J 185 GLN cc_start: 0.9006 (mt0) cc_final: 0.8768 (mp10) REVERT: J 229 MET cc_start: 0.8851 (mmm) cc_final: 0.8160 (mmm) REVERT: J 246 GLU cc_start: 0.9135 (tp30) cc_final: 0.8689 (tp30) REVERT: J 250 GLU cc_start: 0.8930 (tp30) cc_final: 0.8665 (tp30) REVERT: J 256 LEU cc_start: 0.9545 (mm) cc_final: 0.9255 (mm) REVERT: K 116 ARG cc_start: 0.8864 (ttm-80) cc_final: 0.8629 (ttm110) REVERT: K 187 LEU cc_start: 0.9258 (tt) cc_final: 0.8758 (mt) REVERT: K 199 LEU cc_start: 0.8872 (mm) cc_final: 0.8426 (tp) REVERT: K 204 PHE cc_start: 0.9418 (t80) cc_final: 0.8922 (t80) REVERT: K 210 MET cc_start: 0.8984 (tpt) cc_final: 0.8773 (tpp) REVERT: K 214 MET cc_start: 0.9422 (mmp) cc_final: 0.8858 (ttt) REVERT: K 229 MET cc_start: 0.9460 (mmp) cc_final: 0.9248 (mmm) REVERT: K 250 GLU cc_start: 0.9355 (tt0) cc_final: 0.8746 (tt0) REVERT: K 275 TYR cc_start: 0.7153 (m-80) cc_final: 0.6749 (m-10) REVERT: L 56 CYS cc_start: 0.8641 (p) cc_final: 0.8425 (m) REVERT: L 76 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7549 (ptt-90) REVERT: L 95 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8548 (ptm160) REVERT: L 97 HIS cc_start: 0.7045 (m-70) cc_final: 0.6426 (m-70) REVERT: L 98 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7804 (mp10) REVERT: L 149 LEU cc_start: 0.8821 (tp) cc_final: 0.8400 (tp) REVERT: L 185 GLN cc_start: 0.9517 (tp-100) cc_final: 0.9221 (tm-30) REVERT: L 210 MET cc_start: 0.9554 (ptm) cc_final: 0.8972 (ppp) REVERT: L 223 ASN cc_start: 0.9675 (t0) cc_final: 0.9211 (p0) REVERT: L 229 MET cc_start: 0.9106 (mpp) cc_final: 0.8751 (ptp) REVERT: L 240 TYR cc_start: 0.8518 (m-80) cc_final: 0.7978 (t80) outliers start: 89 outliers final: 66 residues processed: 651 average time/residue: 0.1582 time to fit residues: 167.0802 Evaluate side-chains 649 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 574 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 269 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [147, 35, 88, 28, 104, 240, 90, 30, 27, 217, 278] chunk 147 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.090961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.063010 restraints weight = 94301.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065149 restraints weight = 49500.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.066562 restraints weight = 32407.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067517 restraints weight = 24251.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068103 restraints weight = 19849.976| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26665 Z= 0.142 Angle : 0.778 14.190 36129 Z= 0.381 Chirality : 0.044 0.239 4072 Planarity : 0.004 0.105 4356 Dihedral : 15.377 178.298 4197 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.03 % Favored : 97.75 % Rotamer: Outliers : 3.06 % Allowed : 24.69 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3060 helix: 1.11 (0.12), residues: 1836 sheet: 1.38 (0.29), residues: 314 loop : 0.16 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 254 TYR 0.019 0.001 TYR G 93 PHE 0.016 0.001 PHE H 204 TRP 0.033 0.002 TRP K 211 HIS 0.009 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (26664) covalent geometry : angle 0.77790 / 0.38 (36129) hydrogen bonds : bond 0.04615 / 3.15 ( 1355) hydrogen bonds : angle 4.75465 / 3.41 ( 3957) Misc. bond : bond 0.00115 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 588 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 CYS cc_start: 0.8793 (p) cc_final: 0.8561 (t) REVERT: A 240 TYR cc_start: 0.9443 (m-80) cc_final: 0.9082 (t80) REVERT: B 107 LYS cc_start: 0.9557 (ttmm) cc_final: 0.9143 (ptpp) REVERT: B 144 ASP cc_start: 0.8242 (t70) cc_final: 0.7858 (t0) REVERT: B 145 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7283 (mt-10) REVERT: B 159 ASP cc_start: 0.9127 (t70) cc_final: 0.8683 (t0) REVERT: B 163 ASP cc_start: 0.8994 (m-30) cc_final: 0.8609 (m-30) REVERT: B 211 TRP cc_start: 0.9200 (m100) cc_final: 0.8524 (m100) REVERT: C 38 GLN cc_start: 0.8811 (tp40) cc_final: 0.8298 (tp40) REVERT: C 80 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8228 (tp-100) REVERT: C 98 GLN cc_start: 0.9038 (mm110) cc_final: 0.8700 (mm-40) REVERT: C 139 GLU cc_start: 0.8717 (mp0) cc_final: 0.8315 (mp0) REVERT: C 199 LEU cc_start: 0.8517 (tp) cc_final: 0.7947 (tp) REVERT: C 207 THR cc_start: 0.9798 (m) cc_final: 0.9583 (p) REVERT: C 214 MET cc_start: 0.9523 (tpp) cc_final: 0.9234 (mmm) REVERT: C 223 ASN cc_start: 0.9231 (t0) cc_final: 0.8921 (t0) REVERT: D 118 THR cc_start: 0.9104 (m) cc_final: 0.8835 (p) REVERT: D 152 GLU cc_start: 0.8545 (mp0) cc_final: 0.8255 (mp0) REVERT: D 196 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: D 246 GLU cc_start: 0.9252 (tt0) cc_final: 0.8788 (pp20) REVERT: E 75 TYR cc_start: 0.8782 (t80) cc_final: 0.8507 (t80) REVERT: E 80 GLN cc_start: 0.8850 (pm20) cc_final: 0.8340 (pm20) REVERT: E 98 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7969 (mm110) REVERT: E 132 VAL cc_start: 0.9815 (t) cc_final: 0.9579 (p) REVERT: E 159 ASP cc_start: 0.9082 (t70) cc_final: 0.8673 (t0) REVERT: E 163 ASP cc_start: 0.8604 (m-30) cc_final: 0.8380 (m-30) REVERT: E 185 GLN cc_start: 0.9374 (mm-40) cc_final: 0.8935 (mp10) REVERT: E 253 ILE cc_start: 0.9809 (tt) cc_final: 0.9546 (pt) REVERT: E 270 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8665 (pt0) REVERT: F 37 GLN cc_start: 0.9175 (pp30) cc_final: 0.8920 (pp30) REVERT: F 116 ARG cc_start: 0.8482 (mmp80) cc_final: 0.8278 (mmp80) REVERT: F 140 MET cc_start: 0.9031 (ppp) cc_final: 0.8696 (ppp) REVERT: F 145 GLU cc_start: 0.9101 (tp30) cc_final: 0.8591 (tp30) REVERT: F 154 PHE cc_start: 0.8425 (m-80) cc_final: 0.8116 (m-80) REVERT: F 185 GLN cc_start: 0.9324 (tp-100) cc_final: 0.8978 (tp-100) REVERT: F 196 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: F 204 PHE cc_start: 0.9609 (t80) cc_final: 0.9100 (t80) REVERT: F 211 TRP cc_start: 0.9173 (t-100) cc_final: 0.8846 (t60) REVERT: F 229 MET cc_start: 0.8383 (mtt) cc_final: 0.8175 (mmm) REVERT: G 53 ARG cc_start: 0.8760 (mmm-85) cc_final: 0.8487 (mmm-85) REVERT: G 75 TYR cc_start: 0.8491 (m-10) cc_final: 0.8109 (m-10) REVERT: G 107 LYS cc_start: 0.9460 (ptpt) cc_final: 0.9133 (pttm) REVERT: G 140 MET cc_start: 0.8706 (ttp) cc_final: 0.8139 (ttp) REVERT: G 183 ASP cc_start: 0.8792 (t0) cc_final: 0.8373 (t70) REVERT: G 196 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7065 (t80) REVERT: G 210 MET cc_start: 0.7736 (ttt) cc_final: 0.6991 (ttp) REVERT: G 214 MET cc_start: 0.8986 (mmt) cc_final: 0.8348 (mpp) REVERT: H 127 ASP cc_start: 0.8941 (m-30) cc_final: 0.8607 (m-30) REVERT: H 139 GLU cc_start: 0.9030 (mp0) cc_final: 0.8774 (pm20) REVERT: H 148 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.9031 (ptp-170) REVERT: H 163 ASP cc_start: 0.8693 (m-30) cc_final: 0.8313 (m-30) REVERT: H 183 ASP cc_start: 0.8380 (t70) cc_final: 0.8040 (t70) REVERT: H 185 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9137 (mm110) REVERT: H 214 MET cc_start: 0.8732 (mtm) cc_final: 0.8489 (mtm) REVERT: H 250 GLU cc_start: 0.8910 (tp30) cc_final: 0.8681 (tm-30) REVERT: I 54 LYS cc_start: 0.9095 (tttt) cc_final: 0.8861 (ttpt) REVERT: I 61 GLU cc_start: 0.8154 (mp0) cc_final: 0.7803 (mp0) REVERT: I 140 MET cc_start: 0.8969 (ttp) cc_final: 0.8679 (ttm) REVERT: I 210 MET cc_start: 0.9169 (ppp) cc_final: 0.8729 (ppp) REVERT: I 211 TRP cc_start: 0.9044 (t-100) cc_final: 0.8774 (t-100) REVERT: I 229 MET cc_start: 0.9603 (mmm) cc_final: 0.9235 (mmm) REVERT: I 250 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8119 (tm-30) REVERT: J 75 TYR cc_start: 0.8700 (m-80) cc_final: 0.8422 (m-10) REVERT: J 162 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8407 (mm-30) REVERT: J 163 ASP cc_start: 0.9227 (t70) cc_final: 0.8837 (p0) REVERT: J 176 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8635 (tt) REVERT: J 180 ILE cc_start: 0.9187 (mt) cc_final: 0.8971 (mt) REVERT: J 185 GLN cc_start: 0.8997 (mt0) cc_final: 0.8790 (mp10) REVERT: J 229 MET cc_start: 0.8834 (mmm) cc_final: 0.8164 (mmm) REVERT: J 246 GLU cc_start: 0.9170 (tp30) cc_final: 0.8763 (tp30) REVERT: J 250 GLU cc_start: 0.8930 (tp30) cc_final: 0.8660 (tp30) REVERT: J 256 LEU cc_start: 0.9546 (mm) cc_final: 0.9301 (mm) REVERT: K 116 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8630 (ttm110) REVERT: K 176 LEU cc_start: 0.9633 (tp) cc_final: 0.9358 (mt) REVERT: K 199 LEU cc_start: 0.8893 (mm) cc_final: 0.8429 (tp) REVERT: K 204 PHE cc_start: 0.9424 (t80) cc_final: 0.8918 (t80) REVERT: K 210 MET cc_start: 0.8968 (tpt) cc_final: 0.8761 (tpp) REVERT: K 214 MET cc_start: 0.9429 (mmp) cc_final: 0.8875 (ttp) REVERT: K 250 GLU cc_start: 0.9345 (tt0) cc_final: 0.8721 (tt0) REVERT: K 275 TYR cc_start: 0.7090 (m-80) cc_final: 0.6557 (m-10) REVERT: L 38 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8838 (tp-100) REVERT: L 76 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7832 (ptt180) REVERT: L 95 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8554 (ptm160) REVERT: L 97 HIS cc_start: 0.7015 (m-70) cc_final: 0.6367 (m-70) REVERT: L 98 GLN cc_start: 0.8633 (mm-40) cc_final: 0.7874 (mp10) REVERT: L 149 LEU cc_start: 0.8850 (tp) cc_final: 0.8439 (tp) REVERT: L 159 ASP cc_start: 0.9344 (m-30) cc_final: 0.9062 (p0) REVERT: L 185 GLN cc_start: 0.9525 (tp-100) cc_final: 0.9260 (tm-30) REVERT: L 223 ASN cc_start: 0.9670 (t0) cc_final: 0.9268 (p0) REVERT: L 229 MET cc_start: 0.9106 (mpp) cc_final: 0.8604 (ptp) REVERT: L 240 TYR cc_start: 0.8552 (m-80) cc_final: 0.7986 (t80) REVERT: L 274 GLU cc_start: 0.9053 (tt0) cc_final: 0.8668 (pt0) outliers start: 82 outliers final: 65 residues processed: 635 average time/residue: 0.1547 time to fit residues: 159.2665 Evaluate side-chains 637 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 563 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 269 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [74, 229, 102, 161, 256, 129, 278, 203, 43, 282, 208] chunk 74 optimal weight: 4.9990 chunk 229 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 278 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 208 optimal weight: 0.0470 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.091407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063325 restraints weight = 93766.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065491 restraints weight = 49487.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066898 restraints weight = 32433.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067828 restraints weight = 24331.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068399 restraints weight = 20001.146| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26665 Z= 0.143 Angle : 0.811 15.527 36129 Z= 0.397 Chirality : 0.045 0.350 4072 Planarity : 0.005 0.101 4356 Dihedral : 15.333 178.666 4197 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.16 % Favored : 97.61 % Rotamer: Outliers : 2.80 % Allowed : 25.21 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.15), residues: 3060 helix: 1.04 (0.12), residues: 1848 sheet: 1.36 (0.29), residues: 314 loop : 0.16 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 27 TYR 0.026 0.001 TYR D 93 PHE 0.017 0.001 PHE J 204 TRP 0.034 0.002 TRP K 211 HIS 0.010 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (26664) covalent geometry : angle 0.81149 / 0.40 (36129) hydrogen bonds : bond 0.04589 / 3.14 ( 1355) hydrogen bonds : angle 4.76603 / 3.42 ( 3957) Misc. bond : bond 0.00113 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 581 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 CYS cc_start: 0.8795 (p) cc_final: 0.8438 (t) REVERT: A 80 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8028 (pp30) REVERT: A 185 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8794 (mm-40) REVERT: A 240 TYR cc_start: 0.9436 (m-80) cc_final: 0.9075 (t80) REVERT: B 107 LYS cc_start: 0.9549 (ttmm) cc_final: 0.9131 (ptpp) REVERT: B 144 ASP cc_start: 0.8244 (t70) cc_final: 0.7860 (t0) REVERT: B 145 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7232 (mt-10) REVERT: B 159 ASP cc_start: 0.9129 (t70) cc_final: 0.8681 (t0) REVERT: B 163 ASP cc_start: 0.8982 (m-30) cc_final: 0.8581 (m-30) REVERT: B 211 TRP cc_start: 0.9242 (m100) cc_final: 0.8536 (m100) REVERT: C 38 GLN cc_start: 0.8956 (tp40) cc_final: 0.8469 (tp40) REVERT: C 80 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8226 (tp-100) REVERT: C 98 GLN cc_start: 0.9038 (mm110) cc_final: 0.8698 (mm-40) REVERT: C 139 GLU cc_start: 0.8703 (mp0) cc_final: 0.8323 (mp0) REVERT: C 196 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: C 199 LEU cc_start: 0.8499 (tp) cc_final: 0.7904 (tp) REVERT: C 207 THR cc_start: 0.9795 (m) cc_final: 0.9581 (p) REVERT: C 214 MET cc_start: 0.9509 (tpp) cc_final: 0.9248 (mmm) REVERT: C 223 ASN cc_start: 0.9220 (t0) cc_final: 0.8886 (t0) REVERT: C 260 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9005 (tp) REVERT: D 118 THR cc_start: 0.9071 (m) cc_final: 0.8815 (p) REVERT: D 145 GLU cc_start: 0.8798 (pt0) cc_final: 0.8516 (pt0) REVERT: D 152 GLU cc_start: 0.8599 (mp0) cc_final: 0.8325 (mp0) REVERT: D 196 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8782 (m-80) REVERT: D 246 GLU cc_start: 0.9252 (tt0) cc_final: 0.8792 (pp20) REVERT: E 75 TYR cc_start: 0.8764 (t80) cc_final: 0.8482 (t80) REVERT: E 80 GLN cc_start: 0.8856 (pm20) cc_final: 0.8343 (pm20) REVERT: E 132 VAL cc_start: 0.9817 (t) cc_final: 0.9584 (p) REVERT: E 159 ASP cc_start: 0.9072 (t70) cc_final: 0.8653 (t0) REVERT: E 163 ASP cc_start: 0.8532 (m-30) cc_final: 0.8303 (m-30) REVERT: E 185 GLN cc_start: 0.9370 (mm-40) cc_final: 0.8935 (mp10) REVERT: E 253 ILE cc_start: 0.9810 (tt) cc_final: 0.9550 (pt) REVERT: E 270 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8678 (pt0) REVERT: F 37 GLN cc_start: 0.9159 (pp30) cc_final: 0.8863 (pp30) REVERT: F 140 MET cc_start: 0.9029 (ppp) cc_final: 0.8675 (ppp) REVERT: F 145 GLU cc_start: 0.9148 (tp30) cc_final: 0.8617 (tp30) REVERT: F 154 PHE cc_start: 0.8461 (m-80) cc_final: 0.8161 (m-80) REVERT: F 185 GLN cc_start: 0.9341 (tp-100) cc_final: 0.8983 (tp-100) REVERT: F 196 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: F 204 PHE cc_start: 0.9614 (t80) cc_final: 0.9114 (t80) REVERT: F 210 MET cc_start: 0.9347 (tpp) cc_final: 0.9031 (mtt) REVERT: F 211 TRP cc_start: 0.9164 (t-100) cc_final: 0.8781 (t60) REVERT: F 229 MET cc_start: 0.8391 (mtt) cc_final: 0.8189 (mmm) REVERT: G 53 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8501 (mmm-85) REVERT: G 75 TYR cc_start: 0.8523 (m-10) cc_final: 0.8118 (m-10) REVERT: G 93 TYR cc_start: 0.8498 (t80) cc_final: 0.8174 (t80) REVERT: G 107 LYS cc_start: 0.9463 (ptpt) cc_final: 0.9132 (pttm) REVERT: G 140 MET cc_start: 0.8687 (ttp) cc_final: 0.8132 (ttp) REVERT: G 183 ASP cc_start: 0.8791 (t0) cc_final: 0.8364 (t70) REVERT: G 196 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6972 (t80) REVERT: G 210 MET cc_start: 0.7733 (ttt) cc_final: 0.7002 (ttp) REVERT: G 214 MET cc_start: 0.8985 (mmt) cc_final: 0.8341 (mpp) REVERT: H 127 ASP cc_start: 0.8929 (m-30) cc_final: 0.8573 (m-30) REVERT: H 139 GLU cc_start: 0.9018 (mp0) cc_final: 0.8777 (pm20) REVERT: H 148 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.9019 (ptp-170) REVERT: H 163 ASP cc_start: 0.8683 (m-30) cc_final: 0.8299 (m-30) REVERT: H 183 ASP cc_start: 0.8285 (t70) cc_final: 0.7926 (t70) REVERT: H 250 GLU cc_start: 0.8913 (tp30) cc_final: 0.8646 (tm-30) REVERT: I 54 LYS cc_start: 0.9115 (tttt) cc_final: 0.8870 (ttpt) REVERT: I 61 GLU cc_start: 0.8187 (mp0) cc_final: 0.7853 (mp0) REVERT: I 140 MET cc_start: 0.8961 (ttp) cc_final: 0.8653 (ttm) REVERT: I 210 MET cc_start: 0.9146 (ppp) cc_final: 0.8445 (ppp) REVERT: I 211 TRP cc_start: 0.9044 (t-100) cc_final: 0.8781 (t-100) REVERT: I 229 MET cc_start: 0.9598 (mmm) cc_final: 0.9220 (mmm) REVERT: I 250 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8036 (tm-30) REVERT: J 75 TYR cc_start: 0.8700 (m-80) cc_final: 0.8423 (m-10) REVERT: J 162 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8397 (mm-30) REVERT: J 163 ASP cc_start: 0.9206 (t70) cc_final: 0.8837 (p0) REVERT: J 176 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8587 (tt) REVERT: J 180 ILE cc_start: 0.9209 (mt) cc_final: 0.8993 (mt) REVERT: J 229 MET cc_start: 0.8829 (mmm) cc_final: 0.8171 (mmm) REVERT: J 246 GLU cc_start: 0.9182 (tp30) cc_final: 0.8758 (tp30) REVERT: J 250 GLU cc_start: 0.8914 (tp30) cc_final: 0.8643 (tp30) REVERT: J 256 LEU cc_start: 0.9518 (mm) cc_final: 0.9275 (mm) REVERT: K 176 LEU cc_start: 0.9630 (tp) cc_final: 0.9358 (mt) REVERT: K 199 LEU cc_start: 0.8900 (mm) cc_final: 0.8423 (tp) REVERT: K 204 PHE cc_start: 0.9449 (t80) cc_final: 0.8923 (t80) REVERT: K 210 MET cc_start: 0.9059 (tpt) cc_final: 0.8857 (tpp) REVERT: K 214 MET cc_start: 0.9430 (mmp) cc_final: 0.8872 (ttp) REVERT: K 250 GLU cc_start: 0.9340 (tt0) cc_final: 0.8990 (tt0) REVERT: L 76 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7772 (ptt180) REVERT: L 95 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8507 (ptm160) REVERT: L 97 HIS cc_start: 0.6914 (m-70) cc_final: 0.6252 (m-70) REVERT: L 98 GLN cc_start: 0.8612 (mm-40) cc_final: 0.7828 (mp10) REVERT: L 149 LEU cc_start: 0.8828 (tp) cc_final: 0.8425 (tp) REVERT: L 159 ASP cc_start: 0.9360 (m-30) cc_final: 0.9090 (p0) REVERT: L 185 GLN cc_start: 0.9538 (tp-100) cc_final: 0.9309 (tm-30) REVERT: L 210 MET cc_start: 0.9566 (ptm) cc_final: 0.9101 (ppp) REVERT: L 223 ASN cc_start: 0.9686 (t0) cc_final: 0.9290 (p0) REVERT: L 229 MET cc_start: 0.9129 (mpp) cc_final: 0.8627 (ptp) REVERT: L 240 TYR cc_start: 0.8597 (m-80) cc_final: 0.8016 (t80) REVERT: L 250 GLU cc_start: 0.8774 (pt0) cc_final: 0.8207 (pt0) outliers start: 75 outliers final: 60 residues processed: 627 average time/residue: 0.1555 time to fit residues: 159.3779 Evaluate side-chains 639 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 569 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 269 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [233, 280, 138, 64, 205, 57, 74, 273, 279, 70, 127] chunk 233 optimal weight: 0.0770 chunk 280 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 273 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.091577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063432 restraints weight = 93892.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.065581 restraints weight = 49658.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066986 restraints weight = 32712.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067873 restraints weight = 24607.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068508 restraints weight = 20377.828| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.287 26665 Z= 0.226 Angle : 0.912 58.992 36129 Z= 0.470 Chirality : 0.045 0.448 4072 Planarity : 0.005 0.097 4356 Dihedral : 15.328 178.674 4197 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.19 % Favored : 97.58 % Rotamer: Outliers : 2.98 % Allowed : 25.36 % Favored : 71.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.15), residues: 3060 helix: 1.03 (0.12), residues: 1848 sheet: 1.36 (0.29), residues: 314 loop : 0.17 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 189 TYR 0.062 0.002 TYR L 275 PHE 0.016 0.001 PHE J 204 TRP 0.032 0.002 TRP K 211 HIS 0.009 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (26664) covalent geometry : angle 0.91195 / 0.47 (36129) hydrogen bonds : bond 0.04603 / 3.14 ( 1355) hydrogen bonds : angle 4.77124 / 3.42 ( 3957) Misc. bond : bond 0.00124 / 0.07 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6401.43 seconds wall clock time: 110 minutes 22.31 seconds (6622.31 seconds total)