Starting phenix.real_space_refine on Sun Jul 5 05:59:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m9b_23722/07_2026/7m9b_23722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m9b_23722/07_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_23722/07_2026/7m9b_23722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m9b_23722/07_2026/7m9b_23722.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m9b_23722/07_2026/7m9b_23722.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m9b_23722/07_2026/7m9b_23722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m9b_23722/07_2026/7m9b_23722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m9b_23722/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 4.41, per 1000 atoms: 0.17 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: 2.06 Conformation dependent library (CDL) restraints added in 775.7 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: 2.24 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: 4.18 Time building geometry restraints manager: 2.75 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: 0.940 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.340 Find NCS groups from input model: 0.680 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- 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 : 0.677 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 0.67727 / 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 : 0.718 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: 0.8194 (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: 0.7101 (t) REVERT: C 196 PHE cc_start: 0.7620 (t80) cc_final: 0.6874 (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 156 ASP cc_start: 0.7235 (m-30) cc_final: 0.7035 (m-30) REVERT: H 159 ASP cc_start: 0.7100 (m-30) cc_final: 0.6815 (m-30) REVERT: I 99 LYS cc_start: 0.7410 (mttt) cc_final: 0.7016 (mttm) REVERT: I 170 LEU cc_start: 0.9291 (mt) cc_final: 0.9061 (mt) REVERT: I 198 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7896 (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: 0.7101 (t80) REVERT: J 123 SER cc_start: 0.8816 (p) cc_final: 0.8564 (p) REVERT: J 144 ASP cc_start: 0.8272 (t0) cc_final: 0.7843 (t0) REVERT: J 245 ASP cc_start: 0.7971 (t0) cc_final: 0.7748 (t0) REVERT: K 46 LEU cc_start: 0.8224 (mt) cc_final: 0.7815 (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: 0.1768 time to fit residues: 380.1607 Evaluate side-chains 720 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 718 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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: 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: 1.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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 37 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.094271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.065934 restraints weight = 92370.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.068193 restraints weight = 48272.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069698 restraints weight = 31460.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.070671 restraints weight = 23469.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.071277 restraints weight = 19232.022| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26665 Z= 0.192 Angle : 0.859 11.304 36129 Z= 0.434 Chirality : 0.048 0.263 4072 Planarity : 0.006 0.068 4356 Dihedral : 16.127 178.845 4199 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 3.84 % Allowed : 17.90 % Favored : 78.25 % 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: 0.81 (0.14), residues: 3060 helix: 0.77 (0.12), residues: 1845 sheet: 1.13 (0.36), residues: 204 loop : 0.23 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 231 TYR 0.030 0.002 TYR A 75 PHE 0.021 0.002 PHE L 154 TRP 0.028 0.002 TRP L 20 HIS 0.015 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (26664) covalent geometry : angle 0.85945 / 0.43 (36129) hydrogen bonds : bond 0.06578 / 4.44 ( 1355) hydrogen bonds : angle 5.18309 / 3.74 ( 3957) Misc. bond : bond 0.00138 / 0.07 ( 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 898 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 795 time to evaluate : 0.901 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: A 140 MET cc_start: 0.8550 (tpp) cc_final: 0.8250 (mmm) REVERT: A 144 ASP cc_start: 0.7502 (t0) cc_final: 0.7224 (t0) REVERT: A 199 LEU cc_start: 0.1339 (OUTLIER) cc_final: 0.1117 (pp) REVERT: B 93 TYR cc_start: 0.8740 (t80) cc_final: 0.8262 (t80) REVERT: B 145 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7712 (mt-10) REVERT: B 159 ASP cc_start: 0.9318 (t70) cc_final: 0.8614 (t0) REVERT: B 182 ARG cc_start: 0.9388 (mtp85) cc_final: 0.9066 (ptp-110) REVERT: C 46 LEU cc_start: 0.9667 (mt) cc_final: 0.9407 (mp) REVERT: C 80 GLN cc_start: 0.8395 (tp-100) cc_final: 0.7920 (tp-100) REVERT: C 185 GLN cc_start: 0.8088 (mp10) cc_final: 0.7582 (mp10) REVERT: C 199 LEU cc_start: 0.8429 (tp) cc_final: 0.7925 (tp) REVERT: C 223 ASN cc_start: 0.8611 (t0) cc_final: 0.8389 (t0) REVERT: D 111 GLU cc_start: 0.8508 (pp20) cc_final: 0.8306 (pp20) REVERT: D 138 VAL cc_start: 0.9304 (t) cc_final: 0.9058 (p) REVERT: D 145 GLU cc_start: 0.8701 (pt0) cc_final: 0.8270 (pt0) REVERT: D 159 ASP cc_start: 0.9270 (m-30) cc_final: 0.8813 (m-30) REVERT: D 210 MET cc_start: 0.9192 (ttt) cc_final: 0.8796 (ttp) REVERT: D 214 MET cc_start: 0.8781 (mmm) cc_final: 0.8524 (mmm) REVERT: D 246 GLU cc_start: 0.9315 (tt0) cc_final: 0.8887 (pp20) REVERT: E 46 LEU cc_start: 0.9707 (mt) cc_final: 0.9474 (mt) REVERT: E 75 TYR cc_start: 0.8682 (t80) cc_final: 0.8423 (t80) REVERT: E 80 GLN cc_start: 0.8650 (pm20) cc_final: 0.8232 (pm20) REVERT: E 132 VAL cc_start: 0.9699 (t) cc_final: 0.9442 (p) REVERT: E 159 ASP cc_start: 0.9272 (t0) cc_final: 0.8949 (t0) REVERT: E 163 ASP cc_start: 0.8643 (m-30) cc_final: 0.8389 (m-30) REVERT: E 250 GLU cc_start: 0.9328 (tp30) cc_final: 0.8941 (tp30) REVERT: E 274 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7471 (mt-10) REVERT: F 145 GLU cc_start: 0.8751 (tp30) cc_final: 0.8512 (tp30) REVERT: F 204 PHE cc_start: 0.9490 (t80) cc_final: 0.9086 (t80) REVERT: F 214 MET cc_start: 0.8793 (ttm) cc_final: 0.8468 (ttt) REVERT: F 232 ILE cc_start: 0.9460 (mt) cc_final: 0.8897 (tp) REVERT: G 143 ILE cc_start: 0.8663 (mm) cc_final: 0.8272 (tp) REVERT: G 162 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8426 (mp0) REVERT: G 183 ASP cc_start: 0.8264 (t0) cc_final: 0.7976 (t0) REVERT: H 127 ASP cc_start: 0.8951 (m-30) cc_final: 0.8655 (m-30) REVERT: H 148 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.8873 (ptp-170) REVERT: H 154 PHE cc_start: 0.9615 (m-80) cc_final: 0.9284 (m-80) REVERT: H 156 ASP cc_start: 0.9163 (m-30) cc_final: 0.8700 (m-30) REVERT: H 159 ASP cc_start: 0.8335 (m-30) cc_final: 0.7892 (m-30) REVERT: H 183 ASP cc_start: 0.8341 (t70) cc_final: 0.7913 (t70) REVERT: I 140 MET cc_start: 0.8979 (ttp) cc_final: 0.8757 (ttm) REVERT: I 170 LEU cc_start: 0.9661 (mt) cc_final: 0.9405 (mt) REVERT: I 185 GLN cc_start: 0.9197 (mt0) cc_final: 0.8960 (mp10) REVERT: I 207 THR cc_start: 0.9779 (m) cc_final: 0.9577 (p) REVERT: I 229 MET cc_start: 0.9438 (mmm) cc_final: 0.9078 (mmm) REVERT: I 232 ILE cc_start: 0.9477 (mt) cc_final: 0.8937 (tt) REVERT: J 75 TYR cc_start: 0.8709 (m-80) cc_final: 0.8373 (m-10) REVERT: J 185 GLN cc_start: 0.8903 (mt0) cc_final: 0.8398 (mp10) REVERT: J 229 MET cc_start: 0.9045 (mmm) cc_final: 0.8550 (mmm) REVERT: J 274 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: K 42 LEU cc_start: 0.9685 (tp) cc_final: 0.9453 (tp) REVERT: K 199 LEU cc_start: 0.8708 (mm) cc_final: 0.8116 (tp) REVERT: K 210 MET cc_start: 0.8893 (tpt) cc_final: 0.8416 (tpp) REVERT: K 214 MET cc_start: 0.9381 (mmm) cc_final: 0.9151 (mmm) REVERT: K 250 GLU cc_start: 0.9237 (tt0) cc_final: 0.8760 (tm-30) REVERT: L 75 TYR cc_start: 0.8754 (m-10) cc_final: 0.8414 (m-80) REVERT: L 97 HIS cc_start: 0.7729 (m-70) cc_final: 0.7492 (m-70) REVERT: L 168 VAL cc_start: 0.9616 (m) cc_final: 0.9382 (p) REVERT: L 250 GLU cc_start: 0.8796 (pt0) cc_final: 0.8206 (pt0) REVERT: L 254 ARG cc_start: 0.9504 (ptp-110) cc_final: 0.9099 (ptp-170) outliers start: 103 outliers final: 58 residues processed: 855 average time/residue: 0.1615 time to fit residues: 216.8457 Evaluate side-chains 703 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 642 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 199 LEU 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 129 THR 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 117 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 J residue 230 LEU Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 274 GLU 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: chunk 259 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 224 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 185 GLN D 269 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** F 213 GLN 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 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.092785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064301 restraints weight = 92728.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.066537 restraints weight = 49047.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.068001 restraints weight = 32151.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068927 restraints weight = 24117.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.069595 restraints weight = 19885.990| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26665 Z= 0.171 Angle : 0.780 16.596 36129 Z= 0.393 Chirality : 0.045 0.248 4072 Planarity : 0.005 0.055 4356 Dihedral : 16.047 175.104 4199 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.84 % Rotamer: Outliers : 3.77 % Allowed : 19.84 % Favored : 76.39 % 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: 1.00 (0.15), residues: 3060 helix: 0.89 (0.12), residues: 1878 sheet: 1.40 (0.36), residues: 204 loop : 0.28 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 182 TYR 0.030 0.002 TYR A 240 PHE 0.025 0.002 PHE G 106 TRP 0.020 0.002 TRP K 20 HIS 0.021 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (26664) covalent geometry : angle 0.77968 / 0.39 (36129) hydrogen bonds : bond 0.05828 / 3.95 ( 1355) hydrogen bonds : angle 4.97672 / 3.59 ( 3957) Misc. bond : bond 0.00052 / 0.03 ( 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 788 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 687 time to evaluate : 1.027 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: B 145 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7941 (mp0) REVERT: B 159 ASP cc_start: 0.9086 (t70) cc_final: 0.8840 (t0) REVERT: B 182 ARG cc_start: 0.9465 (mtp85) cc_final: 0.9115 (ptp-110) REVERT: B 211 TRP cc_start: 0.9085 (m100) cc_final: 0.8164 (m100) REVERT: C 46 LEU cc_start: 0.9684 (mt) cc_final: 0.9422 (mp) REVERT: C 80 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7869 (tp-100) REVERT: C 98 GLN cc_start: 0.8938 (tp40) cc_final: 0.8702 (mm-40) REVERT: C 139 GLU cc_start: 0.8665 (mp0) cc_final: 0.8430 (mp0) REVERT: C 185 GLN cc_start: 0.8203 (mp10) cc_final: 0.7725 (mp10) REVERT: C 199 LEU cc_start: 0.8417 (tp) cc_final: 0.7986 (tp) REVERT: C 223 ASN cc_start: 0.8842 (t0) cc_final: 0.8434 (t0) REVERT: D 159 ASP cc_start: 0.9255 (m-30) cc_final: 0.8888 (m-30) REVERT: D 246 GLU cc_start: 0.9275 (tt0) cc_final: 0.8831 (pp20) REVERT: E 46 LEU cc_start: 0.9760 (mt) cc_final: 0.9538 (mt) REVERT: E 75 TYR cc_start: 0.8734 (t80) cc_final: 0.8456 (t80) REVERT: E 80 GLN cc_start: 0.8736 (pm20) cc_final: 0.8183 (pm20) REVERT: E 132 VAL cc_start: 0.9747 (t) cc_final: 0.9469 (p) REVERT: E 159 ASP cc_start: 0.9293 (t0) cc_final: 0.8916 (t0) REVERT: E 163 ASP cc_start: 0.8660 (m-30) cc_final: 0.8400 (m-30) REVERT: E 274 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7631 (mt-10) REVERT: F 81 GLN cc_start: 0.8717 (tp40) cc_final: 0.8509 (mm110) REVERT: F 125 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8881 (m-80) REVERT: F 145 GLU cc_start: 0.8895 (tp30) cc_final: 0.8595 (tp30) REVERT: F 154 PHE cc_start: 0.9026 (m-80) cc_final: 0.8795 (m-80) REVERT: F 204 PHE cc_start: 0.9463 (t80) cc_final: 0.9133 (t80) REVERT: G 53 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8329 (mmm-85) REVERT: G 93 TYR cc_start: 0.8833 (t80) cc_final: 0.8398 (t80) REVERT: G 140 MET cc_start: 0.8880 (ttp) cc_final: 0.7901 (mtp) REVERT: G 150 LYS cc_start: 0.8618 (tttt) cc_final: 0.8405 (mtmm) REVERT: G 183 ASP cc_start: 0.8282 (t0) cc_final: 0.7958 (t0) REVERT: G 185 GLN cc_start: 0.9088 (tt0) cc_final: 0.8787 (tm-30) REVERT: G 190 PHE cc_start: 0.8800 (m-10) cc_final: 0.8400 (m-10) REVERT: G 196 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7984 (t80) REVERT: G 211 TRP cc_start: 0.9014 (t60) cc_final: 0.8784 (t60) REVERT: G 214 MET cc_start: 0.8645 (mmt) cc_final: 0.7958 (mpp) REVERT: H 127 ASP cc_start: 0.8959 (m-30) cc_final: 0.8641 (m-30) REVERT: H 148 ARG cc_start: 0.9407 (OUTLIER) cc_final: 0.8882 (ptp-170) REVERT: H 156 ASP cc_start: 0.9223 (m-30) cc_final: 0.8802 (m-30) REVERT: H 159 ASP cc_start: 0.8425 (m-30) cc_final: 0.8046 (m-30) REVERT: H 169 VAL cc_start: 0.9793 (t) cc_final: 0.9583 (p) REVERT: H 183 ASP cc_start: 0.8253 (t70) cc_final: 0.7895 (t70) REVERT: H 224 LEU cc_start: 0.9599 (mm) cc_final: 0.9307 (mm) REVERT: I 140 MET cc_start: 0.8968 (ttp) cc_final: 0.8671 (ttm) REVERT: I 142 ILE cc_start: 0.9246 (mt) cc_final: 0.9013 (mm) REVERT: I 170 LEU cc_start: 0.9686 (mt) cc_final: 0.9365 (mt) REVERT: I 229 MET cc_start: 0.9514 (mmm) cc_final: 0.9127 (mmm) REVERT: I 232 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9053 (tt) REVERT: I 250 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8202 (tm-30) REVERT: J 75 TYR cc_start: 0.8750 (m-80) cc_final: 0.8427 (m-10) REVERT: J 111 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8664 (mt-10) REVERT: J 176 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8447 (tt) REVERT: J 180 ILE cc_start: 0.9277 (mt) cc_final: 0.8972 (mp) REVERT: J 185 GLN cc_start: 0.8968 (mt0) cc_final: 0.8601 (mp10) REVERT: J 229 MET cc_start: 0.8957 (mmm) cc_final: 0.8344 (mmm) REVERT: K 63 ARG cc_start: 0.9487 (mmm160) cc_final: 0.9181 (mmm-85) REVERT: K 199 LEU cc_start: 0.8807 (mm) cc_final: 0.8187 (tp) REVERT: K 210 MET cc_start: 0.8973 (tpt) cc_final: 0.8557 (tpt) REVERT: K 250 GLU cc_start: 0.9241 (tt0) cc_final: 0.8618 (tm-30) REVERT: L 75 TYR cc_start: 0.8645 (m-10) cc_final: 0.8328 (m-80) REVERT: L 98 GLN cc_start: 0.8570 (mp10) cc_final: 0.8161 (mm-40) REVERT: L 223 ASN cc_start: 0.9602 (t0) cc_final: 0.9171 (p0) REVERT: L 254 ARG cc_start: 0.9524 (ptp-110) cc_final: 0.9209 (ptp-170) outliers start: 101 outliers final: 67 residues processed: 746 average time/residue: 0.1453 time to fit residues: 173.6610 Evaluate side-chains 692 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 619 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 117 VAL Chi-restraints excluded: chain B residue 215 VAL 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 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 168 VAL 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 129 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 232 ILE 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 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 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 232 ILE 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 129 THR 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 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: chunk 141 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 195 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN E 213 GLN H 185 GLN I 213 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.092447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064263 restraints weight = 92815.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.066474 restraints weight = 48650.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067934 restraints weight = 31765.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068864 restraints weight = 23755.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.069511 restraints weight = 19615.074| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26665 Z= 0.160 Angle : 0.776 15.105 36129 Z= 0.389 Chirality : 0.045 0.334 4072 Planarity : 0.004 0.060 4356 Dihedral : 15.930 175.395 4197 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 3.77 % Allowed : 20.55 % Favored : 75.68 % 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: 1.11 (0.15), residues: 3060 helix: 0.96 (0.12), residues: 1889 sheet: 1.41 (0.36), residues: 204 loop : 0.39 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 158 TYR 0.031 0.001 TYR A 240 PHE 0.023 0.002 PHE J 204 TRP 0.021 0.002 TRP L 211 HIS 0.020 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (26664) covalent geometry : angle 0.77595 / 0.39 (36129) hydrogen bonds : bond 0.05332 / 3.62 ( 1355) hydrogen bonds : angle 4.83820 / 3.48 ( 3957) Misc. bond : bond 0.00096 / 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 771 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 670 time to evaluate : 0.720 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: A 56 CYS cc_start: 0.8986 (p) cc_final: 0.8352 (t) REVERT: B 144 ASP cc_start: 0.8144 (t70) cc_final: 0.7081 (t0) REVERT: B 145 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7322 (mp0) REVERT: B 159 ASP cc_start: 0.9137 (t70) cc_final: 0.8864 (t0) REVERT: B 163 ASP cc_start: 0.8911 (m-30) cc_final: 0.8662 (m-30) REVERT: B 211 TRP cc_start: 0.9131 (m100) cc_final: 0.8252 (m100) REVERT: C 46 LEU cc_start: 0.9693 (mt) cc_final: 0.9427 (mp) REVERT: C 80 GLN cc_start: 0.8540 (tp-100) cc_final: 0.8000 (tp-100) REVERT: C 139 GLU cc_start: 0.8676 (mp0) cc_final: 0.8349 (mp0) REVERT: C 173 THR cc_start: 0.8087 (p) cc_final: 0.7419 (t) REVERT: C 184 GLU cc_start: 0.8460 (pm20) cc_final: 0.8137 (pm20) REVERT: C 185 GLN cc_start: 0.8256 (mp10) cc_final: 0.7534 (mp10) REVERT: C 199 LEU cc_start: 0.8426 (tp) cc_final: 0.7888 (tp) REVERT: C 223 ASN cc_start: 0.9099 (t0) cc_final: 0.8743 (t0) REVERT: C 260 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8989 (tp) REVERT: C 269 GLN cc_start: 0.9036 (pp30) cc_final: 0.8744 (pp30) REVERT: D 175 ARG cc_start: 0.9232 (mmm-85) cc_final: 0.8845 (mmm-85) REVERT: D 229 MET cc_start: 0.8701 (ptp) cc_final: 0.8475 (ptp) REVERT: D 246 GLU cc_start: 0.9237 (tt0) cc_final: 0.9010 (tt0) REVERT: E 75 TYR cc_start: 0.8777 (t80) cc_final: 0.8499 (t80) REVERT: E 80 GLN cc_start: 0.8754 (pm20) cc_final: 0.8127 (pm20) REVERT: E 132 VAL cc_start: 0.9769 (t) cc_final: 0.9512 (p) REVERT: E 149 LEU cc_start: 0.9389 (mm) cc_final: 0.9102 (mm) REVERT: E 159 ASP cc_start: 0.9243 (t70) cc_final: 0.8847 (t0) REVERT: E 163 ASP cc_start: 0.8715 (m-30) cc_final: 0.8418 (m-30) REVERT: E 210 MET cc_start: 0.9462 (ptp) cc_final: 0.9079 (ptp) REVERT: E 229 MET cc_start: 0.8930 (mmt) cc_final: 0.8112 (mmp) REVERT: E 250 GLU cc_start: 0.9430 (tp30) cc_final: 0.9184 (tp30) REVERT: E 270 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8574 (pt0) REVERT: F 145 GLU cc_start: 0.8913 (tp30) cc_final: 0.8611 (tp30) REVERT: F 149 LEU cc_start: 0.8979 (tt) cc_final: 0.8686 (tt) REVERT: F 154 PHE cc_start: 0.9007 (m-80) cc_final: 0.8806 (m-80) REVERT: F 204 PHE cc_start: 0.9498 (t80) cc_final: 0.9071 (t80) REVERT: F 211 TRP cc_start: 0.9434 (t-100) cc_final: 0.9148 (t-100) REVERT: F 214 MET cc_start: 0.8948 (ttm) cc_final: 0.8523 (ttm) REVERT: G 75 TYR cc_start: 0.8449 (m-10) cc_final: 0.8115 (m-10) REVERT: G 140 MET cc_start: 0.8910 (ttp) cc_final: 0.8341 (mtp) REVERT: G 162 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: G 183 ASP cc_start: 0.8316 (t0) cc_final: 0.7932 (t0) REVERT: G 185 GLN cc_start: 0.9052 (tt0) cc_final: 0.8718 (tp40) REVERT: G 196 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7653 (t80) REVERT: H 127 ASP cc_start: 0.8954 (m-30) cc_final: 0.8636 (m-30) REVERT: H 148 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.8737 (ptp90) REVERT: H 156 ASP cc_start: 0.9287 (m-30) cc_final: 0.9042 (m-30) REVERT: H 183 ASP cc_start: 0.8171 (t70) cc_final: 0.7796 (t70) REVERT: I 140 MET cc_start: 0.8951 (ttp) cc_final: 0.8722 (ttm) REVERT: I 154 PHE cc_start: 0.9291 (m-80) cc_final: 0.8938 (m-80) REVERT: I 210 MET cc_start: 0.8955 (ppp) cc_final: 0.8415 (ppp) REVERT: I 229 MET cc_start: 0.9554 (mmm) cc_final: 0.9154 (mmm) REVERT: I 232 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9006 (tt) REVERT: I 250 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8144 (tm-30) REVERT: J 75 TYR cc_start: 0.8698 (m-80) cc_final: 0.8381 (m-10) REVERT: J 111 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8656 (mt-10) REVERT: J 176 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8622 (tt) REVERT: J 180 ILE cc_start: 0.9212 (mt) cc_final: 0.8979 (mp) REVERT: J 185 GLN cc_start: 0.9028 (mt0) cc_final: 0.8712 (mp10) REVERT: J 229 MET cc_start: 0.8971 (mmm) cc_final: 0.8285 (mmm) REVERT: K 63 ARG cc_start: 0.9504 (mmm160) cc_final: 0.9134 (mmm-85) REVERT: K 199 LEU cc_start: 0.8859 (mm) cc_final: 0.8343 (tp) REVERT: K 210 MET cc_start: 0.8946 (tpt) cc_final: 0.7675 (tpp) REVERT: K 214 MET cc_start: 0.9396 (mmp) cc_final: 0.8467 (mtp) REVERT: K 250 GLU cc_start: 0.9257 (tt0) cc_final: 0.8664 (tm-30) REVERT: L 36 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9093 (mm) REVERT: L 37 GLN cc_start: 0.9502 (pm20) cc_final: 0.9038 (pm20) REVERT: L 56 CYS cc_start: 0.8386 (p) cc_final: 0.7992 (m) REVERT: L 75 TYR cc_start: 0.8623 (m-10) cc_final: 0.8286 (m-80) REVERT: L 98 GLN cc_start: 0.8396 (mp10) cc_final: 0.7390 (mm-40) REVERT: L 99 LYS cc_start: 0.9189 (mppt) cc_final: 0.8782 (mmmt) REVERT: L 210 MET cc_start: 0.9462 (ptm) cc_final: 0.9111 (ptp) REVERT: L 223 ASN cc_start: 0.9622 (t0) cc_final: 0.9036 (p0) REVERT: L 254 ARG cc_start: 0.9553 (ptp-110) cc_final: 0.9221 (ptp-170) outliers start: 101 outliers final: 62 residues processed: 725 average time/residue: 0.1517 time to fit residues: 175.6068 Evaluate side-chains 668 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 598 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 117 VAL Chi-restraints excluded: chain B residue 118 THR 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 229 MET 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 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 129 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 232 ILE 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 39 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU 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 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 159 ASP Chi-restraints excluded: chain I residue 232 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 256 LEU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 141 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: chunk 150 optimal weight: 40.0000 chunk 269 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN E 185 GLN H 185 GLN I 37 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.090153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062132 restraints weight = 93937.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.064256 restraints weight = 49598.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.065649 restraints weight = 32595.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066534 restraints weight = 24515.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067156 restraints weight = 20273.314| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26665 Z= 0.201 Angle : 0.765 14.998 36129 Z= 0.384 Chirality : 0.045 0.238 4072 Planarity : 0.004 0.060 4356 Dihedral : 15.823 178.605 4197 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.71 % Rotamer: Outliers : 4.44 % Allowed : 21.07 % Favored : 74.49 % 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: 1.05 (0.12), residues: 1879 sheet: 1.32 (0.28), residues: 314 loop : 0.20 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 158 TYR 0.035 0.002 TYR L 240 PHE 0.020 0.002 PHE G 190 TRP 0.018 0.002 TRP K 211 HIS 0.015 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (26664) covalent geometry : angle 0.76525 / 0.38 (36129) hydrogen bonds : bond 0.05186 / 3.49 ( 1355) hydrogen bonds : angle 4.91352 / 3.54 ( 3957) Misc. bond : bond 0.00041 / 0.02 ( 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 718 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 599 time to evaluate : 1.099 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: A 56 CYS cc_start: 0.8907 (p) cc_final: 0.8414 (t) REVERT: B 140 MET cc_start: 0.9456 (ttp) cc_final: 0.9084 (tmm) REVERT: B 144 ASP cc_start: 0.8203 (t70) cc_final: 0.7124 (t0) REVERT: B 145 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7109 (mp0) REVERT: B 159 ASP cc_start: 0.9158 (t70) cc_final: 0.8854 (t0) REVERT: B 163 ASP cc_start: 0.9056 (m-30) cc_final: 0.8768 (m-30) REVERT: B 211 TRP cc_start: 0.9178 (m100) cc_final: 0.8566 (m100) REVERT: C 38 GLN cc_start: 0.9029 (tp40) cc_final: 0.8518 (tp40) REVERT: C 46 LEU cc_start: 0.9699 (mt) cc_final: 0.9427 (mp) REVERT: C 80 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8009 (tp-100) REVERT: C 139 GLU cc_start: 0.8691 (mp0) cc_final: 0.8351 (mp0) REVERT: C 166 ILE cc_start: 0.9655 (mt) cc_final: 0.9432 (mm) REVERT: C 184 GLU cc_start: 0.8600 (pm20) cc_final: 0.8135 (pm20) REVERT: C 196 PHE cc_start: 0.8808 (t80) cc_final: 0.8072 (t80) REVERT: C 199 LEU cc_start: 0.8330 (tp) cc_final: 0.7826 (tp) REVERT: C 223 ASN cc_start: 0.9195 (t0) cc_final: 0.8783 (t0) REVERT: C 260 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9022 (tp) REVERT: C 269 GLN cc_start: 0.9075 (pp30) cc_final: 0.8628 (pp30) REVERT: D 175 ARG cc_start: 0.9215 (mmm-85) cc_final: 0.8961 (mmm-85) REVERT: D 210 MET cc_start: 0.9285 (ttt) cc_final: 0.9032 (ttp) REVERT: E 21 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8900 (pt) REVERT: E 75 TYR cc_start: 0.8786 (t80) cc_final: 0.8515 (t80) REVERT: E 80 GLN cc_start: 0.8911 (pm20) cc_final: 0.8373 (pm20) REVERT: E 98 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8243 (mm-40) REVERT: E 132 VAL cc_start: 0.9791 (t) cc_final: 0.9543 (p) REVERT: E 159 ASP cc_start: 0.9221 (t70) cc_final: 0.8828 (t0) REVERT: E 163 ASP cc_start: 0.8700 (m-30) cc_final: 0.8407 (m-30) REVERT: E 229 MET cc_start: 0.8977 (mmt) cc_final: 0.8602 (mmp) REVERT: E 250 GLU cc_start: 0.9486 (tp30) cc_final: 0.9236 (tp30) REVERT: E 270 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8612 (pt0) REVERT: F 37 GLN cc_start: 0.9130 (pp30) cc_final: 0.8903 (pp30) REVERT: F 145 GLU cc_start: 0.9046 (tp30) cc_final: 0.8622 (tp30) REVERT: F 149 LEU cc_start: 0.9063 (tt) cc_final: 0.8771 (tt) REVERT: F 154 PHE cc_start: 0.9050 (m-80) cc_final: 0.8837 (m-80) REVERT: F 204 PHE cc_start: 0.9554 (t80) cc_final: 0.9077 (t80) REVERT: F 211 TRP cc_start: 0.9380 (t-100) cc_final: 0.9168 (t-100) REVERT: G 75 TYR cc_start: 0.8557 (m-10) cc_final: 0.8266 (m-10) REVERT: G 107 LYS cc_start: 0.9449 (ptpt) cc_final: 0.9149 (pttm) REVERT: G 140 MET cc_start: 0.8716 (ttp) cc_final: 0.8397 (ttp) REVERT: G 183 ASP cc_start: 0.8425 (t0) cc_final: 0.8059 (t0) REVERT: G 196 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7533 (t80) REVERT: G 210 MET cc_start: 0.7608 (ttt) cc_final: 0.7030 (ttt) REVERT: G 214 MET cc_start: 0.8842 (mmt) cc_final: 0.8181 (mpp) REVERT: H 127 ASP cc_start: 0.8988 (m-30) cc_final: 0.8664 (m-30) REVERT: H 144 ASP cc_start: 0.7973 (t0) cc_final: 0.7700 (t0) REVERT: H 148 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.8819 (ptp90) REVERT: H 156 ASP cc_start: 0.9283 (m-30) cc_final: 0.9078 (m-30) REVERT: H 183 ASP cc_start: 0.8299 (t70) cc_final: 0.7625 (t70) REVERT: H 229 MET cc_start: 0.9030 (ptt) cc_final: 0.8721 (ppp) REVERT: H 246 GLU cc_start: 0.9341 (tm-30) cc_final: 0.9030 (pp20) REVERT: I 140 MET cc_start: 0.8986 (ttp) cc_final: 0.8749 (ttm) REVERT: I 210 MET cc_start: 0.8883 (ppp) cc_final: 0.8489 (ppp) REVERT: I 229 MET cc_start: 0.9602 (mmm) cc_final: 0.9232 (mmm) REVERT: I 232 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.8988 (tt) REVERT: I 250 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8143 (tm-30) REVERT: J 75 TYR cc_start: 0.8722 (m-80) cc_final: 0.8411 (m-10) REVERT: J 111 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8661 (mt-10) REVERT: J 176 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8643 (tt) REVERT: J 180 ILE cc_start: 0.9258 (mt) cc_final: 0.8986 (mp) REVERT: J 185 GLN cc_start: 0.9019 (mt0) cc_final: 0.8628 (mp10) REVERT: J 229 MET cc_start: 0.8971 (mmm) cc_final: 0.8289 (mmm) REVERT: K 199 LEU cc_start: 0.8735 (mm) cc_final: 0.8107 (tp) REVERT: K 210 MET cc_start: 0.8998 (tpt) cc_final: 0.7753 (tpp) REVERT: K 214 MET cc_start: 0.9411 (mmp) cc_final: 0.8514 (mtp) REVERT: K 250 GLU cc_start: 0.9259 (tt0) cc_final: 0.8583 (tm-30) REVERT: L 36 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9089 (mm) REVERT: L 37 GLN cc_start: 0.9528 (pm20) cc_final: 0.9151 (pm20) REVERT: L 75 TYR cc_start: 0.8664 (m-10) cc_final: 0.8321 (m-80) REVERT: L 98 GLN cc_start: 0.8305 (mp10) cc_final: 0.7959 (mm-40) REVERT: L 210 MET cc_start: 0.9619 (ptm) cc_final: 0.9307 (ppp) REVERT: L 223 ASN cc_start: 0.9663 (t0) cc_final: 0.9314 (p0) REVERT: L 229 MET cc_start: 0.9104 (mpp) cc_final: 0.8541 (ptp) outliers start: 119 outliers final: 81 residues processed: 673 average time/residue: 0.1514 time to fit residues: 162.6688 Evaluate side-chains 651 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 561 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 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 118 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 225 LYS 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 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET 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 216 LEU Chi-restraints excluded: chain E residue 21 LEU 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 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 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 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 124 ASP 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 140 MET Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 152 GLU 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 H residue 275 TYR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 55 SER 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 264 ASP Chi-restraints excluded: chain J residue 100 CYS 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 109 ILE Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain L residue 36 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: chunk 18 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN G 185 GLN H 185 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.089362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061300 restraints weight = 94129.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063381 restraints weight = 49854.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064760 restraints weight = 32883.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065665 restraints weight = 24783.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.066221 restraints weight = 20451.463| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26665 Z= 0.183 Angle : 0.756 15.017 36129 Z= 0.378 Chirality : 0.044 0.209 4072 Planarity : 0.004 0.058 4356 Dihedral : 15.684 179.242 4197 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.25 % Favored : 97.58 % Rotamer: Outliers : 4.36 % Allowed : 22.16 % Favored : 73.48 % 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: 1.22 (0.15), residues: 3060 helix: 1.07 (0.12), residues: 1869 sheet: 1.29 (0.28), residues: 314 loop : 0.29 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 175 TYR 0.019 0.001 TYR L 240 PHE 0.020 0.002 PHE J 204 TRP 0.020 0.002 TRP K 211 HIS 0.012 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (26664) covalent geometry : angle 0.75572 / 0.38 (36129) hydrogen bonds : bond 0.05085 / 3.45 ( 1355) hydrogen bonds : angle 4.89371 / 3.51 ( 3957) Misc. bond : bond 0.00048 / 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 698 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 581 time to evaluate : 1.056 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: 0.8857 (OUTLIER) cc_final: 0.8465 (t) REVERT: B 140 MET cc_start: 0.9447 (ttp) cc_final: 0.8848 (tmm) REVERT: B 144 ASP cc_start: 0.8178 (t70) cc_final: 0.7741 (t0) REVERT: B 145 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7184 (mt-10) REVERT: B 159 ASP cc_start: 0.9172 (t70) cc_final: 0.8822 (t0) REVERT: B 163 ASP cc_start: 0.9090 (m-30) cc_final: 0.8795 (m-30) REVERT: B 211 TRP cc_start: 0.9212 (m100) cc_final: 0.8475 (m100) REVERT: C 38 GLN cc_start: 0.8998 (tp40) cc_final: 0.8595 (tp40) REVERT: C 46 LEU cc_start: 0.9709 (mt) cc_final: 0.9458 (mp) REVERT: C 80 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8042 (tp-100) REVERT: C 98 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8746 (mm-40) REVERT: C 139 GLU cc_start: 0.8739 (mp0) cc_final: 0.8369 (mp0) REVERT: C 166 ILE cc_start: 0.9641 (mt) cc_final: 0.9396 (mm) REVERT: C 184 GLU cc_start: 0.8681 (pm20) cc_final: 0.8231 (pm20) REVERT: C 196 PHE cc_start: 0.8967 (t80) cc_final: 0.8291 (t80) REVERT: C 199 LEU cc_start: 0.8320 (tp) cc_final: 0.7801 (tp) REVERT: C 223 ASN cc_start: 0.9229 (t0) cc_final: 0.8822 (t0) REVERT: C 260 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9031 (tp) REVERT: C 269 GLN cc_start: 0.9067 (pp30) cc_final: 0.8788 (pp30) REVERT: D 175 ARG cc_start: 0.9227 (mmm-85) cc_final: 0.8975 (mmm-85) REVERT: D 246 GLU cc_start: 0.9270 (tt0) cc_final: 0.8832 (pp20) REVERT: E 75 TYR cc_start: 0.8812 (t80) cc_final: 0.8550 (t80) REVERT: E 80 GLN cc_start: 0.8856 (pm20) cc_final: 0.8312 (pm20) REVERT: E 98 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8171 (mm-40) REVERT: E 132 VAL cc_start: 0.9800 (t) cc_final: 0.9563 (p) REVERT: E 159 ASP cc_start: 0.9207 (t70) cc_final: 0.8823 (t0) REVERT: E 163 ASP cc_start: 0.8687 (m-30) cc_final: 0.8406 (m-30) REVERT: E 229 MET cc_start: 0.8984 (mmt) cc_final: 0.8583 (mmp) REVERT: E 250 GLU cc_start: 0.9470 (tp30) cc_final: 0.9181 (tp30) REVERT: E 270 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8574 (pt0) REVERT: F 37 GLN cc_start: 0.9164 (pp30) cc_final: 0.8905 (pp30) REVERT: F 145 GLU cc_start: 0.9111 (tp30) cc_final: 0.8668 (tp30) REVERT: F 149 LEU cc_start: 0.9058 (tt) cc_final: 0.8721 (tt) REVERT: F 154 PHE cc_start: 0.9070 (m-80) cc_final: 0.8833 (m-80) REVERT: F 204 PHE cc_start: 0.9575 (t80) cc_final: 0.9104 (t80) REVERT: F 214 MET cc_start: 0.9067 (ttm) cc_final: 0.8711 (ttm) REVERT: G 75 TYR cc_start: 0.8615 (m-10) cc_final: 0.8299 (m-10) REVERT: G 107 LYS cc_start: 0.9467 (ptpt) cc_final: 0.9166 (pttm) REVERT: G 140 MET cc_start: 0.8685 (ttp) cc_final: 0.8361 (ttp) REVERT: G 183 ASP cc_start: 0.8467 (t0) cc_final: 0.8150 (t0) REVERT: G 196 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7579 (t80) REVERT: H 127 ASP cc_start: 0.8991 (m-30) cc_final: 0.8662 (m-30) REVERT: H 144 ASP cc_start: 0.8031 (t0) cc_final: 0.7749 (t0) REVERT: H 148 ARG cc_start: 0.9399 (OUTLIER) cc_final: 0.8829 (ptp90) REVERT: H 183 ASP cc_start: 0.8345 (t70) cc_final: 0.7921 (t70) REVERT: H 229 MET cc_start: 0.9060 (ptt) cc_final: 0.8815 (ppp) REVERT: I 140 MET cc_start: 0.9003 (ttp) cc_final: 0.8750 (ttm) REVERT: I 210 MET cc_start: 0.8996 (ppp) cc_final: 0.8350 (ppp) REVERT: I 211 TRP cc_start: 0.9137 (t-100) cc_final: 0.8857 (t-100) REVERT: I 229 MET cc_start: 0.9580 (mmm) cc_final: 0.9240 (mmm) REVERT: I 232 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9116 (tt) REVERT: I 250 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8055 (tm-30) REVERT: J 75 TYR cc_start: 0.8667 (m-80) cc_final: 0.8354 (m-10) REVERT: J 111 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8723 (mt-10) REVERT: J 176 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8649 (tt) REVERT: J 180 ILE cc_start: 0.9209 (mt) cc_final: 0.8996 (mt) REVERT: J 185 GLN cc_start: 0.8951 (mt0) cc_final: 0.8629 (mp10) REVERT: J 229 MET cc_start: 0.8922 (mmm) cc_final: 0.8245 (mmm) REVERT: K 116 ARG cc_start: 0.8880 (ttm-80) cc_final: 0.8665 (ttm110) REVERT: K 199 LEU cc_start: 0.8739 (mm) cc_final: 0.8002 (tp) REVERT: K 204 PHE cc_start: 0.9376 (t80) cc_final: 0.8859 (t80) REVERT: K 210 MET cc_start: 0.8992 (tpt) cc_final: 0.7721 (tpp) REVERT: K 214 MET cc_start: 0.9421 (mmp) cc_final: 0.8547 (mtp) REVERT: K 229 MET cc_start: 0.9433 (mmp) cc_final: 0.9214 (mmm) REVERT: K 250 GLU cc_start: 0.9336 (tt0) cc_final: 0.8753 (tt0) REVERT: K 275 TYR cc_start: 0.6945 (m-80) cc_final: 0.6639 (m-10) REVERT: L 36 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9099 (mm) REVERT: L 37 GLN cc_start: 0.9521 (pm20) cc_final: 0.9262 (pm20) REVERT: L 75 TYR cc_start: 0.8654 (m-10) cc_final: 0.8354 (m-80) REVERT: L 196 PHE cc_start: 0.8235 (m-10) cc_final: 0.7816 (m-10) REVERT: L 210 MET cc_start: 0.9574 (ptm) cc_final: 0.9055 (ppp) REVERT: L 223 ASN cc_start: 0.9659 (t0) cc_final: 0.9276 (p0) REVERT: L 240 TYR cc_start: 0.8550 (m-80) cc_final: 0.7785 (t80) outliers start: 117 outliers final: 88 residues processed: 649 average time/residue: 0.1511 time to fit residues: 158.2961 Evaluate side-chains 640 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 543 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 141 LEU 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 196 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 233 LEU 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 179 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 113 LEU 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 183 ASP 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 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 141 LEU 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 124 ASP Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 163 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 185 GLN 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 140 MET Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 152 GLU 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 H residue 275 TYR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 55 SER 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 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 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 36 LEU Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 269 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 291 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 245 optimal weight: 0.0020 chunk 102 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 281 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 208 optimal weight: 0.5980 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN E 213 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.090660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.062741 restraints weight = 93503.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.064857 restraints weight = 49411.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066261 restraints weight = 32445.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067160 restraints weight = 24376.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067726 restraints weight = 20091.463| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26665 Z= 0.143 Angle : 0.770 16.411 36129 Z= 0.381 Chirality : 0.044 0.251 4072 Planarity : 0.004 0.058 4356 Dihedral : 15.531 178.336 4197 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.16 % Favored : 97.61 % Rotamer: Outliers : 3.88 % Allowed : 23.20 % Favored : 72.92 % 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: 1.27 (0.15), residues: 3060 helix: 1.10 (0.12), residues: 1867 sheet: 1.36 (0.29), residues: 314 loop : 0.31 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 158 TYR 0.019 0.001 TYR D 93 PHE 0.022 0.002 PHE J 204 TRP 0.020 0.002 TRP A 211 HIS 0.010 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (26664) covalent geometry : angle 0.77039 / 0.38 (36129) hydrogen bonds : bond 0.04865 / 3.32 ( 1355) hydrogen bonds : angle 4.78127 / 3.43 ( 3957) Misc. bond : bond 0.00101 / 0.05 ( 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 705 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 601 time to evaluate : 1.031 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: 0.8777 (p) cc_final: 0.8427 (t) REVERT: B 140 MET cc_start: 0.9384 (ttp) cc_final: 0.8532 (tmm) REVERT: B 144 ASP cc_start: 0.8132 (t70) cc_final: 0.7001 (t0) REVERT: B 145 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7011 (mp0) REVERT: B 159 ASP cc_start: 0.9165 (t70) cc_final: 0.8759 (t0) REVERT: B 163 ASP cc_start: 0.9018 (m-30) cc_final: 0.8668 (m-30) REVERT: B 185 GLN cc_start: 0.9577 (tp40) cc_final: 0.9269 (tp-100) REVERT: B 211 TRP cc_start: 0.9230 (m100) cc_final: 0.8474 (m100) REVERT: C 38 GLN cc_start: 0.8902 (tp40) cc_final: 0.8531 (tp40) REVERT: C 46 LEU cc_start: 0.9701 (mt) cc_final: 0.9433 (mp) REVERT: C 80 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8056 (tp-100) REVERT: C 98 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8708 (mm-40) REVERT: C 139 GLU cc_start: 0.8744 (mp0) cc_final: 0.8340 (mp0) REVERT: C 162 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7873 (mp0) REVERT: C 166 ILE cc_start: 0.9631 (mt) cc_final: 0.9378 (mm) REVERT: C 173 THR cc_start: 0.7896 (p) cc_final: 0.7241 (t) REVERT: C 184 GLU cc_start: 0.8588 (pm20) cc_final: 0.8138 (pm20) REVERT: C 196 PHE cc_start: 0.8979 (t80) cc_final: 0.8302 (t80) REVERT: C 199 LEU cc_start: 0.8337 (tp) cc_final: 0.7982 (tp) REVERT: C 210 MET cc_start: 0.9350 (tpt) cc_final: 0.8905 (mmm) REVERT: C 213 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8568 (pp30) REVERT: C 214 MET cc_start: 0.9541 (tpp) cc_final: 0.9340 (mmm) REVERT: C 223 ASN cc_start: 0.9226 (t0) cc_final: 0.8890 (t0) REVERT: C 260 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9014 (tp) REVERT: D 145 GLU cc_start: 0.8822 (pt0) cc_final: 0.8483 (pt0) REVERT: D 246 GLU cc_start: 0.9277 (tt0) cc_final: 0.8802 (pp20) REVERT: E 75 TYR cc_start: 0.8715 (t80) cc_final: 0.8436 (t80) REVERT: E 80 GLN cc_start: 0.8821 (pm20) cc_final: 0.8278 (pm20) REVERT: E 98 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8209 (mm110) REVERT: E 132 VAL cc_start: 0.9802 (t) cc_final: 0.9562 (p) REVERT: E 159 ASP cc_start: 0.9131 (t70) cc_final: 0.8732 (t0) REVERT: E 163 ASP cc_start: 0.8633 (m-30) cc_final: 0.8410 (m-30) REVERT: E 229 MET cc_start: 0.8959 (mmt) cc_final: 0.8590 (mmp) REVERT: E 250 GLU cc_start: 0.9459 (tp30) cc_final: 0.9137 (tp30) REVERT: E 270 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8566 (pt0) REVERT: F 37 GLN cc_start: 0.9150 (pp30) cc_final: 0.8882 (pp30) REVERT: F 116 ARG cc_start: 0.8477 (mmp80) cc_final: 0.8260 (mmp80) REVERT: F 145 GLU cc_start: 0.9105 (tp30) cc_final: 0.8563 (tp30) REVERT: F 149 LEU cc_start: 0.8950 (tt) cc_final: 0.8558 (tt) REVERT: F 154 PHE cc_start: 0.9054 (m-80) cc_final: 0.8810 (m-80) REVERT: F 196 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: F 204 PHE cc_start: 0.9580 (t80) cc_final: 0.9092 (t80) REVERT: F 211 TRP cc_start: 0.9396 (t-100) cc_final: 0.8762 (t60) REVERT: F 248 LEU cc_start: 0.9688 (mt) cc_final: 0.9327 (pp) REVERT: G 53 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8437 (mmm-85) REVERT: G 75 TYR cc_start: 0.8478 (m-10) cc_final: 0.8183 (m-10) REVERT: G 107 LYS cc_start: 0.9471 (ptpt) cc_final: 0.9150 (pttm) REVERT: G 140 MET cc_start: 0.8818 (ttp) cc_final: 0.8306 (ttp) REVERT: G 183 ASP cc_start: 0.8486 (t0) cc_final: 0.7950 (t70) REVERT: G 185 GLN cc_start: 0.9154 (tt0) cc_final: 0.8872 (tm-30) REVERT: G 210 MET cc_start: 0.7561 (ttt) cc_final: 0.6948 (ttt) REVERT: G 214 MET cc_start: 0.8801 (mmt) cc_final: 0.8068 (mpp) REVERT: H 127 ASP cc_start: 0.8981 (m-30) cc_final: 0.8645 (m-30) REVERT: H 144 ASP cc_start: 0.8137 (t0) cc_final: 0.7935 (t0) REVERT: H 148 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.8882 (ptp90) REVERT: H 183 ASP cc_start: 0.8246 (t70) cc_final: 0.7845 (t70) REVERT: H 229 MET cc_start: 0.9019 (ptt) cc_final: 0.8777 (ppp) REVERT: I 140 MET cc_start: 0.8951 (ttp) cc_final: 0.8681 (ttm) REVERT: I 210 MET cc_start: 0.9076 (ppp) cc_final: 0.8267 (ppp) REVERT: I 211 TRP cc_start: 0.9080 (t-100) cc_final: 0.8804 (t-100) REVERT: I 214 MET cc_start: 0.8871 (mmm) cc_final: 0.8663 (mmm) REVERT: I 229 MET cc_start: 0.9552 (mmm) cc_final: 0.9209 (mmm) REVERT: I 232 ILE cc_start: 0.9528 (mt) cc_final: 0.9109 (tt) REVERT: I 250 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7983 (tm-30) REVERT: J 75 TYR cc_start: 0.8668 (m-80) cc_final: 0.8358 (m-10) REVERT: J 111 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8756 (mt-10) REVERT: J 162 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8429 (mm-30) REVERT: J 163 ASP cc_start: 0.9270 (OUTLIER) cc_final: 0.8830 (p0) REVERT: J 176 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8613 (tt) REVERT: J 180 ILE cc_start: 0.9175 (mt) cc_final: 0.8944 (mt) REVERT: J 229 MET cc_start: 0.8892 (mmm) cc_final: 0.8205 (mmm) REVERT: J 250 GLU cc_start: 0.8948 (tp30) cc_final: 0.8671 (tp30) REVERT: K 199 LEU cc_start: 0.8849 (mm) cc_final: 0.8130 (tp) REVERT: K 204 PHE cc_start: 0.9370 (t80) cc_final: 0.8830 (t80) REVERT: K 210 MET cc_start: 0.8969 (tpt) cc_final: 0.7654 (tpp) REVERT: K 214 MET cc_start: 0.9401 (mmp) cc_final: 0.8517 (mtp) REVERT: K 229 MET cc_start: 0.9436 (mmp) cc_final: 0.9206 (mmm) REVERT: K 250 GLU cc_start: 0.9322 (tt0) cc_final: 0.8739 (tt0) REVERT: K 275 TYR cc_start: 0.6942 (m-80) cc_final: 0.6588 (m-10) REVERT: L 38 GLN cc_start: 0.8901 (tt0) cc_final: 0.8633 (tp40) REVERT: L 56 CYS cc_start: 0.8526 (p) cc_final: 0.8123 (m) REVERT: L 76 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8022 (ptt180) REVERT: L 149 LEU cc_start: 0.8884 (tp) cc_final: 0.8511 (tp) REVERT: L 185 GLN cc_start: 0.9440 (tp-100) cc_final: 0.9089 (tm-30) REVERT: L 223 ASN cc_start: 0.9649 (t0) cc_final: 0.9323 (p0) REVERT: L 229 MET cc_start: 0.9123 (ptp) cc_final: 0.8626 (ptp) REVERT: L 240 TYR cc_start: 0.8489 (m-80) cc_final: 0.7784 (t80) outliers start: 104 outliers final: 67 residues processed: 662 average time/residue: 0.1460 time to fit residues: 155.3669 Evaluate side-chains 636 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 561 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 196 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 187 LEU 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 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 216 LEU 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 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 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 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 142 ILE 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 140 MET 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 H residue 275 TYR 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 J residue 111 GLU 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 75 TYR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 76 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: chunk 285 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 274 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3631 r_free = 0.3631 target = 0.090801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.062767 restraints weight = 94367.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.064883 restraints weight = 50002.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066261 restraints weight = 32915.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067184 restraints weight = 24744.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067782 restraints weight = 20399.909| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.6470 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= 0.140 Angle : 0.776 13.960 36129 Z= 0.384 Chirality : 0.044 0.293 4072 Planarity : 0.004 0.057 4356 Dihedral : 15.455 177.541 4197 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.99 % Favored : 97.78 % Rotamer: Outliers : 3.36 % Allowed : 23.76 % Favored : 72.88 % 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: 1.34 (0.15), residues: 3060 helix: 1.12 (0.12), residues: 1858 sheet: 1.54 (0.27), residues: 347 loop : 0.33 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 182 TYR 0.023 0.001 TYR D 93 PHE 0.020 0.001 PHE C 204 TRP 0.019 0.002 TRP A 211 HIS 0.010 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (26664) covalent geometry : angle 0.77569 / 0.38 (36129) hydrogen bonds : bond 0.04732 / 3.22 ( 1355) hydrogen bonds : angle 4.79632 / 3.43 ( 3957) Misc. bond : bond 0.00104 / 0.05 ( 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 675 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 585 time to evaluate : 0.901 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: A 56 CYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8311 (t) REVERT: A 140 MET cc_start: 0.9149 (tpt) cc_final: 0.8867 (tpt) REVERT: B 140 MET cc_start: 0.9369 (ttp) cc_final: 0.8522 (tmm) REVERT: B 144 ASP cc_start: 0.8235 (t70) cc_final: 0.7141 (t0) REVERT: B 145 GLU cc_start: 0.8109 (mt-10) cc_final: 0.6975 (mp0) REVERT: B 159 ASP cc_start: 0.9149 (t70) cc_final: 0.8724 (t0) REVERT: B 163 ASP cc_start: 0.9009 (m-30) cc_final: 0.8635 (m-30) REVERT: B 211 TRP cc_start: 0.9198 (m100) cc_final: 0.8437 (m100) REVERT: C 38 GLN cc_start: 0.9057 (tp40) cc_final: 0.8345 (tp40) REVERT: C 46 LEU cc_start: 0.9718 (mt) cc_final: 0.9457 (mp) REVERT: C 80 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8196 (tp-100) REVERT: C 139 GLU cc_start: 0.8758 (mp0) cc_final: 0.8337 (mp0) REVERT: C 162 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7738 (mp0) REVERT: C 166 ILE cc_start: 0.9529 (mt) cc_final: 0.9232 (mm) REVERT: C 184 GLU cc_start: 0.8528 (pm20) cc_final: 0.8147 (pm20) REVERT: C 196 PHE cc_start: 0.8966 (t80) cc_final: 0.8303 (t80) REVERT: C 199 LEU cc_start: 0.8495 (tp) cc_final: 0.8091 (tp) REVERT: C 223 ASN cc_start: 0.9229 (t0) cc_final: 0.8901 (t0) REVERT: C 260 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9007 (tp) REVERT: C 269 GLN cc_start: 0.9003 (pp30) cc_final: 0.8791 (pp30) REVERT: D 118 THR cc_start: 0.9119 (m) cc_final: 0.8823 (p) REVERT: D 246 GLU cc_start: 0.9253 (tt0) cc_final: 0.8786 (pp20) REVERT: E 75 TYR cc_start: 0.8733 (t80) cc_final: 0.8452 (t80) REVERT: E 80 GLN cc_start: 0.8816 (pm20) cc_final: 0.8272 (pm20) REVERT: E 98 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8189 (mm110) REVERT: E 132 VAL cc_start: 0.9804 (t) cc_final: 0.9559 (p) REVERT: E 145 GLU cc_start: 0.8250 (tp30) cc_final: 0.7871 (tm-30) REVERT: E 159 ASP cc_start: 0.9087 (t70) cc_final: 0.8680 (t0) REVERT: E 163 ASP cc_start: 0.8582 (m-30) cc_final: 0.8361 (m-30) REVERT: E 229 MET cc_start: 0.8938 (mmt) cc_final: 0.8561 (mmp) REVERT: E 250 GLU cc_start: 0.9444 (tp30) cc_final: 0.9118 (tp30) REVERT: E 270 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8634 (pt0) REVERT: F 37 GLN cc_start: 0.9177 (pp30) cc_final: 0.8910 (pp30) REVERT: F 140 MET cc_start: 0.9077 (ppp) cc_final: 0.8701 (ppp) REVERT: F 145 GLU cc_start: 0.9142 (tp30) cc_final: 0.8585 (tp30) REVERT: F 154 PHE cc_start: 0.9053 (m-80) cc_final: 0.8837 (m-80) REVERT: F 156 ASP cc_start: 0.9106 (m-30) cc_final: 0.8897 (t70) REVERT: F 196 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: F 204 PHE cc_start: 0.9599 (t80) cc_final: 0.9114 (t80) REVERT: F 211 TRP cc_start: 0.9374 (t-100) cc_final: 0.8582 (t60) REVERT: F 214 MET cc_start: 0.8938 (ttm) cc_final: 0.8658 (ttm) REVERT: F 248 LEU cc_start: 0.9702 (mt) cc_final: 0.9368 (pp) REVERT: G 53 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8494 (mmm-85) REVERT: G 75 TYR cc_start: 0.8514 (m-10) cc_final: 0.8179 (m-10) REVERT: G 93 TYR cc_start: 0.8583 (t80) cc_final: 0.8329 (t80) REVERT: G 107 LYS cc_start: 0.9467 (ptpt) cc_final: 0.9124 (pttm) REVERT: G 140 MET cc_start: 0.8772 (ttp) cc_final: 0.8205 (ttp) REVERT: G 183 ASP cc_start: 0.8538 (t0) cc_final: 0.8307 (t70) REVERT: G 196 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7403 (t80) REVERT: G 210 MET cc_start: 0.7674 (ttt) cc_final: 0.7062 (ttt) REVERT: G 214 MET cc_start: 0.8964 (mmt) cc_final: 0.8330 (mpp) REVERT: H 127 ASP cc_start: 0.8957 (m-30) cc_final: 0.8620 (m-30) REVERT: H 139 GLU cc_start: 0.8894 (mp0) cc_final: 0.8586 (pm20) REVERT: H 144 ASP cc_start: 0.8127 (t0) cc_final: 0.7802 (t0) REVERT: H 148 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.8895 (ptp90) REVERT: H 183 ASP cc_start: 0.8248 (t70) cc_final: 0.7858 (t70) REVERT: H 214 MET cc_start: 0.8885 (mtm) cc_final: 0.8651 (ptp) REVERT: I 140 MET cc_start: 0.8897 (ttp) cc_final: 0.8628 (ttm) REVERT: I 162 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8532 (mm-30) REVERT: I 210 MET cc_start: 0.9118 (ppp) cc_final: 0.8319 (ppp) REVERT: I 211 TRP cc_start: 0.9094 (t-100) cc_final: 0.8833 (t-100) REVERT: I 214 MET cc_start: 0.8932 (mmm) cc_final: 0.8675 (mmm) REVERT: I 229 MET cc_start: 0.9541 (mmm) cc_final: 0.9201 (mmm) REVERT: I 250 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7952 (tm-30) REVERT: J 75 TYR cc_start: 0.8666 (m-80) cc_final: 0.8371 (m-10) REVERT: J 159 ASP cc_start: 0.8964 (t0) cc_final: 0.8422 (t0) REVERT: J 162 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8342 (mm-30) REVERT: J 163 ASP cc_start: 0.9259 (t70) cc_final: 0.8831 (p0) REVERT: J 176 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8604 (tt) REVERT: J 180 ILE cc_start: 0.9199 (mt) cc_final: 0.8971 (mt) REVERT: J 185 GLN cc_start: 0.9154 (mp10) cc_final: 0.8615 (mp10) REVERT: J 229 MET cc_start: 0.8846 (mmm) cc_final: 0.8174 (mmm) REVERT: J 256 LEU cc_start: 0.9551 (mm) cc_final: 0.9261 (mm) REVERT: K 116 ARG cc_start: 0.8874 (ttm-80) cc_final: 0.8661 (ttm110) REVERT: K 140 MET cc_start: 0.8982 (ppp) cc_final: 0.8259 (ppp) REVERT: K 199 LEU cc_start: 0.8883 (mm) cc_final: 0.8198 (tp) REVERT: K 204 PHE cc_start: 0.9389 (t80) cc_final: 0.8809 (t80) REVERT: K 210 MET cc_start: 0.8992 (tpt) cc_final: 0.7824 (tpp) REVERT: K 214 MET cc_start: 0.9387 (mmp) cc_final: 0.8526 (mtp) REVERT: K 250 GLU cc_start: 0.9354 (tt0) cc_final: 0.8745 (tt0) REVERT: K 275 TYR cc_start: 0.7180 (m-80) cc_final: 0.6754 (m-10) REVERT: L 27 ARG cc_start: 0.9386 (ptp-110) cc_final: 0.9113 (ptp-110) REVERT: L 56 CYS cc_start: 0.8681 (p) cc_final: 0.8453 (m) REVERT: L 76 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7578 (ptt-90) REVERT: L 149 LEU cc_start: 0.8913 (tp) cc_final: 0.8470 (tp) REVERT: L 159 ASP cc_start: 0.9324 (m-30) cc_final: 0.9043 (p0) REVERT: L 185 GLN cc_start: 0.9515 (tp-100) cc_final: 0.9228 (tm-30) REVERT: L 223 ASN cc_start: 0.9642 (t0) cc_final: 0.9269 (p0) REVERT: L 229 MET cc_start: 0.9141 (ptp) cc_final: 0.8830 (ptp) REVERT: L 240 TYR cc_start: 0.8544 (m-80) cc_final: 0.7953 (t80) REVERT: L 254 ARG cc_start: 0.9595 (ptp-110) cc_final: 0.9333 (ptp-110) outliers start: 90 outliers final: 68 residues processed: 638 average time/residue: 0.1491 time to fit residues: 153.1775 Evaluate side-chains 639 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 563 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 56 CYS 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 248 LEU Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 187 LEU 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 179 VAL 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 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 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 196 PHE 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 142 ILE 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 140 MET Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 160 ILE 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 H residue 275 TYR 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 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 75 TYR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain L residue 76 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: chunk 147 optimal weight: 6.9990 chunk 35 optimal weight: 0.0570 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 104 optimal weight: 0.0010 chunk 240 optimal weight: 0.0570 chunk 90 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 overall best weight: 0.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN C 193 HIS ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.091674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063594 restraints weight = 94735.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065785 restraints weight = 49444.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.067213 restraints weight = 32207.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.068153 restraints weight = 24116.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.068703 restraints weight = 19826.134| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26665 Z= 0.141 Angle : 0.798 14.522 36129 Z= 0.394 Chirality : 0.045 0.252 4072 Planarity : 0.004 0.058 4356 Dihedral : 15.397 177.765 4197 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.16 % Favored : 97.61 % Rotamer: Outliers : 2.76 % Allowed : 24.69 % Favored : 72.55 % 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: 1.31 (0.15), residues: 3060 helix: 1.15 (0.12), residues: 1826 sheet: 1.60 (0.27), residues: 347 loop : 0.16 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 158 TYR 0.019 0.001 TYR D 93 PHE 0.016 0.001 PHE F 190 TRP 0.028 0.002 TRP K 20 HIS 0.009 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (26664) covalent geometry : angle 0.79844 / 0.39 (36129) hydrogen bonds : bond 0.04609 / 3.16 ( 1355) hydrogen bonds : angle 4.75169 / 3.40 ( 3957) Misc. bond : bond 0.00171 / 0.09 ( 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 663 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 589 time to evaluate : 0.884 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: 0.8723 (OUTLIER) cc_final: 0.8513 (t) REVERT: A 80 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8724 (mm110) REVERT: A 140 MET cc_start: 0.9140 (tpt) cc_final: 0.8836 (tpt) REVERT: A 170 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9279 (pp) REVERT: B 140 MET cc_start: 0.9363 (ttp) cc_final: 0.8498 (tmm) REVERT: B 144 ASP cc_start: 0.8245 (t70) cc_final: 0.7144 (t0) REVERT: B 145 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7003 (mp0) REVERT: B 159 ASP cc_start: 0.9139 (t70) cc_final: 0.8670 (t0) REVERT: B 163 ASP cc_start: 0.9038 (m-30) cc_final: 0.8637 (m-30) REVERT: B 211 TRP cc_start: 0.9236 (m100) cc_final: 0.8455 (m100) REVERT: C 38 GLN cc_start: 0.8927 (tp40) cc_final: 0.8544 (tp40) REVERT: C 80 GLN cc_start: 0.8789 (tp-100) cc_final: 0.8222 (tp-100) REVERT: C 139 GLU cc_start: 0.8755 (mp0) cc_final: 0.8353 (mp0) REVERT: C 184 GLU cc_start: 0.8542 (pm20) cc_final: 0.8154 (pm20) REVERT: C 199 LEU cc_start: 0.8512 (tp) cc_final: 0.7940 (tp) REVERT: C 207 THR cc_start: 0.9806 (m) cc_final: 0.9605 (p) REVERT: C 210 MET cc_start: 0.9378 (tpt) cc_final: 0.9015 (mmm) REVERT: C 213 GLN cc_start: 0.9306 (tm-30) cc_final: 0.8629 (pp30) REVERT: C 223 ASN cc_start: 0.9228 (t0) cc_final: 0.8917 (t0) REVERT: C 260 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9011 (tp) REVERT: C 269 GLN cc_start: 0.8974 (pp30) cc_final: 0.8694 (pp30) REVERT: D 118 THR cc_start: 0.9088 (m) cc_final: 0.8821 (p) REVERT: D 246 GLU cc_start: 0.9282 (tt0) cc_final: 0.8799 (pp20) REVERT: E 75 TYR cc_start: 0.8830 (t80) cc_final: 0.8558 (t80) REVERT: E 80 GLN cc_start: 0.8843 (pm20) cc_final: 0.8331 (pm20) REVERT: E 132 VAL cc_start: 0.9808 (t) cc_final: 0.9567 (p) REVERT: E 159 ASP cc_start: 0.9082 (t70) cc_final: 0.8647 (t0) REVERT: E 163 ASP cc_start: 0.8538 (m-30) cc_final: 0.8287 (m-30) REVERT: E 229 MET cc_start: 0.8951 (mmt) cc_final: 0.8571 (mmp) REVERT: E 250 GLU cc_start: 0.9442 (tp30) cc_final: 0.9107 (tp30) REVERT: E 270 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8654 (pt0) REVERT: F 37 GLN cc_start: 0.9168 (pp30) cc_final: 0.8913 (pp30) REVERT: F 140 MET cc_start: 0.9067 (ppp) cc_final: 0.8719 (ppp) REVERT: F 145 GLU cc_start: 0.9145 (tp30) cc_final: 0.8566 (tp30) REVERT: F 154 PHE cc_start: 0.9057 (m-80) cc_final: 0.8788 (m-80) REVERT: F 156 ASP cc_start: 0.9122 (m-30) cc_final: 0.8911 (t70) REVERT: F 196 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: F 204 PHE cc_start: 0.9595 (t80) cc_final: 0.9086 (t80) REVERT: F 210 MET cc_start: 0.9259 (tpp) cc_final: 0.9020 (mtt) REVERT: F 211 TRP cc_start: 0.9123 (t-100) cc_final: 0.8500 (t60) REVERT: F 248 LEU cc_start: 0.9677 (mt) cc_final: 0.9352 (pp) REVERT: G 53 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8470 (mmm-85) REVERT: G 75 TYR cc_start: 0.8558 (m-10) cc_final: 0.8178 (m-10) REVERT: G 93 TYR cc_start: 0.8544 (t80) cc_final: 0.8227 (t80) REVERT: G 107 LYS cc_start: 0.9451 (ptpt) cc_final: 0.9114 (pttm) REVERT: G 140 MET cc_start: 0.8724 (ttp) cc_final: 0.8149 (ttp) REVERT: G 183 ASP cc_start: 0.8692 (t0) cc_final: 0.8360 (t70) REVERT: G 196 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7206 (t80) REVERT: G 210 MET cc_start: 0.7691 (ttt) cc_final: 0.7076 (ttt) REVERT: G 214 MET cc_start: 0.8981 (mmt) cc_final: 0.8373 (mpp) REVERT: H 54 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8340 (ptmt) REVERT: H 93 TYR cc_start: 0.8865 (t80) cc_final: 0.8633 (t80) REVERT: H 127 ASP cc_start: 0.9005 (m-30) cc_final: 0.8659 (m-30) REVERT: H 139 GLU cc_start: 0.8907 (mp0) cc_final: 0.8573 (pm20) REVERT: H 144 ASP cc_start: 0.8000 (t0) cc_final: 0.7392 (t0) REVERT: H 148 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8860 (ptp90) REVERT: H 183 ASP cc_start: 0.8217 (t70) cc_final: 0.7820 (t70) REVERT: H 214 MET cc_start: 0.8730 (mtm) cc_final: 0.8489 (mtm) REVERT: I 140 MET cc_start: 0.8919 (ttp) cc_final: 0.8627 (ttm) REVERT: I 162 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8465 (mm-30) REVERT: I 188 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8899 (tm-30) REVERT: I 210 MET cc_start: 0.9187 (ppp) cc_final: 0.8371 (ppp) REVERT: I 211 TRP cc_start: 0.9127 (t-100) cc_final: 0.8828 (t-100) REVERT: I 214 MET cc_start: 0.8980 (mmm) cc_final: 0.8668 (mmm) REVERT: I 229 MET cc_start: 0.9550 (mmm) cc_final: 0.9212 (mmm) REVERT: I 250 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7973 (tm-30) REVERT: I 275 TYR cc_start: 0.6631 (m-10) cc_final: 0.6040 (m-10) REVERT: J 75 TYR cc_start: 0.8706 (m-80) cc_final: 0.8410 (m-10) REVERT: J 159 ASP cc_start: 0.8976 (t0) cc_final: 0.8434 (t0) REVERT: J 162 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8399 (mm-30) REVERT: J 163 ASP cc_start: 0.9274 (t70) cc_final: 0.8816 (p0) REVERT: J 176 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8601 (tt) REVERT: J 180 ILE cc_start: 0.9208 (mt) cc_final: 0.8979 (mt) REVERT: J 185 GLN cc_start: 0.9140 (mp10) cc_final: 0.8557 (mp10) REVERT: J 229 MET cc_start: 0.8882 (mmm) cc_final: 0.8221 (mmm) REVERT: J 256 LEU cc_start: 0.9550 (mm) cc_final: 0.9299 (mm) REVERT: K 116 ARG cc_start: 0.8889 (ttm-80) cc_final: 0.8633 (ttm110) REVERT: K 176 LEU cc_start: 0.9629 (tp) cc_final: 0.9349 (mt) REVERT: K 199 LEU cc_start: 0.8874 (mm) cc_final: 0.8188 (tp) REVERT: K 204 PHE cc_start: 0.9405 (t80) cc_final: 0.8850 (t80) REVERT: K 210 MET cc_start: 0.9000 (tpt) cc_final: 0.8749 (tpp) REVERT: K 214 MET cc_start: 0.9410 (mmp) cc_final: 0.8886 (ttp) REVERT: K 250 GLU cc_start: 0.9343 (tt0) cc_final: 0.8986 (tt0) REVERT: K 275 TYR cc_start: 0.7009 (m-80) cc_final: 0.6734 (m-10) REVERT: L 27 ARG cc_start: 0.9405 (ptp-110) cc_final: 0.9134 (ptp-110) REVERT: L 38 GLN cc_start: 0.8979 (tt0) cc_final: 0.8764 (tp-100) REVERT: L 76 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7786 (ptt180) REVERT: L 149 LEU cc_start: 0.8850 (tp) cc_final: 0.8462 (tp) REVERT: L 159 ASP cc_start: 0.9363 (m-30) cc_final: 0.9098 (p0) REVERT: L 185 GLN cc_start: 0.9557 (tp-100) cc_final: 0.9274 (tm-30) REVERT: L 223 ASN cc_start: 0.9687 (t0) cc_final: 0.9354 (p0) REVERT: L 229 MET cc_start: 0.9169 (ptp) cc_final: 0.8898 (ptp) REVERT: L 240 TYR cc_start: 0.8594 (m-80) cc_final: 0.8013 (t80) outliers start: 74 outliers final: 56 residues processed: 630 average time/residue: 0.1477 time to fit residues: 149.7897 Evaluate side-chains 632 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 568 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 56 CYS 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 188 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 187 LEU 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 260 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 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 117 VAL Chi-restraints excluded: chain E residue 129 THR 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 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 196 PHE 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 142 ILE 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 140 MET 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 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 275 TYR 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 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 75 TYR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 76 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: chunk 74 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 278 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 208 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.090068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062231 restraints weight = 94705.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064366 restraints weight = 49372.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065761 restraints weight = 32184.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066676 restraints weight = 24054.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067274 restraints weight = 19766.416| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26665 Z= 0.169 Angle : 0.806 14.522 36129 Z= 0.401 Chirality : 0.045 0.313 4072 Planarity : 0.004 0.055 4356 Dihedral : 15.378 175.077 4197 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.09 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 25.18 % Favored : 72.03 % 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: 1.30 (0.15), residues: 3060 helix: 1.12 (0.12), residues: 1837 sheet: 1.57 (0.27), residues: 347 loop : 0.22 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 175 TYR 0.023 0.001 TYR D 93 PHE 0.020 0.002 PHE C 204 TRP 0.045 0.002 TRP K 20 HIS 0.009 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (26664) covalent geometry : angle 0.80587 / 0.40 (36129) hydrogen bonds : bond 0.04830 / 3.26 ( 1355) hydrogen bonds : angle 4.87235 / 3.48 ( 3957) Misc. bond : bond 0.00162 / 0.09 ( 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 624 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 549 time to evaluate : 0.928 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: A 80 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8659 (mm110) REVERT: A 140 MET cc_start: 0.9128 (tpt) cc_final: 0.8869 (tpp) REVERT: A 175 ARG cc_start: 0.9207 (ptt180) cc_final: 0.8854 (ptt90) REVERT: B 140 MET cc_start: 0.9406 (ttp) cc_final: 0.8811 (tmm) REVERT: B 144 ASP cc_start: 0.8277 (t70) cc_final: 0.7160 (t0) REVERT: B 145 GLU cc_start: 0.8078 (mt-10) cc_final: 0.6966 (mp0) REVERT: B 159 ASP cc_start: 0.9131 (t70) cc_final: 0.8684 (t0) REVERT: B 163 ASP cc_start: 0.9018 (m-30) cc_final: 0.8634 (m-30) REVERT: B 211 TRP cc_start: 0.9192 (m100) cc_final: 0.8423 (m100) REVERT: C 38 GLN cc_start: 0.9044 (tp40) cc_final: 0.8386 (tp40) REVERT: C 80 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8261 (tp-100) REVERT: C 139 GLU cc_start: 0.8766 (mp0) cc_final: 0.8341 (mp0) REVERT: C 184 GLU cc_start: 0.8640 (pm20) cc_final: 0.8245 (pm20) REVERT: C 199 LEU cc_start: 0.8490 (tp) cc_final: 0.8060 (tp) REVERT: C 210 MET cc_start: 0.9513 (tpt) cc_final: 0.9204 (mmm) REVERT: C 223 ASN cc_start: 0.9226 (t0) cc_final: 0.8898 (t0) REVERT: C 269 GLN cc_start: 0.8994 (pp30) cc_final: 0.8722 (pp30) REVERT: D 140 MET cc_start: 0.8802 (ttp) cc_final: 0.8565 (ptp) REVERT: D 246 GLU cc_start: 0.9278 (tt0) cc_final: 0.8832 (pp20) REVERT: E 75 TYR cc_start: 0.8822 (t80) cc_final: 0.8535 (t80) REVERT: E 80 GLN cc_start: 0.8881 (pm20) cc_final: 0.8368 (pm20) REVERT: E 132 VAL cc_start: 0.9820 (t) cc_final: 0.9582 (p) REVERT: E 159 ASP cc_start: 0.9117 (t70) cc_final: 0.8584 (t0) REVERT: E 163 ASP cc_start: 0.8550 (m-30) cc_final: 0.8328 (m-30) REVERT: E 185 GLN cc_start: 0.9382 (mm-40) cc_final: 0.9112 (mp10) REVERT: E 229 MET cc_start: 0.9026 (mmt) cc_final: 0.8646 (mmp) REVERT: E 250 GLU cc_start: 0.9455 (tp30) cc_final: 0.9124 (tp30) REVERT: E 270 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8697 (pt0) REVERT: F 37 GLN cc_start: 0.9214 (pp30) cc_final: 0.8919 (pp30) REVERT: F 140 MET cc_start: 0.9065 (ppp) cc_final: 0.8734 (ppp) REVERT: F 145 GLU cc_start: 0.9216 (tp30) cc_final: 0.8648 (tp30) REVERT: F 154 PHE cc_start: 0.9057 (m-80) cc_final: 0.8787 (m-80) REVERT: F 160 ILE cc_start: 0.9504 (mm) cc_final: 0.9282 (mm) REVERT: F 196 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: F 204 PHE cc_start: 0.9602 (t80) cc_final: 0.9119 (t80) REVERT: G 53 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8505 (mmm-85) REVERT: G 75 TYR cc_start: 0.8524 (m-10) cc_final: 0.8174 (m-10) REVERT: G 93 TYR cc_start: 0.8621 (t80) cc_final: 0.8269 (t80) REVERT: G 107 LYS cc_start: 0.9405 (ptpt) cc_final: 0.9085 (pttm) REVERT: G 140 MET cc_start: 0.8607 (ttp) cc_final: 0.7990 (ttp) REVERT: G 183 ASP cc_start: 0.9015 (t0) cc_final: 0.8538 (t0) REVERT: G 196 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7135 (t80) REVERT: G 210 MET cc_start: 0.7776 (ttt) cc_final: 0.7138 (ttt) REVERT: G 214 MET cc_start: 0.9030 (mmt) cc_final: 0.8411 (mpp) REVERT: H 127 ASP cc_start: 0.8983 (m-30) cc_final: 0.8645 (m-30) REVERT: H 139 GLU cc_start: 0.8910 (mp0) cc_final: 0.8586 (pm20) REVERT: H 148 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.8864 (ptp90) REVERT: H 183 ASP cc_start: 0.8246 (t70) cc_final: 0.7830 (t70) REVERT: I 61 GLU cc_start: 0.7356 (tt0) cc_final: 0.7142 (tt0) REVERT: I 140 MET cc_start: 0.8963 (ttp) cc_final: 0.8669 (ttm) REVERT: I 162 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8631 (mm-30) REVERT: I 164 LEU cc_start: 0.9052 (mt) cc_final: 0.8763 (mp) REVERT: I 188 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8911 (tm-30) REVERT: I 210 MET cc_start: 0.9208 (ppp) cc_final: 0.8397 (ppp) REVERT: I 214 MET cc_start: 0.8962 (mmm) cc_final: 0.8628 (mmm) REVERT: I 229 MET cc_start: 0.9574 (mmm) cc_final: 0.9214 (mmm) REVERT: I 250 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8089 (tm-30) REVERT: J 75 TYR cc_start: 0.8716 (m-80) cc_final: 0.8428 (m-10) REVERT: J 159 ASP cc_start: 0.9011 (t0) cc_final: 0.8505 (t0) REVERT: J 163 ASP cc_start: 0.9289 (t70) cc_final: 0.8837 (p0) REVERT: J 176 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8628 (tt) REVERT: J 180 ILE cc_start: 0.9211 (mt) cc_final: 0.8992 (mt) REVERT: J 185 GLN cc_start: 0.9090 (mp10) cc_final: 0.8697 (mp10) REVERT: J 229 MET cc_start: 0.8816 (mmm) cc_final: 0.8149 (mmm) REVERT: J 256 LEU cc_start: 0.9547 (mm) cc_final: 0.9301 (mm) REVERT: K 116 ARG cc_start: 0.8882 (ttm-80) cc_final: 0.8624 (ttm110) REVERT: K 140 MET cc_start: 0.8883 (ppp) cc_final: 0.8123 (ppp) REVERT: K 176 LEU cc_start: 0.9640 (tp) cc_final: 0.9339 (mt) REVERT: K 187 LEU cc_start: 0.9263 (tt) cc_final: 0.8771 (mt) REVERT: K 199 LEU cc_start: 0.8891 (mm) cc_final: 0.8164 (tp) REVERT: K 204 PHE cc_start: 0.9461 (t80) cc_final: 0.8880 (t80) REVERT: K 210 MET cc_start: 0.9002 (tpt) cc_final: 0.8739 (tpp) REVERT: K 214 MET cc_start: 0.9407 (mmp) cc_final: 0.8875 (ttp) REVERT: K 250 GLU cc_start: 0.9352 (tt0) cc_final: 0.8930 (tt0) REVERT: K 275 TYR cc_start: 0.7052 (m-80) cc_final: 0.6847 (m-10) REVERT: L 27 ARG cc_start: 0.9396 (ptp-110) cc_final: 0.9127 (ptp-110) REVERT: L 38 GLN cc_start: 0.8934 (tt0) cc_final: 0.8694 (tp-100) REVERT: L 76 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7787 (ptt180) REVERT: L 149 LEU cc_start: 0.8775 (tp) cc_final: 0.8521 (tp) REVERT: L 159 ASP cc_start: 0.9351 (m-30) cc_final: 0.9089 (p0) REVERT: L 185 GLN cc_start: 0.9555 (tp-100) cc_final: 0.9334 (tm-30) REVERT: L 210 MET cc_start: 0.9510 (ptm) cc_final: 0.9197 (ppp) REVERT: L 223 ASN cc_start: 0.9690 (t0) cc_final: 0.9346 (p0) REVERT: L 229 MET cc_start: 0.9185 (ptp) cc_final: 0.8894 (ptp) REVERT: L 240 TYR cc_start: 0.8607 (m-80) cc_final: 0.8027 (t80) outliers start: 75 outliers final: 59 residues processed: 597 average time/residue: 0.1499 time to fit residues: 144.2883 Evaluate side-chains 597 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 533 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 186 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 187 LEU 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 D residue 31 LYS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL 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 117 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 166 ILE 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 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 142 ILE 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 66 LYS 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 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 J residue 28 LEU 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 244 LEU Chi-restraints excluded: chain L residue 76 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: chunk 233 optimal weight: 0.5980 chunk 280 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN ** 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** ** L 98 GLN ** 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 = 0.3600 r_free = 0.3600 target = 0.089389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.061686 restraints weight = 94537.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063784 restraints weight = 49541.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.065165 restraints weight = 32341.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066041 restraints weight = 24181.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.066640 restraints weight = 19965.323| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26665 Z= 0.184 Angle : 0.825 14.277 36129 Z= 0.411 Chirality : 0.046 0.273 4072 Planarity : 0.004 0.078 4356 Dihedral : 15.346 178.408 4197 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.03 % Favored : 97.68 % Rotamer: Outliers : 2.69 % Allowed : 25.66 % Favored : 71.65 % 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: 1.29 (0.15), residues: 3060 helix: 1.12 (0.12), residues: 1837 sheet: 1.58 (0.27), residues: 347 loop : 0.20 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 27 TYR 0.023 0.001 TYR D 93 PHE 0.015 0.001 PHE F 190 TRP 0.033 0.002 TRP K 20 HIS 0.009 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (26664) covalent geometry : angle 0.82500 / 0.41 (36129) hydrogen bonds : bond 0.04805 / 3.26 ( 1355) hydrogen bonds : angle 4.95333 / 3.56 ( 3957) Misc. bond : bond 0.00390 / 0.21 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5673.11 seconds wall clock time: 98 minutes 23.34 seconds (5903.34 seconds total)