Starting phenix.real_space_refine on Mon May 4 06:06:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9omy_70624/05_2026/9omy_70624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9omy_70624/05_2026/9omy_70624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9omy_70624/05_2026/9omy_70624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9omy_70624/05_2026/9omy_70624.map" model { file = "/net/cci-nas-00/data/ceres_data/9omy_70624/05_2026/9omy_70624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9omy_70624/05_2026/9omy_70624.cif" } resolution = 3.25 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= 0.031 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 18 5.49 5 S 98 5.16 5 C 11572 2.51 5 N 3292 2.21 5 O 3464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18444 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2256 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 287} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2364 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 8, 'TRANS': 300} Chain breaks: 1 Chain: "C" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1986 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "X" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2523 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 307} Chain breaks: 2 Chain: "D" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2256 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 287} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2364 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 8, 'TRANS': 300} Chain breaks: 1 Chain: "F" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1986 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "G" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2523 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 307} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.74, per 1000 atoms: 0.26 Number of scatterers: 18444 At special positions: 0 Unit cell: (152.25, 112.23, 118.32, 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 98 16.00 P 18 15.00 O 3464 8.00 N 3292 7.00 C 11572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 863.4 milliseconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4380 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 18 sheets defined 45.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.687A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.919A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.751A pdb=" N LYS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.565A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 189 removed outlier: 3.803A pdb=" N ASP A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.610A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 260 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 36 through 43 removed outlier: 3.883A pdb=" N LYS B 40 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.512A pdb=" N SER B 97 " --> pdb=" O HIS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 134 through 144 removed outlier: 3.544A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.700A pdb=" N ALA B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 189 removed outlier: 3.542A pdb=" N LEU B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.773A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.677A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.706A pdb=" N GLN B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.502A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 165 through 188 removed outlier: 3.663A pdb=" N ASP C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 3.952A pdb=" N ARG C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 194' Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 265 through 276 removed outlier: 3.569A pdb=" N ASN C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 20 removed outlier: 3.649A pdb=" N ALA X 19 " --> pdb=" O ALA X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 28 Processing helix chain 'X' and resid 33 through 40 removed outlier: 4.265A pdb=" N ARG X 37 " --> pdb=" O PRO X 33 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU X 38 " --> pdb=" O ASP X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 58 Processing helix chain 'X' and resid 64 through 71 Processing helix chain 'X' and resid 75 through 80 removed outlier: 3.820A pdb=" N HIS X 79 " --> pdb=" O PHE X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 94 Processing helix chain 'X' and resid 112 through 124 Processing helix chain 'X' and resid 147 through 157 removed outlier: 3.587A pdb=" N ALA X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 162 Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 186 through 197 Processing helix chain 'X' and resid 198 through 203 Processing helix chain 'X' and resid 215 through 223 removed outlier: 4.221A pdb=" N PHE X 219 " --> pdb=" O VAL X 215 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 250 removed outlier: 3.838A pdb=" N ARG X 233 " --> pdb=" O ALA X 229 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER X 237 " --> pdb=" O ARG X 233 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA X 240 " --> pdb=" O GLN X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 285 through 290 Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.679A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.503A pdb=" N ALA D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 95 Processing helix chain 'D' and resid 106 through 113 removed outlier: 3.749A pdb=" N LYS D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 145 through 146 No H-bonds generated for 'chain 'D' and resid 145 through 146' Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.535A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 189 removed outlier: 3.838A pdb=" N ASP D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 212 removed outlier: 3.615A pdb=" N THR D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 260 Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.884A pdb=" N LYS E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 89 through 97 removed outlier: 3.508A pdb=" N SER E 97 " --> pdb=" O HIS E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 134 through 144 removed outlier: 3.546A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.688A pdb=" N ALA E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 189 removed outlier: 3.851A pdb=" N ASP E 187 " --> pdb=" O SER E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 211 removed outlier: 3.776A pdb=" N THR E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 removed outlier: 3.686A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.720A pdb=" N GLN E 242 " --> pdb=" O LEU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 removed outlier: 3.534A pdb=" N ALA E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 112 Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 165 through 188 removed outlier: 3.677A pdb=" N ASP F 171 " --> pdb=" O ASP F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 removed outlier: 3.953A pdb=" N ARG F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 189 through 194' Processing helix chain 'F' and resid 200 through 207 Processing helix chain 'F' and resid 215 through 233 Proline residue: F 227 - end of helix removed outlier: 3.852A pdb=" N SER F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 249 Processing helix chain 'F' and resid 255 through 264 removed outlier: 3.553A pdb=" N THR F 259 " --> pdb=" O LEU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 276 removed outlier: 3.568A pdb=" N ASN F 275 " --> pdb=" O SER F 271 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 removed outlier: 3.649A pdb=" N ALA G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 Processing helix chain 'G' and resid 33 through 40 removed outlier: 4.265A pdb=" N ARG G 37 " --> pdb=" O PRO G 33 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU G 38 " --> pdb=" O ASP G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 58 Processing helix chain 'G' and resid 64 through 71 Processing helix chain 'G' and resid 75 through 80 removed outlier: 3.883A pdb=" N HIS G 79 " --> pdb=" O PHE G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 94 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 147 through 157 removed outlier: 3.596A pdb=" N ALA G 156 " --> pdb=" O GLN G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 162 Processing helix chain 'G' and resid 166 through 171 Processing helix chain 'G' and resid 186 through 197 Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 215 through 223 removed outlier: 4.231A pdb=" N PHE G 219 " --> pdb=" O VAL G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 250 removed outlier: 3.839A pdb=" N ARG G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 237 " --> pdb=" O ARG G 233 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA G 240 " --> pdb=" O GLN G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.358A pdb=" N TYR B 159 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 219 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N THR B 266 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL B 221 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLN B 268 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 193 removed outlier: 5.580A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A 217 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 221 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.785A pdb=" N THR B 87 " --> pdb=" O ILE X 181 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA X 137 " --> pdb=" O PHE X 180 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLY X 136 " --> pdb=" O ALA X 207 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU X 209 " --> pdb=" O GLY X 136 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU X 297 " --> pdb=" O VAL X 317 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL X 317 " --> pdb=" O LEU X 297 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP X 299 " --> pdb=" O LEU X 315 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU X 315 " --> pdb=" O ASP X 299 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 210 removed outlier: 5.989A pdb=" N VAL C 156 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP C 242 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 158 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 311 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS C 316 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG C 322 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.566A pdb=" N VAL C 298 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 81 through 82 Processing sheet with id=AA9, first strand: chain 'X' and resid 330 through 333 Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.362A pdb=" N TYR E 159 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLN E 268 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE E 122 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU E 300 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU E 124 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU E 302 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE E 126 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LYS E 304 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB3, first strand: chain 'D' and resid 190 through 193 removed outlier: 5.581A pdb=" N LYS D 156 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA D 217 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL D 264 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET D 125 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU D 124 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU D 302 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE D 126 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N LYS D 304 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.771A pdb=" N THR E 87 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA G 137 " --> pdb=" O PHE G 180 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLY G 136 " --> pdb=" O ALA G 207 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 209 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU G 297 " --> pdb=" O VAL G 317 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL G 317 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP G 299 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU G 315 " --> pdb=" O ASP G 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB6, first strand: chain 'F' and resid 208 through 210 removed outlier: 6.467A pdb=" N GLU F 154 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE F 240 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL F 156 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP F 242 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE F 158 " --> pdb=" O ASP F 242 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA F 279 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE F 311 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS F 316 " --> pdb=" O LEU F 323 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG F 322 " --> pdb=" O PHE F 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 286 through 288 removed outlier: 3.570A pdb=" N VAL F 298 " --> pdb=" O THR F 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 81 through 82 Processing sheet with id=AB9, first strand: chain 'G' and resid 330 through 333 782 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 2.27 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: 6202 1.34 - 1.46: 3756 1.46 - 1.58: 8620 1.58 - 1.70: 22 1.70 - 1.82: 148 Bond restraints: 18748 Sorted by residual: bond pdb=" N3B ANP X 401 " pdb=" PG ANP X 401 " ideal model delta sigma weight residual 1.795 1.595 0.200 2.00e-02 2.50e+03 9.96e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.596 0.199 2.00e-02 2.50e+03 9.92e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.596 0.199 2.00e-02 2.50e+03 9.86e+01 bond pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 1.795 1.599 0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.599 0.196 2.00e-02 2.50e+03 9.56e+01 ... (remaining 18743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 25085 2.70 - 5.41: 241 5.41 - 8.11: 33 8.11 - 10.82: 3 10.82 - 13.52: 12 Bond angle restraints: 25374 Sorted by residual: angle pdb=" N ILE C 244 " pdb=" CA ILE C 244 " pdb=" C ILE C 244 " ideal model delta sigma weight residual 112.90 108.19 4.71 9.60e-01 1.09e+00 2.41e+01 angle pdb=" O GLY F 243 " pdb=" C GLY F 243 " pdb=" N ILE F 244 " ideal model delta sigma weight residual 122.70 116.83 5.87 1.30e+00 5.92e-01 2.04e+01 angle pdb=" CB MET A 243 " pdb=" CG MET A 243 " pdb=" SD MET A 243 " ideal model delta sigma weight residual 112.70 126.22 -13.52 3.00e+00 1.11e-01 2.03e+01 angle pdb=" CB MET D 243 " pdb=" CG MET D 243 " pdb=" SD MET D 243 " ideal model delta sigma weight residual 112.70 126.22 -13.52 3.00e+00 1.11e-01 2.03e+01 angle pdb=" N LEU X 116 " pdb=" CA LEU X 116 " pdb=" C LEU X 116 " ideal model delta sigma weight residual 112.90 107.15 5.75 1.31e+00 5.83e-01 1.93e+01 ... (remaining 25369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 11187 36.00 - 72.00: 266 72.00 - 108.00: 33 108.00 - 143.99: 4 143.99 - 179.99: 2 Dihedral angle restraints: 11492 sinusoidal: 4706 harmonic: 6786 Sorted by residual: dihedral pdb=" O1A ANP G 401 " pdb=" O3A ANP G 401 " pdb=" PA ANP G 401 " pdb=" PB ANP G 401 " ideal model delta sinusoidal sigma weight residual 83.11 -96.90 -179.99 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A ANP X 401 " pdb=" O3A ANP X 401 " pdb=" PA ANP X 401 " pdb=" PB ANP X 401 " ideal model delta sinusoidal sigma weight residual 83.11 -90.83 173.94 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B ANP X 401 " pdb=" N3B ANP X 401 " pdb=" PB ANP X 401 " pdb=" PG ANP X 401 " ideal model delta sinusoidal sigma weight residual 35.15 -107.74 142.89 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 11489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2596 0.066 - 0.132: 311 0.132 - 0.198: 18 0.198 - 0.264: 5 0.264 - 0.330: 4 Chirality restraints: 2934 Sorted by residual: chirality pdb=" C3' ANP G 401 " pdb=" C2' ANP G 401 " pdb=" C4' ANP G 401 " pdb=" O3' ANP G 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C3' ANP X 401 " pdb=" C2' ANP X 401 " pdb=" C4' ANP X 401 " pdb=" O3' ANP X 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2931 not shown) Planarity restraints: 3246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 243 " -0.031 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C GLY F 243 " 0.103 2.00e-02 2.50e+03 pdb=" O GLY F 243 " -0.038 2.00e-02 2.50e+03 pdb=" N ILE F 244 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 82 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO B 83 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 83 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 83 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 82 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO E 83 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 83 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 83 " -0.033 5.00e-02 4.00e+02 ... (remaining 3243 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 484 2.70 - 3.25: 18347 3.25 - 3.80: 29913 3.80 - 4.35: 40103 4.35 - 4.90: 67074 Nonbonded interactions: 155921 Sorted by model distance: nonbonded pdb=" O GLY F 243 " pdb=" N ALA F 245 " model vdw 2.146 3.120 nonbonded pdb=" CG2 VAL F 241 " pdb=" CD1 ILE F 244 " model vdw 2.156 3.880 nonbonded pdb=" OG1 THR A 225 " pdb=" OD1 ASN A 267 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR G 114 " pdb=" O2A ANP G 401 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR D 225 " pdb=" OD1 ASN D 267 " model vdw 2.177 3.040 ... (remaining 155916 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 337) selection = (chain 'B' and (resid 32 through 221 or (resid 222 through 224 and (name N or na \ me CA or name C or name O or name CB )) or resid 225 through 271 or resid 284 th \ rough 337)) selection = (chain 'D' and resid 32 through 337) selection = (chain 'E' and (resid 32 through 221 or (resid 222 through 224 and (name N or na \ me CA or name C or name O or name CB )) or resid 225 through 271 or resid 284 th \ rough 337)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'X' } 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 individual isotropic 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: 2.960 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.020 Find NCS groups from input model: 0.430 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.008 0.703 18749 Z= 0.592 Angle : 0.717 13.524 25374 Z= 0.366 Chirality : 0.045 0.330 2934 Planarity : 0.004 0.068 3246 Dihedral : 16.179 179.992 7112 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.67 % Favored : 95.16 % Rotamer: Outliers : 0.77 % Allowed : 17.47 % Favored : 81.75 % 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: -1.57 (0.17), residues: 2336 helix: -0.16 (0.18), residues: 890 sheet: -1.72 (0.29), residues: 334 loop : -1.50 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 249 TYR 0.011 0.001 TYR E 54 PHE 0.011 0.001 PHE F 246 TRP 0.004 0.000 TRP C 317 HIS 0.006 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00576 (18748) covalent geometry : angle 0.71689 (25374) hydrogen bonds : bond 0.21986 ( 782) hydrogen bonds : angle 8.15515 ( 2244) Misc. bond : bond 0.70316 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 0.747 Fit side-chains REVERT: C 151 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7233 (t) REVERT: X 115 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7559 (mp10) outliers start: 15 outliers final: 5 residues processed: 233 average time/residue: 0.1588 time to fit residues: 55.7819 Evaluate side-chains 223 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 331 THR Chi-restraints excluded: chain D residue 176 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 30.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 119 GLN ** 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 = 0.4537 r_free = 0.4537 target = 0.230568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.179772 restraints weight = 18755.940| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.15 r_work: 0.3688 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18749 Z= 0.157 Angle : 0.560 7.755 25374 Z= 0.280 Chirality : 0.043 0.191 2934 Planarity : 0.004 0.058 3246 Dihedral : 11.974 174.982 2773 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 3.30 % Allowed : 16.65 % Favored : 80.05 % 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: -1.40 (0.17), residues: 2336 helix: 0.05 (0.17), residues: 944 sheet: -1.62 (0.28), residues: 332 loop : -1.54 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 249 TYR 0.014 0.001 TYR D 191 PHE 0.011 0.001 PHE B 248 TRP 0.003 0.000 TRP C 317 HIS 0.003 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00363 (18748) covalent geometry : angle 0.56007 (25374) hydrogen bonds : bond 0.03729 ( 782) hydrogen bonds : angle 5.68925 ( 2244) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 253 time to evaluate : 0.756 Fit side-chains REVERT: A 84 MET cc_start: 0.8200 (tpp) cc_final: 0.7929 (tpp) REVERT: C 237 ARG cc_start: 0.7252 (mmp-170) cc_final: 0.6509 (mmp-170) REVERT: X 155 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7051 (mmt) REVERT: X 296 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8130 (mt) REVERT: D 84 MET cc_start: 0.8179 (tpp) cc_final: 0.7942 (tpp) REVERT: G 155 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7047 (mmt) outliers start: 64 outliers final: 32 residues processed: 291 average time/residue: 0.1519 time to fit residues: 66.9578 Evaluate side-chains 276 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 155 MET Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 301 LEU Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 333 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 62 optimal weight: 0.6980 chunk 187 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 168 optimal weight: 0.3980 chunk 199 optimal weight: 2.9990 chunk 52 optimal weight: 0.0170 chunk 231 optimal weight: 0.5980 chunk 217 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.237055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186427 restraints weight = 19171.556| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.28 r_work: 0.3714 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18749 Z= 0.114 Angle : 0.509 7.482 25374 Z= 0.253 Chirality : 0.042 0.182 2934 Planarity : 0.004 0.051 3246 Dihedral : 10.048 178.947 2761 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 3.30 % Allowed : 18.30 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.17), residues: 2336 helix: 0.35 (0.17), residues: 946 sheet: -1.62 (0.28), residues: 336 loop : -1.51 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 249 TYR 0.011 0.001 TYR B 315 PHE 0.009 0.001 PHE E 248 TRP 0.003 0.000 TRP F 317 HIS 0.002 0.000 HIS X 79 Details of bonding type rmsd covalent geometry : bond 0.00261 (18748) covalent geometry : angle 0.50917 (25374) hydrogen bonds : bond 0.03041 ( 782) hydrogen bonds : angle 5.16149 ( 2244) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 0.694 Fit side-chains REVERT: A 114 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7483 (mt0) REVERT: B 255 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7658 (mt) REVERT: C 237 ARG cc_start: 0.7287 (mmp-170) cc_final: 0.6519 (mmp-170) REVERT: D 114 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7547 (mt0) REVERT: D 167 ARG cc_start: 0.8192 (mtm110) cc_final: 0.7756 (mmm160) REVERT: E 255 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7686 (mt) REVERT: F 237 ARG cc_start: 0.7252 (mmm-85) cc_final: 0.7032 (mmm-85) outliers start: 64 outliers final: 37 residues processed: 304 average time/residue: 0.1454 time to fit residues: 66.6250 Evaluate side-chains 284 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 333 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 173 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 101 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 183 HIS D 94 GLN D 101 GLN G 71 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.228808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.178819 restraints weight = 18887.909| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.25 r_work: 0.3662 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18749 Z= 0.177 Angle : 0.554 8.557 25374 Z= 0.273 Chirality : 0.044 0.193 2934 Planarity : 0.004 0.051 3246 Dihedral : 9.877 172.987 2759 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 4.23 % Allowed : 17.99 % Favored : 77.78 % 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: -1.26 (0.17), residues: 2336 helix: 0.28 (0.17), residues: 952 sheet: -1.91 (0.27), residues: 358 loop : -1.43 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 229 TYR 0.010 0.001 TYR E 315 PHE 0.014 0.001 PHE B 248 TRP 0.001 0.000 TRP F 305 HIS 0.003 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00422 (18748) covalent geometry : angle 0.55372 (25374) hydrogen bonds : bond 0.03142 ( 782) hydrogen bonds : angle 5.19041 ( 2244) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 252 time to evaluate : 0.455 Fit side-chains REVERT: A 114 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7742 (mt0) REVERT: A 167 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7755 (mmm160) REVERT: C 237 ARG cc_start: 0.7250 (mmp-170) cc_final: 0.6466 (mmp-170) REVERT: C 322 ARG cc_start: 0.7519 (ptp-170) cc_final: 0.7312 (ptp-170) REVERT: X 154 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8161 (mp) REVERT: X 155 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7140 (mmt) REVERT: D 167 ARG cc_start: 0.8125 (mtm110) cc_final: 0.7697 (mmm160) REVERT: E 216 TYR cc_start: 0.8691 (m-80) cc_final: 0.8071 (m-80) REVERT: G 154 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8151 (mp) REVERT: G 155 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7150 (mmt) outliers start: 82 outliers final: 54 residues processed: 301 average time/residue: 0.1372 time to fit residues: 62.6542 Evaluate side-chains 301 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 142 THR Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 155 MET Chi-restraints excluded: chain X residue 178 GLN Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 326 SER Chi-restraints excluded: chain X residue 331 THR Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 333 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 118 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN G 71 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.220167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.166344 restraints weight = 18947.029| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.49 r_work: 0.3525 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 18749 Z= 0.348 Angle : 0.723 10.312 25374 Z= 0.354 Chirality : 0.049 0.196 2934 Planarity : 0.005 0.048 3246 Dihedral : 11.228 172.744 2759 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.96 % Rotamer: Outliers : 4.90 % Allowed : 18.30 % Favored : 76.80 % 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: -1.66 (0.17), residues: 2336 helix: -0.05 (0.17), residues: 954 sheet: -2.09 (0.28), residues: 340 loop : -1.68 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 193 TYR 0.022 0.002 TYR A 191 PHE 0.024 0.002 PHE B 248 TRP 0.003 0.001 TRP G 288 HIS 0.005 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00838 (18748) covalent geometry : angle 0.72286 (25374) hydrogen bonds : bond 0.03904 ( 782) hydrogen bonds : angle 5.60877 ( 2244) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 265 time to evaluate : 0.851 Fit side-chains REVERT: A 324 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6960 (mm-30) REVERT: C 237 ARG cc_start: 0.7387 (mmp-170) cc_final: 0.6630 (mmp-170) REVERT: X 155 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7043 (mmt) REVERT: X 192 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7424 (tm-30) REVERT: F 154 GLU cc_start: 0.8676 (mp0) cc_final: 0.7829 (mp0) REVERT: G 155 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7047 (mmt) REVERT: G 192 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7441 (tm-30) REVERT: G 296 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8160 (mt) outliers start: 95 outliers final: 65 residues processed: 321 average time/residue: 0.1457 time to fit residues: 71.6285 Evaluate side-chains 318 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 250 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 142 THR Chi-restraints excluded: chain X residue 155 MET Chi-restraints excluded: chain X residue 178 GLN Chi-restraints excluded: chain X residue 189 THR Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 326 SER Chi-restraints excluded: chain X residue 331 THR Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 343 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 1 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN G 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.224629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.172554 restraints weight = 18563.790| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.30 r_work: 0.3616 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18749 Z= 0.143 Angle : 0.557 8.611 25374 Z= 0.275 Chirality : 0.044 0.213 2934 Planarity : 0.004 0.057 3246 Dihedral : 10.023 173.398 2759 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 3.30 % Allowed : 20.26 % Favored : 76.44 % 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: -1.40 (0.17), residues: 2336 helix: 0.25 (0.17), residues: 936 sheet: -1.98 (0.27), residues: 354 loop : -1.58 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.013 0.001 TYR A 315 PHE 0.012 0.001 PHE G 75 TRP 0.003 0.001 TRP C 305 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00336 (18748) covalent geometry : angle 0.55677 (25374) hydrogen bonds : bond 0.03022 ( 782) hydrogen bonds : angle 5.18474 ( 2244) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 256 time to evaluate : 0.764 Fit side-chains REVERT: A 167 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7658 (mmm160) REVERT: C 237 ARG cc_start: 0.7310 (mmp-170) cc_final: 0.6460 (mmp-170) REVERT: X 154 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8214 (mp) REVERT: X 155 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7062 (mmt) REVERT: X 296 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8094 (mt) REVERT: D 167 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7603 (mmm160) REVERT: D 211 MET cc_start: 0.8110 (mmt) cc_final: 0.7810 (mmt) REVERT: F 154 GLU cc_start: 0.8595 (mp0) cc_final: 0.7521 (mp0) REVERT: G 155 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7005 (mmt) outliers start: 64 outliers final: 54 residues processed: 301 average time/residue: 0.1510 time to fit residues: 68.9253 Evaluate side-chains 304 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 142 THR Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 155 MET Chi-restraints excluded: chain X residue 178 GLN Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 305 GLU Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 326 SER Chi-restraints excluded: chain X residue 331 THR Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 343 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 228 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.221886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165936 restraints weight = 18883.812| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.16 r_work: 0.3622 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18749 Z= 0.145 Angle : 0.552 10.724 25374 Z= 0.271 Chirality : 0.043 0.189 2934 Planarity : 0.004 0.052 3246 Dihedral : 9.621 173.839 2759 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 4.18 % Allowed : 19.69 % Favored : 76.13 % 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: -1.19 (0.17), residues: 2336 helix: 0.39 (0.17), residues: 944 sheet: -1.79 (0.28), residues: 350 loop : -1.49 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.012 0.001 TYR D 191 PHE 0.014 0.001 PHE G 75 TRP 0.002 0.001 TRP C 317 HIS 0.004 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00344 (18748) covalent geometry : angle 0.55162 (25374) hydrogen bonds : bond 0.02877 ( 782) hydrogen bonds : angle 5.04192 ( 2244) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 254 time to evaluate : 0.728 Fit side-chains REVERT: A 167 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7500 (mmm160) REVERT: C 237 ARG cc_start: 0.7172 (mmp-170) cc_final: 0.6813 (mmp-170) REVERT: C 285 GLN cc_start: 0.7581 (mt0) cc_final: 0.6776 (mp10) REVERT: X 154 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8116 (mp) REVERT: X 155 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7006 (mmt) REVERT: X 296 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8213 (mt) REVERT: D 84 MET cc_start: 0.8238 (tpp) cc_final: 0.7893 (tpp) REVERT: D 167 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7522 (mmm160) REVERT: F 154 GLU cc_start: 0.8567 (mp0) cc_final: 0.7425 (mp0) REVERT: G 155 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7009 (mmt) REVERT: G 296 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8228 (mt) outliers start: 81 outliers final: 65 residues processed: 311 average time/residue: 0.1504 time to fit residues: 71.3549 Evaluate side-chains 313 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 243 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 142 THR Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 155 MET Chi-restraints excluded: chain X residue 178 GLN Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 305 GLU Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 326 SER Chi-restraints excluded: chain X residue 331 THR Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 343 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 228 optimal weight: 0.5980 chunk 28 optimal weight: 0.0070 chunk 161 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 211 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 234 HIS G 71 GLN G 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.223104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172443 restraints weight = 18564.260| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.34 r_work: 0.3608 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18749 Z= 0.120 Angle : 0.537 11.447 25374 Z= 0.263 Chirality : 0.042 0.173 2934 Planarity : 0.004 0.054 3246 Dihedral : 9.159 174.026 2758 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.28 % Rotamer: Outliers : 3.56 % Allowed : 20.52 % Favored : 75.93 % 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: -1.05 (0.17), residues: 2336 helix: 0.57 (0.17), residues: 934 sheet: -1.81 (0.28), residues: 362 loop : -1.40 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.011 0.001 TYR E 315 PHE 0.015 0.001 PHE G 75 TRP 0.002 0.000 TRP C 305 HIS 0.004 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00281 (18748) covalent geometry : angle 0.53746 (25374) hydrogen bonds : bond 0.02788 ( 782) hydrogen bonds : angle 4.93668 ( 2244) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 255 time to evaluate : 0.862 Fit side-chains REVERT: A 101 GLN cc_start: 0.7538 (mt0) cc_final: 0.7337 (mt0) REVERT: A 167 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7526 (mmm160) REVERT: C 237 ARG cc_start: 0.7056 (mmp-170) cc_final: 0.6719 (mmp-170) REVERT: C 285 GLN cc_start: 0.7426 (mt0) cc_final: 0.6638 (mp10) REVERT: X 154 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8017 (mp) REVERT: X 155 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7102 (mmt) REVERT: X 296 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8114 (mt) REVERT: D 167 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7491 (mmm160) REVERT: F 132 THR cc_start: 0.5810 (OUTLIER) cc_final: 0.5509 (p) REVERT: G 155 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7113 (mmt) outliers start: 69 outliers final: 57 residues processed: 302 average time/residue: 0.1521 time to fit residues: 69.1646 Evaluate side-chains 301 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 142 THR Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 155 MET Chi-restraints excluded: chain X residue 178 GLN Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 305 GLU Chi-restraints excluded: chain X residue 326 SER Chi-restraints excluded: chain X residue 331 THR Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 172 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 159 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN G 67 GLN G 71 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.222216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170649 restraints weight = 18555.045| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.32 r_work: 0.3601 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18749 Z= 0.133 Angle : 0.549 11.668 25374 Z= 0.268 Chirality : 0.043 0.163 2934 Planarity : 0.004 0.055 3246 Dihedral : 9.085 172.498 2758 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.97 % Allowed : 20.31 % Favored : 75.72 % 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: -0.96 (0.17), residues: 2336 helix: 0.69 (0.17), residues: 910 sheet: -1.84 (0.27), residues: 370 loop : -1.31 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.011 0.001 TYR D 178 PHE 0.015 0.001 PHE G 75 TRP 0.002 0.000 TRP C 305 HIS 0.004 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00314 (18748) covalent geometry : angle 0.54879 (25374) hydrogen bonds : bond 0.02785 ( 782) hydrogen bonds : angle 4.90023 ( 2244) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 243 time to evaluate : 0.690 Fit side-chains REVERT: A 167 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7528 (mmm160) REVERT: C 237 ARG cc_start: 0.7086 (mmp-170) cc_final: 0.6753 (mmp-170) REVERT: C 285 GLN cc_start: 0.7436 (mt0) cc_final: 0.6671 (mp10) REVERT: X 154 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7983 (mp) REVERT: X 155 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7075 (mmt) REVERT: X 296 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8098 (mt) REVERT: D 167 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7500 (mmm160) REVERT: F 132 THR cc_start: 0.5874 (OUTLIER) cc_final: 0.5515 (p) REVERT: F 237 ARG cc_start: 0.7171 (mmm-85) cc_final: 0.6825 (mmm-85) REVERT: G 67 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: G 155 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7088 (mmt) REVERT: G 296 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8115 (mt) outliers start: 77 outliers final: 65 residues processed: 299 average time/residue: 0.1450 time to fit residues: 66.2582 Evaluate side-chains 308 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 142 THR Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 155 MET Chi-restraints excluded: chain X residue 178 GLN Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 305 GLU Chi-restraints excluded: chain X residue 326 SER Chi-restraints excluded: chain X residue 331 THR Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 83 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 112 optimal weight: 0.4980 chunk 216 optimal weight: 0.0370 chunk 88 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 242 GLN X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN G 67 GLN G 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.224215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173789 restraints weight = 18617.850| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.30 r_work: 0.3615 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18749 Z= 0.110 Angle : 0.534 12.255 25374 Z= 0.260 Chirality : 0.042 0.163 2934 Planarity : 0.004 0.058 3246 Dihedral : 8.846 171.245 2758 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.51 % Allowed : 20.31 % Favored : 76.19 % 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: -0.83 (0.18), residues: 2336 helix: 0.74 (0.17), residues: 932 sheet: -1.69 (0.28), residues: 356 loop : -1.26 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.012 0.001 TYR D 178 PHE 0.019 0.001 PHE G 75 TRP 0.002 0.000 TRP C 305 HIS 0.003 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00253 (18748) covalent geometry : angle 0.53369 (25374) hydrogen bonds : bond 0.02657 ( 782) hydrogen bonds : angle 4.78843 ( 2244) Misc. bond : bond 0.00062 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 237 time to evaluate : 0.627 Fit side-chains REVERT: A 167 ARG cc_start: 0.8036 (mtm110) cc_final: 0.7557 (mmm160) REVERT: B 216 TYR cc_start: 0.8782 (m-80) cc_final: 0.8090 (m-80) REVERT: C 237 ARG cc_start: 0.7071 (mmp-170) cc_final: 0.6742 (mmp-170) REVERT: C 285 GLN cc_start: 0.7386 (mt0) cc_final: 0.6621 (mp10) REVERT: X 154 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7940 (mp) REVERT: X 155 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7092 (mmt) REVERT: X 296 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8090 (mt) REVERT: D 167 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7482 (mmm160) REVERT: F 132 THR cc_start: 0.5815 (OUTLIER) cc_final: 0.5556 (p) REVERT: G 67 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: G 296 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8090 (mt) outliers start: 68 outliers final: 61 residues processed: 289 average time/residue: 0.1444 time to fit residues: 63.8637 Evaluate side-chains 295 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 228 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 142 THR Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 155 MET Chi-restraints excluded: chain X residue 178 GLN Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 296 LEU Chi-restraints excluded: chain X residue 305 GLU Chi-restraints excluded: chain X residue 326 SER Chi-restraints excluded: chain X residue 331 THR Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 221 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN X 71 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN E 267 ASN G 67 GLN G 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.222216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.170581 restraints weight = 18694.856| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.34 r_work: 0.3593 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18749 Z= 0.140 Angle : 0.555 12.166 25374 Z= 0.271 Chirality : 0.043 0.163 2934 Planarity : 0.004 0.059 3246 Dihedral : 8.941 171.080 2758 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.71 % Allowed : 19.95 % Favored : 76.34 % 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: -0.84 (0.18), residues: 2336 helix: 0.64 (0.17), residues: 944 sheet: -1.72 (0.28), residues: 360 loop : -1.18 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 212 TYR 0.012 0.001 TYR D 178 PHE 0.016 0.001 PHE G 75 TRP 0.003 0.000 TRP C 305 HIS 0.004 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00332 (18748) covalent geometry : angle 0.55516 (25374) hydrogen bonds : bond 0.02785 ( 782) hydrogen bonds : angle 4.85284 ( 2244) Misc. bond : bond 0.00075 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4431.08 seconds wall clock time: 76 minutes 58.47 seconds (4618.47 seconds total)