Starting phenix.real_space_refine on Mon Sep 14 20:42:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k7y_9945/09_2026/6k7y_9945.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7y_9945/09_2026/6k7y_9945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k7y_9945/09_2026/6k7y_9945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7y_9945/09_2026/6k7y_9945.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6k7y_9945/09_2026/6k7y_9945.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k7y_9945/09_2026/6k7y_9945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k7y_9945/09_2026/6k7y_9945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7y_9945/09_2026/6k7y_9945.map" } resolution = 3.6 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= 0.103 sd= 1.837 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 32 5.49 5 S 132 5.16 5 C 21450 2.51 5 N 5390 2.21 5 O 5950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 325 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32956 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "C" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2274 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "D" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "E" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "F" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "H" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "I" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2406 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2602 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "N" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "O" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "P" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2274 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "Q" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "R" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "T" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "U" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "V" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2406 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "W" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2602 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {' CA': 1, 'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 220 Unusual residues: {'CDL': 1, 'PLX': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {' CA': 1, 'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 220 Unusual residues: {'CDL': 1, 'PLX': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.51, per 1000 atoms: 0.23 Number of scatterers: 32956 At special positions: 0 Unit cell: (212.745, 99.281, 184.379, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 132 16.00 P 32 15.00 O 5950 8.00 N 5390 7.00 C 21450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7396 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 20 sheets defined 65.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.729A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 170 through 190 removed outlier: 4.106A pdb=" N ALA A 174 " --> pdb=" O HIS A 170 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 213 removed outlier: 3.501A pdb=" N HIS A 195 " --> pdb=" O CYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 256 removed outlier: 3.859A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 286 Proline residue: A 265 - end of helix removed outlier: 3.783A pdb=" N TYR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 311 Processing helix chain 'A' and resid 313 through 328 removed outlier: 3.685A pdb=" N TYR A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.521A pdb=" N PHE B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 175 through 256 removed outlier: 4.888A pdb=" N GLU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Proline residue: B 216 - end of helix removed outlier: 4.047A pdb=" N LYS B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 286 Proline residue: B 265 - end of helix removed outlier: 3.601A pdb=" N THR B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 307 Processing helix chain 'B' and resid 313 through 340 removed outlier: 3.897A pdb=" N ASP B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Proline residue: B 337 - end of helix Processing helix chain 'C' and resid 107 through 118 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 171 through 191 removed outlier: 4.250A pdb=" N ASP C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C 179 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 256 removed outlier: 3.567A pdb=" N ASP C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 4.200A pdb=" N LYS C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 Proline residue: C 265 - end of helix removed outlier: 3.528A pdb=" N TYR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 310 removed outlier: 3.902A pdb=" N LYS C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 334 removed outlier: 3.727A pdb=" N ALA C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'D' and resid 107 through 120 removed outlier: 4.557A pdb=" N ASP D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 171 through 190 Processing helix chain 'D' and resid 191 through 211 Processing helix chain 'D' and resid 214 through 254 removed outlier: 3.704A pdb=" N LYS D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 234 " --> pdb=" O LYS D 230 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 286 Proline residue: D 265 - end of helix removed outlier: 3.628A pdb=" N PHE D 282 " --> pdb=" O MET D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 310 removed outlier: 3.642A pdb=" N LYS D 308 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 335 removed outlier: 3.647A pdb=" N ALA D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 95 removed outlier: 3.899A pdb=" N ILE E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE E 75 " --> pdb=" O PHE E 71 " (cutoff:3.500A) Proline residue: E 76 - end of helix removed outlier: 3.546A pdb=" N HIS E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 95 removed outlier: 4.109A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE F 75 " --> pdb=" O PHE F 71 " (cutoff:3.500A) Proline residue: F 76 - end of helix Processing helix chain 'G' and resid 65 through 95 removed outlier: 4.042A pdb=" N ILE G 73 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G 75 " --> pdb=" O PHE G 71 " (cutoff:3.500A) Proline residue: G 76 - end of helix Processing helix chain 'H' and resid 65 through 95 removed outlier: 3.832A pdb=" N PHE H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Proline residue: H 76 - end of helix removed outlier: 3.664A pdb=" N HIS H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 121 Processing helix chain 'I' and resid 123 through 131 removed outlier: 4.065A pdb=" N PHE I 128 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 157 Processing helix chain 'I' and resid 193 through 201 removed outlier: 3.641A pdb=" N THR I 197 " --> pdb=" O SER I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 218 Processing helix chain 'I' and resid 219 through 231 Processing helix chain 'I' and resid 239 through 249 Processing helix chain 'I' and resid 278 through 283 Processing helix chain 'I' and resid 292 through 315 Processing helix chain 'I' and resid 323 through 335 Processing helix chain 'I' and resid 341 through 353 removed outlier: 4.250A pdb=" N LYS I 350 " --> pdb=" O GLN I 346 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS I 351 " --> pdb=" O ARG I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 373 removed outlier: 3.505A pdb=" N VAL I 364 " --> pdb=" O THR I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 381 removed outlier: 3.950A pdb=" N THR I 379 " --> pdb=" O ASN I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 403 Processing helix chain 'I' and resid 409 through 421 Processing helix chain 'I' and resid 433 through 441 Processing helix chain 'I' and resid 456 through 473 Processing helix chain 'J' and resid 84 through 94 Processing helix chain 'J' and resid 105 through 115 Processing helix chain 'J' and resid 128 through 137 Processing helix chain 'J' and resid 138 through 142 Processing helix chain 'J' and resid 148 through 153 Processing helix chain 'J' and resid 159 through 171 removed outlier: 3.963A pdb=" N THR J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 184 Processing helix chain 'J' and resid 193 through 210 removed outlier: 4.151A pdb=" N PHE J 197 " --> pdb=" O GLU J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 239 Processing helix chain 'J' and resid 248 through 272 Processing helix chain 'J' and resid 280 through 291 removed outlier: 4.351A pdb=" N PHE J 290 " --> pdb=" O TRP J 286 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR J 291 " --> pdb=" O LEU J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 306 Processing helix chain 'J' and resid 314 through 327 removed outlier: 3.869A pdb=" N PHE J 318 " --> pdb=" O SER J 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 340 removed outlier: 4.573A pdb=" N MET J 337 " --> pdb=" O ILE J 333 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE J 338 " --> pdb=" O ALA J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 359 Processing helix chain 'J' and resid 363 through 375 removed outlier: 3.527A pdb=" N LEU J 367 " --> pdb=" O SER J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 391 removed outlier: 4.543A pdb=" N PHE J 387 " --> pdb=" O SER J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 417 removed outlier: 4.372A pdb=" N GLN J 408 " --> pdb=" O HIS J 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 120 removed outlier: 3.729A pdb=" N ASP N 119 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 145 Processing helix chain 'N' and resid 170 through 190 removed outlier: 4.106A pdb=" N ALA N 174 " --> pdb=" O HIS N 170 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU N 190 " --> pdb=" O LEU N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 213 removed outlier: 3.501A pdb=" N HIS N 195 " --> pdb=" O CYS N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 256 removed outlier: 3.859A pdb=" N VAL N 220 " --> pdb=" O PRO N 216 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU N 223 " --> pdb=" O LYS N 219 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU N 234 " --> pdb=" O LYS N 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL N 235 " --> pdb=" O ARG N 231 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU N 240 " --> pdb=" O LEU N 236 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR N 254 " --> pdb=" O LEU N 250 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP N 255 " --> pdb=" O ALA N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 286 Proline residue: N 265 - end of helix removed outlier: 3.784A pdb=" N TYR N 279 " --> pdb=" O ALA N 275 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE N 282 " --> pdb=" O MET N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 311 Processing helix chain 'N' and resid 313 through 328 removed outlier: 3.685A pdb=" N TYR N 317 " --> pdb=" O ASP N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 328 through 333 Processing helix chain 'O' and resid 107 through 120 removed outlier: 3.521A pdb=" N PHE O 111 " --> pdb=" O SER O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 145 Processing helix chain 'O' and resid 175 through 256 removed outlier: 4.888A pdb=" N GLU O 193 " --> pdb=" O THR O 189 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN O 194 " --> pdb=" O LEU O 190 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN O 198 " --> pdb=" O GLN O 194 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU O 205 " --> pdb=" O ARG O 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU O 208 " --> pdb=" O ILE O 204 " (cutoff:3.500A) Proline residue: O 216 - end of helix removed outlier: 4.047A pdb=" N LYS O 219 " --> pdb=" O ALA O 215 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL O 220 " --> pdb=" O PRO O 216 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS O 227 " --> pdb=" O GLU O 223 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 286 Proline residue: O 265 - end of helix removed outlier: 3.601A pdb=" N THR O 271 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR O 279 " --> pdb=" O ALA O 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE O 282 " --> pdb=" O MET O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 307 Processing helix chain 'O' and resid 313 through 340 removed outlier: 3.897A pdb=" N ASP O 336 " --> pdb=" O LYS O 332 " (cutoff:3.500A) Proline residue: O 337 - end of helix Processing helix chain 'P' and resid 107 through 118 Processing helix chain 'P' and resid 140 through 145 Processing helix chain 'P' and resid 171 through 191 removed outlier: 4.250A pdb=" N ASP P 178 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL P 179 " --> pdb=" O THR P 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN P 184 " --> pdb=" O LYS P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 256 removed outlier: 3.567A pdb=" N ASP P 209 " --> pdb=" O GLU P 205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU P 212 " --> pdb=" O GLU P 208 " (cutoff:3.500A) Proline residue: P 216 - end of helix removed outlier: 4.200A pdb=" N LYS P 219 " --> pdb=" O ALA P 215 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL P 220 " --> pdb=" O PRO P 216 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS P 227 " --> pdb=" O GLU P 223 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR P 232 " --> pdb=" O ALA P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 286 Proline residue: P 265 - end of helix removed outlier: 3.529A pdb=" N TYR P 279 " --> pdb=" O ALA P 275 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE P 282 " --> pdb=" O MET P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 310 removed outlier: 3.903A pdb=" N LYS P 308 " --> pdb=" O HIS P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 334 removed outlier: 3.727A pdb=" N ALA P 323 " --> pdb=" O GLN P 319 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE P 324 " --> pdb=" O LEU P 320 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA P 325 " --> pdb=" O LYS P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 340 Processing helix chain 'Q' and resid 107 through 120 removed outlier: 4.558A pdb=" N ASP Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 145 Processing helix chain 'Q' and resid 171 through 190 Processing helix chain 'Q' and resid 191 through 211 Processing helix chain 'Q' and resid 214 through 254 removed outlier: 3.703A pdb=" N LYS Q 219 " --> pdb=" O ALA Q 215 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL Q 220 " --> pdb=" O PRO Q 216 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU Q 223 " --> pdb=" O LYS Q 219 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG Q 231 " --> pdb=" O LYS Q 227 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU Q 234 " --> pdb=" O LYS Q 230 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU Q 253 " --> pdb=" O ILE Q 249 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR Q 254 " --> pdb=" O LEU Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 259 through 286 Proline residue: Q 265 - end of helix removed outlier: 3.628A pdb=" N PHE Q 282 " --> pdb=" O MET Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 290 through 310 removed outlier: 3.642A pdb=" N LYS Q 308 " --> pdb=" O HIS Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 313 through 335 removed outlier: 3.647A pdb=" N ALA Q 325 " --> pdb=" O LYS Q 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 95 removed outlier: 3.898A pdb=" N ILE R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) Proline residue: R 76 - end of helix removed outlier: 3.546A pdb=" N HIS R 95 " --> pdb=" O LEU R 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 95 removed outlier: 4.109A pdb=" N ILE S 73 " --> pdb=" O ARG S 69 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE S 75 " --> pdb=" O PHE S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix Processing helix chain 'T' and resid 65 through 95 removed outlier: 4.041A pdb=" N ILE T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE T 75 " --> pdb=" O PHE T 71 " (cutoff:3.500A) Proline residue: T 76 - end of helix Processing helix chain 'U' and resid 65 through 95 removed outlier: 3.832A pdb=" N PHE U 71 " --> pdb=" O LEU U 67 " (cutoff:3.500A) Proline residue: U 76 - end of helix removed outlier: 3.665A pdb=" N HIS U 95 " --> pdb=" O LEU U 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 121 Processing helix chain 'V' and resid 123 through 131 removed outlier: 4.064A pdb=" N PHE V 128 " --> pdb=" O PRO V 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 157 Processing helix chain 'V' and resid 193 through 201 removed outlier: 3.641A pdb=" N THR V 197 " --> pdb=" O SER V 193 " (cutoff:3.500A) Processing helix chain 'V' and resid 205 through 218 Processing helix chain 'V' and resid 219 through 231 Processing helix chain 'V' and resid 239 through 249 Processing helix chain 'V' and resid 278 through 283 Processing helix chain 'V' and resid 292 through 315 Processing helix chain 'V' and resid 323 through 335 Processing helix chain 'V' and resid 341 through 353 removed outlier: 4.250A pdb=" N LYS V 350 " --> pdb=" O GLN V 346 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS V 351 " --> pdb=" O ARG V 347 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 373 removed outlier: 3.506A pdb=" N VAL V 364 " --> pdb=" O THR V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 374 through 381 removed outlier: 3.951A pdb=" N THR V 379 " --> pdb=" O ASN V 375 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 403 Processing helix chain 'V' and resid 409 through 421 Processing helix chain 'V' and resid 433 through 441 Processing helix chain 'V' and resid 456 through 473 Processing helix chain 'W' and resid 84 through 94 Processing helix chain 'W' and resid 105 through 115 Processing helix chain 'W' and resid 128 through 137 Processing helix chain 'W' and resid 138 through 142 Processing helix chain 'W' and resid 148 through 153 Processing helix chain 'W' and resid 159 through 171 removed outlier: 3.964A pdb=" N THR W 171 " --> pdb=" O LEU W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 184 Processing helix chain 'W' and resid 193 through 210 removed outlier: 4.151A pdb=" N PHE W 197 " --> pdb=" O GLU W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 232 through 239 Processing helix chain 'W' and resid 248 through 272 Processing helix chain 'W' and resid 280 through 291 removed outlier: 4.351A pdb=" N PHE W 290 " --> pdb=" O TRP W 286 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR W 291 " --> pdb=" O LEU W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 296 through 306 Processing helix chain 'W' and resid 314 through 327 removed outlier: 3.868A pdb=" N PHE W 318 " --> pdb=" O SER W 314 " (cutoff:3.500A) Processing helix chain 'W' and resid 327 through 340 removed outlier: 4.573A pdb=" N MET W 337 " --> pdb=" O ILE W 333 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE W 338 " --> pdb=" O ALA W 334 " (cutoff:3.500A) Processing helix chain 'W' and resid 346 through 359 Processing helix chain 'W' and resid 363 through 375 removed outlier: 3.527A pdb=" N LEU W 367 " --> pdb=" O SER W 363 " (cutoff:3.500A) Processing helix chain 'W' and resid 383 through 391 removed outlier: 4.543A pdb=" N PHE W 387 " --> pdb=" O SER W 383 " (cutoff:3.500A) Processing helix chain 'W' and resid 404 through 417 removed outlier: 4.372A pdb=" N GLN W 408 " --> pdb=" O HIS W 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.704A pdb=" N GLU A 95 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG A 96 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.798A pdb=" N ARG A 134 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR C 100 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 95 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 80 removed outlier: 3.577A pdb=" N THR B 76 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 128 Processing sheet with id=AA6, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA7, first strand: chain 'C' and resid 126 through 128 Processing sheet with id=AA8, first strand: chain 'D' and resid 126 through 128 Processing sheet with id=AA9, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AB1, first strand: chain 'J' and resid 278 through 279 Processing sheet with id=AB2, first strand: chain 'N' and resid 76 through 80 removed outlier: 3.705A pdb=" N GLU N 95 " --> pdb=" O LEU N 90 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG N 96 " --> pdb=" O ARG Q 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 126 through 128 Processing sheet with id=AB4, first strand: chain 'N' and resid 134 through 135 removed outlier: 6.798A pdb=" N ARG N 134 " --> pdb=" O GLN P 98 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR P 100 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU P 95 " --> pdb=" O LEU P 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 76 through 80 removed outlier: 3.577A pdb=" N THR O 76 " --> pdb=" O SER O 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 125 through 128 Processing sheet with id=AB7, first strand: chain 'O' and resid 134 through 135 Processing sheet with id=AB8, first strand: chain 'P' and resid 126 through 128 Processing sheet with id=AB9, first strand: chain 'Q' and resid 126 through 128 Processing sheet with id=AC1, first strand: chain 'W' and resid 96 through 97 Processing sheet with id=AC2, first strand: chain 'W' and resid 278 through 279 1898 hydrogen bonds defined for protein. 5574 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: 6.83 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5361 1.32 - 1.44: 8482 1.44 - 1.57: 19423 1.57 - 1.69: 64 1.69 - 1.81: 236 Bond restraints: 33566 Sorted by residual: bond pdb=" C ASP B 296 " pdb=" N ARG B 297 " ideal model delta sigma weight residual 1.335 1.402 -0.067 1.31e-02 5.83e+03 2.59e+01 bond pdb=" C1B PLX O 402 " pdb=" N1 PLX O 402 " ideal model delta sigma weight residual 1.501 1.431 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1B PLX B 402 " pdb=" N1 PLX B 402 " ideal model delta sigma weight residual 1.501 1.431 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1B PLX Q 402 " pdb=" N1 PLX Q 402 " ideal model delta sigma weight residual 1.501 1.432 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1B PLX D 401 " pdb=" N1 PLX D 401 " ideal model delta sigma weight residual 1.501 1.432 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 33561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 44526 4.23 - 8.46: 455 8.46 - 12.70: 21 12.70 - 16.93: 4 16.93 - 21.16: 16 Bond angle restraints: 45022 Sorted by residual: angle pdb=" CA2 CDL P 401 " pdb=" OA2 CDL P 401 " pdb=" PA1 CDL P 401 " ideal model delta sigma weight residual 121.27 114.00 7.27 1.00e+00 1.00e+00 5.28e+01 angle pdb=" CA2 CDL C 401 " pdb=" OA2 CDL C 401 " pdb=" PA1 CDL C 401 " ideal model delta sigma weight residual 121.27 114.06 7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" O2 PLX C 404 " pdb=" P1 PLX C 404 " pdb=" O3 PLX C 404 " ideal model delta sigma weight residual 121.72 100.56 21.16 3.00e+00 1.11e-01 4.97e+01 angle pdb=" O2 PLX P 404 " pdb=" P1 PLX P 404 " pdb=" O3 PLX P 404 " ideal model delta sigma weight residual 121.72 100.61 21.11 3.00e+00 1.11e-01 4.95e+01 angle pdb=" O2 PLX A 404 " pdb=" P1 PLX A 404 " pdb=" O3 PLX A 404 " ideal model delta sigma weight residual 121.72 100.91 20.81 3.00e+00 1.11e-01 4.81e+01 ... (remaining 45017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 19885 34.30 - 68.60: 815 68.60 - 102.90: 52 102.90 - 137.20: 2 137.20 - 171.50: 10 Dihedral angle restraints: 20764 sinusoidal: 9378 harmonic: 11386 Sorted by residual: dihedral pdb=" CA THR V 123 " pdb=" C THR V 123 " pdb=" N PRO V 124 " pdb=" CA PRO V 124 " ideal model delta harmonic sigma weight residual 180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA THR I 123 " pdb=" C THR I 123 " pdb=" N PRO I 124 " pdb=" CA PRO I 124 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" C2 PLX B 402 " pdb=" O1 PLX B 402 " pdb=" P1 PLX B 402 " pdb=" O2 PLX B 402 " ideal model delta sinusoidal sigma weight residual 178.46 -10.04 -171.50 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 20761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4834 0.114 - 0.228: 68 0.228 - 0.343: 22 0.343 - 0.457: 0 0.457 - 0.571: 2 Chirality restraints: 4926 Sorted by residual: chirality pdb=" CB4 CDL N 402 " pdb=" CB3 CDL N 402 " pdb=" CB6 CDL N 402 " pdb=" OB6 CDL N 402 " both_signs ideal model delta sigma weight residual False -2.57 -2.00 -0.57 2.00e-01 2.50e+01 8.15e+00 chirality pdb=" CB4 CDL A 402 " pdb=" CB3 CDL A 402 " pdb=" CB6 CDL A 402 " pdb=" OB6 CDL A 402 " both_signs ideal model delta sigma weight residual False -2.57 -2.01 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" C6 PLX P 403 " pdb=" C7 PLX P 403 " pdb=" O6 PLX P 403 " pdb=" O7 PLX P 403 " both_signs ideal model delta sigma weight residual False 2.01 2.35 -0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 4923 not shown) Planarity restraints: 5546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 292 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C PRO B 292 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO B 292 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU B 293 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO O 292 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C PRO O 292 " -0.057 2.00e-02 2.50e+03 pdb=" O PRO O 292 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU O 293 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 297 " 0.197 9.50e-02 1.11e+02 9.10e-02 1.05e+01 pdb=" NE ARG A 297 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 297 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG A 297 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 297 " 0.021 2.00e-02 2.50e+03 ... (remaining 5543 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2727 2.73 - 3.27: 32394 3.27 - 3.82: 51361 3.82 - 4.36: 59636 4.36 - 4.90: 104323 Nonbonded interactions: 250441 Sorted by model distance: nonbonded pdb=" OG SER A 92 " pdb=" OD1 ASP A 119 " model vdw 2.190 3.040 nonbonded pdb=" OG SER N 92 " pdb=" OD1 ASP N 119 " model vdw 2.190 3.040 nonbonded pdb=" NH1 ARG J 343 " pdb=" O PRO J 344 " model vdw 2.217 3.120 nonbonded pdb=" NH1 ARG W 343 " pdb=" O PRO W 344 " model vdw 2.217 3.120 nonbonded pdb=" NH1 ARG Q 297 " pdb=" OA4 CDL Q 401 " model vdw 2.220 3.120 ... (remaining 250436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 73 through 345) selection = (chain 'B' and resid 73 through 345) selection = (chain 'C' and resid 73 through 345) selection = (chain 'D' and resid 73 through 345) selection = (chain 'N' and resid 73 through 345) selection = (chain 'O' and resid 73 through 345) selection = (chain 'P' and resid 73 through 345) selection = (chain 'Q' and resid 73 through 345) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 48 through 101) selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.460 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 0.902 33567 Z= 0.575 Angle : 0.974 21.160 45022 Z= 0.432 Chirality : 0.048 0.571 4926 Planarity : 0.004 0.106 5546 Dihedral : 17.380 171.500 13368 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 0.06 % Allowed : 1.44 % Favored : 98.50 % 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: -1.75 (0.13), residues: 3812 helix: -0.43 (0.10), residues: 2404 sheet: -1.16 (0.30), residues: 232 loop : -2.55 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.000 ARG A 297 TYR 0.013 0.001 TYR I 196 PHE 0.018 0.002 PHE V 296 TRP 0.014 0.001 TRP O 255 HIS 0.004 0.001 HIS J 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.30 (33566) covalent geometry : angle 0.97380 / 0.43 (45022) hydrogen bonds : bond 0.12863 / 8.67 ( 1898) hydrogen bonds : angle 5.14451 / 3.69 ( 5574) Misc. bond : bond 0.90249 / 47.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 439 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7890 (ttm170) REVERT: A 297 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8727 (ttt-90) REVERT: B 329 MET cc_start: 0.7947 (tpt) cc_final: 0.7646 (tpp) REVERT: E 98 PHE cc_start: 0.8706 (t80) cc_final: 0.8441 (t80) REVERT: I 332 LEU cc_start: 0.9585 (tp) cc_final: 0.9337 (tt) REVERT: J 288 LEU cc_start: 0.9357 (mt) cc_final: 0.9129 (mt) REVERT: N 201 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7885 (ttm170) REVERT: O 329 MET cc_start: 0.7950 (tpt) cc_final: 0.7652 (tpp) REVERT: R 98 PHE cc_start: 0.8703 (t80) cc_final: 0.8436 (t80) REVERT: V 112 MET cc_start: 0.8408 (mtm) cc_final: 0.8206 (mtp) REVERT: V 224 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7356 (tm-30) REVERT: V 332 LEU cc_start: 0.9586 (tp) cc_final: 0.9349 (tt) REVERT: V 373 ASN cc_start: 0.8792 (t0) cc_final: 0.8363 (t0) REVERT: W 288 LEU cc_start: 0.9367 (mt) cc_final: 0.9132 (mt) outliers start: 2 outliers final: 0 residues processed: 441 average time/residue: 0.2405 time to fit residues: 163.8556 Evaluate side-chains 327 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 185 GLN A 196 GLN A 298 GLN B 195 HIS B 196 GLN B 213 GLN B 318 ASN C 80 GLN C 172 ASN C 184 GLN C 185 GLN C 196 GLN C 213 GLN D 80 GLN D 114 GLN D 196 GLN D 213 GLN H 95 HIS I 159 ASN I 245 GLN I 348 GLN I 352 HIS I 375 ASN I 385 HIS I 397 GLN I 398 GLN I 411 HIS J 98 HIS J 117 GLN J 235 GLN J 260 GLN J 404 HIS N 80 GLN N 185 GLN N 196 GLN N 298 GLN N 319 GLN O 195 HIS O 213 GLN O 318 ASN P 80 GLN P 172 ASN P 184 GLN P 185 GLN P 196 GLN P 213 GLN Q 80 GLN Q 114 GLN Q 196 GLN Q 213 GLN U 95 HIS V 159 ASN V 245 GLN ** V 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 348 GLN V 352 HIS V 385 HIS V 397 GLN V 398 GLN V 411 HIS W 98 HIS W 117 GLN W 235 GLN W 260 GLN W 404 HIS Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.090716 restraints weight = 57028.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093149 restraints weight = 34584.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094751 restraints weight = 24811.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095670 restraints weight = 19851.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096476 restraints weight = 17289.589| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33567 Z= 0.114 Angle : 0.536 8.280 45022 Z= 0.271 Chirality : 0.040 0.179 4926 Planarity : 0.004 0.042 5546 Dihedral : 15.570 135.778 5574 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.12 % Allowed : 9.41 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3812 helix: 0.78 (0.11), residues: 2430 sheet: -0.50 (0.31), residues: 230 loop : -2.02 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 52 TYR 0.016 0.001 TYR I 196 PHE 0.014 0.001 PHE J 252 TRP 0.006 0.001 TRP A 256 HIS 0.005 0.001 HIS V 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (33566) covalent geometry : angle 0.53600 / 0.27 (45022) hydrogen bonds : bond 0.04153 / 2.76 ( 1898) hydrogen bonds : angle 4.12188 / 2.91 ( 5574) Misc. bond : bond 0.01043 / 0.55 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 362 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.7955 (tpt) cc_final: 0.7666 (tpp) REVERT: D 177 ASN cc_start: 0.8119 (t0) cc_final: 0.7712 (m-40) REVERT: D 242 TYR cc_start: 0.8997 (t80) cc_final: 0.8612 (t80) REVERT: D 284 MET cc_start: 0.8758 (mtp) cc_final: 0.8528 (mtp) REVERT: E 98 PHE cc_start: 0.8680 (t80) cc_final: 0.8445 (t80) REVERT: I 332 LEU cc_start: 0.9504 (tp) cc_final: 0.9224 (tt) REVERT: J 262 GLU cc_start: 0.8677 (tp30) cc_final: 0.8404 (tp30) REVERT: J 264 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: O 329 MET cc_start: 0.7955 (tpt) cc_final: 0.7664 (tpp) REVERT: Q 177 ASN cc_start: 0.8117 (t0) cc_final: 0.7715 (m-40) REVERT: Q 242 TYR cc_start: 0.9013 (t80) cc_final: 0.8609 (t80) REVERT: Q 284 MET cc_start: 0.8773 (mtp) cc_final: 0.8558 (mtp) REVERT: R 98 PHE cc_start: 0.8684 (t80) cc_final: 0.8449 (t80) REVERT: V 332 LEU cc_start: 0.9509 (tp) cc_final: 0.9231 (tt) REVERT: W 262 GLU cc_start: 0.8676 (tp30) cc_final: 0.8398 (tp30) REVERT: W 264 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7680 (mt0) outliers start: 38 outliers final: 20 residues processed: 380 average time/residue: 0.2152 time to fit residues: 133.0661 Evaluate side-chains 341 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 319 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain P residue 319 GLN Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain W residue 264 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 342 optimal weight: 2.9990 chunk 370 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 311 optimal weight: 7.9990 chunk 295 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN D 246 GLN I 159 ASN ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 GLN ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 318 ASN Q 246 GLN V 159 ASN ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 GLN ** W 302 ASN ** 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 = 0.3355 r_free = 0.3355 target = 0.109067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.086217 restraints weight = 57805.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.088234 restraints weight = 36245.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.089518 restraints weight = 26417.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.090471 restraints weight = 21605.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.090676 restraints weight = 19713.069| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 33567 Z= 0.253 Angle : 0.618 7.573 45022 Z= 0.316 Chirality : 0.044 0.181 4926 Planarity : 0.004 0.044 5546 Dihedral : 14.692 122.476 5570 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.68 % Allowed : 12.61 % Favored : 85.71 % 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: 0.11 (0.14), residues: 3812 helix: 0.99 (0.11), residues: 2438 sheet: -0.34 (0.31), residues: 236 loop : -1.83 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 297 TYR 0.016 0.002 TYR I 130 PHE 0.020 0.002 PHE J 252 TRP 0.009 0.001 TRP B 255 HIS 0.006 0.001 HIS W 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.25 (33566) covalent geometry : angle 0.61841 / 0.32 (45022) hydrogen bonds : bond 0.05159 / 3.43 ( 1898) hydrogen bonds : angle 4.16370 / 2.94 ( 5574) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 321 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.8006 (tpt) cc_final: 0.7715 (tpp) REVERT: D 177 ASN cc_start: 0.8102 (t0) cc_final: 0.7866 (t0) REVERT: D 284 MET cc_start: 0.8910 (mtp) cc_final: 0.8623 (mtp) REVERT: I 332 LEU cc_start: 0.9536 (tp) cc_final: 0.9309 (tt) REVERT: J 264 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: O 329 MET cc_start: 0.8010 (tpt) cc_final: 0.7718 (tpp) REVERT: Q 177 ASN cc_start: 0.8105 (t0) cc_final: 0.7876 (t0) REVERT: Q 284 MET cc_start: 0.8916 (mtp) cc_final: 0.8637 (mtp) REVERT: W 264 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7750 (mt0) outliers start: 57 outliers final: 37 residues processed: 356 average time/residue: 0.2029 time to fit residues: 119.5581 Evaluate side-chains 341 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 391 LEU Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 319 GLN Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 318 VAL Chi-restraints excluded: chain V residue 391 LEU Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 169 ILE Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain W residue 264 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 363 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 276 optimal weight: 0.0670 chunk 119 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 375 ASN W 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.087903 restraints weight = 57170.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089951 restraints weight = 35587.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091451 restraints weight = 25875.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.092411 restraints weight = 20914.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092534 restraints weight = 18869.896| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33567 Z= 0.144 Angle : 0.528 7.430 45022 Z= 0.270 Chirality : 0.041 0.171 4926 Planarity : 0.003 0.055 5546 Dihedral : 13.841 116.638 5570 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.91 % Allowed : 14.70 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3812 helix: 1.31 (0.11), residues: 2438 sheet: -0.00 (0.33), residues: 230 loop : -1.68 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 94 TYR 0.015 0.001 TYR I 209 PHE 0.023 0.001 PHE W 252 TRP 0.005 0.001 TRP N 256 HIS 0.003 0.001 HIS W 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (33566) covalent geometry : angle 0.52810 / 0.27 (45022) hydrogen bonds : bond 0.04289 / 2.85 ( 1898) hydrogen bonds : angle 3.97158 / 2.79 ( 5574) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 324 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.8001 (tpt) cc_final: 0.7721 (tpp) REVERT: D 177 ASN cc_start: 0.8020 (t0) cc_final: 0.7653 (m-40) REVERT: D 284 MET cc_start: 0.8869 (mtp) cc_final: 0.8625 (mtp) REVERT: E 98 PHE cc_start: 0.8825 (t80) cc_final: 0.8544 (t80) REVERT: G 93 GLU cc_start: 0.8073 (tp30) cc_final: 0.7864 (tp30) REVERT: I 332 LEU cc_start: 0.9489 (tp) cc_final: 0.9203 (tt) REVERT: J 264 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: O 329 MET cc_start: 0.8010 (tpt) cc_final: 0.7724 (tpp) REVERT: Q 177 ASN cc_start: 0.8023 (t0) cc_final: 0.7654 (m-40) REVERT: Q 284 MET cc_start: 0.8862 (mtp) cc_final: 0.8621 (mtp) REVERT: R 98 PHE cc_start: 0.8827 (t80) cc_final: 0.8547 (t80) REVERT: T 93 GLU cc_start: 0.8022 (tp30) cc_final: 0.7808 (tp30) REVERT: V 332 LEU cc_start: 0.9494 (tp) cc_final: 0.9234 (tt) REVERT: W 264 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7735 (mt0) outliers start: 65 outliers final: 42 residues processed: 363 average time/residue: 0.1927 time to fit residues: 117.8362 Evaluate side-chains 347 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 303 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 391 LEU Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 319 GLN Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 HIS Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 318 VAL Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 326 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 327 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 355 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.084696 restraints weight = 58148.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.087074 restraints weight = 36119.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.088401 restraints weight = 26242.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.089395 restraints weight = 20844.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.089510 restraints weight = 18732.999| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 33567 Z= 0.298 Angle : 0.652 8.586 45022 Z= 0.331 Chirality : 0.046 0.188 4926 Planarity : 0.004 0.060 5546 Dihedral : 14.075 126.277 5570 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.35 % Allowed : 15.84 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: 0.39 (0.14), residues: 3812 helix: 1.17 (0.11), residues: 2444 sheet: 0.02 (0.33), residues: 230 loop : -1.67 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 394 TYR 0.015 0.002 TYR V 209 PHE 0.022 0.002 PHE J 252 TRP 0.007 0.001 TRP B 256 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.30 (33566) covalent geometry : angle 0.65190 / 0.33 (45022) hydrogen bonds : bond 0.05280 / 3.50 ( 1898) hydrogen bonds : angle 4.18509 / 2.95 ( 5574) Misc. bond : bond 0.00115 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 306 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.8045 (tpt) cc_final: 0.7622 (tpp) REVERT: D 284 MET cc_start: 0.8909 (mtp) cc_final: 0.8619 (mtp) REVERT: E 98 PHE cc_start: 0.8802 (t80) cc_final: 0.8522 (t80) REVERT: H 79 TYR cc_start: 0.9021 (t80) cc_final: 0.8709 (t80) REVERT: I 300 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7805 (tp-100) REVERT: J 264 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: O 329 MET cc_start: 0.8047 (tpt) cc_final: 0.7623 (tpp) REVERT: Q 284 MET cc_start: 0.8916 (mtp) cc_final: 0.8629 (mtp) REVERT: R 98 PHE cc_start: 0.8803 (t80) cc_final: 0.8523 (t80) REVERT: U 79 TYR cc_start: 0.9026 (t80) cc_final: 0.8697 (t80) REVERT: V 300 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7817 (tp-100) REVERT: W 264 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.7802 (mt0) outliers start: 80 outliers final: 56 residues processed: 368 average time/residue: 0.1924 time to fit residues: 118.8842 Evaluate side-chains 355 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 295 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain I residue 283 PHE Chi-restraints excluded: chain I residue 300 GLN Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 391 LEU Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain J residue 384 HIS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 319 GLN Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain U residue 92 LEU Chi-restraints excluded: chain V residue 283 PHE Chi-restraints excluded: chain V residue 300 GLN Chi-restraints excluded: chain V residue 318 VAL Chi-restraints excluded: chain V residue 391 LEU Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 298 ILE Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 384 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 7 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 337 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 252 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 184 GLN ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 305 HIS Q 184 GLN ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 305 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.089612 restraints weight = 56708.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092070 restraints weight = 34483.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093530 restraints weight = 24740.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094477 restraints weight = 19346.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094578 restraints weight = 17695.162| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33567 Z= 0.110 Angle : 0.514 9.102 45022 Z= 0.262 Chirality : 0.040 0.198 4926 Planarity : 0.003 0.047 5546 Dihedral : 12.970 112.726 5570 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.32 % Allowed : 16.40 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.14), residues: 3812 helix: 1.62 (0.11), residues: 2430 sheet: 0.41 (0.34), residues: 230 loop : -1.56 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 394 TYR 0.021 0.001 TYR V 196 PHE 0.021 0.001 PHE W 252 TRP 0.006 0.001 TRP A 256 HIS 0.004 0.001 HIS W 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (33566) covalent geometry : angle 0.51433 / 0.26 (45022) hydrogen bonds : bond 0.03917 / 2.60 ( 1898) hydrogen bonds : angle 3.86296 / 2.71 ( 5574) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 337 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.7915 (tpt) cc_final: 0.7664 (tpp) REVERT: D 284 MET cc_start: 0.8840 (mtp) cc_final: 0.8618 (mtp) REVERT: E 85 SER cc_start: 0.9334 (t) cc_final: 0.9129 (t) REVERT: J 118 MET cc_start: 0.7384 (tpp) cc_final: 0.7019 (mmm) REVERT: J 264 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: O 329 MET cc_start: 0.7921 (tpt) cc_final: 0.7664 (tpp) REVERT: P 243 MET cc_start: 0.9384 (mtp) cc_final: 0.9172 (ttp) REVERT: Q 284 MET cc_start: 0.8851 (mtp) cc_final: 0.8634 (mtp) REVERT: R 85 SER cc_start: 0.9335 (t) cc_final: 0.9133 (t) REVERT: W 118 MET cc_start: 0.7400 (tpp) cc_final: 0.7034 (mmm) REVERT: W 264 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7845 (mt0) outliers start: 79 outliers final: 54 residues processed: 391 average time/residue: 0.2014 time to fit residues: 130.8793 Evaluate side-chains 358 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 283 PHE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain J residue 384 HIS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 170 HIS Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 HIS Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 318 VAL Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 384 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 327 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 294 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 184 GLN ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 GLN ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.087502 restraints weight = 57407.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.089920 restraints weight = 35307.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.091401 restraints weight = 25408.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092394 restraints weight = 19757.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092496 restraints weight = 17995.489| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 33567 Z= 0.177 Angle : 0.563 12.618 45022 Z= 0.283 Chirality : 0.042 0.241 4926 Planarity : 0.004 0.053 5546 Dihedral : 13.010 117.840 5570 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.82 % Allowed : 16.43 % Favored : 80.75 % 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: 0.95 (0.14), residues: 3812 helix: 1.64 (0.11), residues: 2432 sheet: 0.41 (0.34), residues: 230 loop : -1.55 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 94 TYR 0.017 0.001 TYR I 209 PHE 0.016 0.001 PHE J 252 TRP 0.005 0.001 TRP Q 260 HIS 0.005 0.001 HIS W 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (33566) covalent geometry : angle 0.56324 / 0.28 (45022) hydrogen bonds : bond 0.04369 / 2.90 ( 1898) hydrogen bonds : angle 3.90355 / 2.75 ( 5574) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 308 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8543 (mt) REVERT: B 329 MET cc_start: 0.7995 (tpt) cc_final: 0.7731 (tpp) REVERT: D 284 MET cc_start: 0.8889 (mtp) cc_final: 0.8619 (mtp) REVERT: I 300 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7669 (tp-100) REVERT: J 264 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: O 141 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8540 (mt) REVERT: O 329 MET cc_start: 0.7999 (tpt) cc_final: 0.7729 (tpp) REVERT: Q 284 MET cc_start: 0.8886 (mtp) cc_final: 0.8617 (mtp) REVERT: V 300 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7698 (tp-100) REVERT: W 264 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7738 (mt0) outliers start: 96 outliers final: 68 residues processed: 372 average time/residue: 0.2020 time to fit residues: 125.7086 Evaluate side-chains 379 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 305 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 283 PHE Chi-restraints excluded: chain I residue 300 GLN Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain J residue 384 HIS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 233 THR Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 243 MET Chi-restraints excluded: chain O residue 259 SER Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 319 GLN Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 170 HIS Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 HIS Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 300 GLN Chi-restraints excluded: chain V residue 318 VAL Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 384 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 256 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 321 optimal weight: 7.9990 chunk 135 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088465 restraints weight = 56972.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.090464 restraints weight = 35633.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092004 restraints weight = 26034.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092749 restraints weight = 20922.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092952 restraints weight = 19145.367| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33567 Z= 0.149 Angle : 0.540 11.490 45022 Z= 0.273 Chirality : 0.041 0.244 4926 Planarity : 0.004 0.066 5546 Dihedral : 12.780 115.325 5570 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.82 % Allowed : 17.08 % Favored : 80.10 % 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: 1.09 (0.14), residues: 3812 helix: 1.75 (0.11), residues: 2428 sheet: 0.50 (0.34), residues: 230 loop : -1.49 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 394 TYR 0.025 0.001 TYR V 196 PHE 0.016 0.001 PHE W 252 TRP 0.004 0.001 TRP N 256 HIS 0.005 0.001 HIS W 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (33566) covalent geometry : angle 0.54041 / 0.27 (45022) hydrogen bonds : bond 0.04163 / 2.76 ( 1898) hydrogen bonds : angle 3.85940 / 2.72 ( 5574) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 313 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8509 (mt) REVERT: B 329 MET cc_start: 0.7906 (tpt) cc_final: 0.7663 (tpp) REVERT: D 284 MET cc_start: 0.8866 (mtp) cc_final: 0.8621 (mtp) REVERT: J 264 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: O 141 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8504 (mt) REVERT: O 329 MET cc_start: 0.7949 (tpt) cc_final: 0.7692 (tpp) REVERT: Q 284 MET cc_start: 0.8863 (mtp) cc_final: 0.8612 (mtp) REVERT: W 264 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7749 (mt0) outliers start: 96 outliers final: 72 residues processed: 374 average time/residue: 0.2029 time to fit residues: 126.5430 Evaluate side-chains 382 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 306 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 233 THR Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 243 MET Chi-restraints excluded: chain O residue 259 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 319 GLN Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 170 HIS Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 HIS Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 283 PHE Chi-restraints excluded: chain V residue 318 VAL Chi-restraints excluded: chain V residue 391 LEU Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 298 ILE Chi-restraints excluded: chain W residue 326 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 91 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 316 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089005 restraints weight = 56721.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.091451 restraints weight = 34835.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092945 restraints weight = 24949.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093957 restraints weight = 19503.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094022 restraints weight = 17718.358| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33567 Z= 0.133 Angle : 0.534 10.739 45022 Z= 0.268 Chirality : 0.041 0.244 4926 Planarity : 0.004 0.072 5546 Dihedral : 12.549 114.217 5570 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.82 % Allowed : 17.70 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.14), residues: 3812 helix: 1.85 (0.11), residues: 2426 sheet: 0.53 (0.35), residues: 230 loop : -1.46 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 394 TYR 0.021 0.001 TYR V 196 PHE 0.018 0.001 PHE I 296 TRP 0.005 0.001 TRP A 256 HIS 0.005 0.001 HIS W 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (33566) covalent geometry : angle 0.53377 / 0.27 (45022) hydrogen bonds : bond 0.04019 / 2.66 ( 1898) hydrogen bonds : angle 3.80787 / 2.68 ( 5574) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 325 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8530 (mt) REVERT: B 234 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8627 (mm) REVERT: B 329 MET cc_start: 0.7896 (tpt) cc_final: 0.7656 (tpp) REVERT: D 284 MET cc_start: 0.8858 (mtp) cc_final: 0.8630 (mtp) REVERT: J 264 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: O 141 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8526 (mt) REVERT: O 234 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8627 (mm) REVERT: O 329 MET cc_start: 0.7883 (tpt) cc_final: 0.7632 (tpp) REVERT: Q 284 MET cc_start: 0.8860 (mtp) cc_final: 0.8625 (mtp) REVERT: V 373 ASN cc_start: 0.8619 (t0) cc_final: 0.8392 (t0) REVERT: W 264 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7767 (mt0) outliers start: 96 outliers final: 70 residues processed: 389 average time/residue: 0.2008 time to fit residues: 130.3109 Evaluate side-chains 386 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 310 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain J residue 384 HIS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 233 THR Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 243 MET Chi-restraints excluded: chain O residue 259 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 319 GLN Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 170 HIS Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 HIS Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 318 VAL Chi-restraints excluded: chain V residue 391 LEU Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 298 ILE Chi-restraints excluded: chain W residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 229 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 303 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.086767 restraints weight = 57607.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.089128 restraints weight = 35576.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090720 restraints weight = 25755.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.091795 restraints weight = 20758.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.092450 restraints weight = 17939.739| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33567 Z= 0.206 Angle : 0.602 12.416 45022 Z= 0.302 Chirality : 0.043 0.234 4926 Planarity : 0.004 0.046 5546 Dihedral : 12.800 118.505 5570 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.47 % Allowed : 17.99 % Favored : 79.54 % 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: 1.06 (0.14), residues: 3812 helix: 1.72 (0.11), residues: 2428 sheet: 0.38 (0.34), residues: 230 loop : -1.48 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 52 TYR 0.020 0.001 TYR V 196 PHE 0.020 0.002 PHE I 296 TRP 0.005 0.001 TRP B 256 HIS 0.005 0.001 HIS W 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (33566) covalent geometry : angle 0.60214 / 0.30 (45022) hydrogen bonds : bond 0.04553 / 3.02 ( 1898) hydrogen bonds : angle 3.93508 / 2.77 ( 5574) Misc. bond : bond 0.00067 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 318 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8584 (mt) REVERT: B 329 MET cc_start: 0.7953 (tpt) cc_final: 0.7688 (tpp) REVERT: D 284 MET cc_start: 0.8900 (mtp) cc_final: 0.8632 (mtp) REVERT: J 264 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: O 141 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8581 (mt) REVERT: O 329 MET cc_start: 0.7993 (tpt) cc_final: 0.7717 (tpp) REVERT: Q 284 MET cc_start: 0.8878 (mtp) cc_final: 0.8603 (mtp) REVERT: U 79 TYR cc_start: 0.8958 (t80) cc_final: 0.8656 (t80) REVERT: W 264 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.7779 (mt0) outliers start: 84 outliers final: 74 residues processed: 373 average time/residue: 0.2002 time to fit residues: 124.0844 Evaluate side-chains 387 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 309 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 248 HIS Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain J residue 384 HIS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 233 THR Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 243 MET Chi-restraints excluded: chain O residue 259 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 319 GLN Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 170 HIS Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 95 HIS Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 318 VAL Chi-restraints excluded: chain V residue 391 LEU Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 248 HIS Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 298 ILE Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 384 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 6 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 118 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 184 GLN ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 GLN ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090176 restraints weight = 56733.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092628 restraints weight = 34417.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094266 restraints weight = 24647.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095385 restraints weight = 19713.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096087 restraints weight = 16917.704| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33567 Z= 0.108 Angle : 0.534 11.044 45022 Z= 0.266 Chirality : 0.040 0.247 4926 Planarity : 0.003 0.047 5546 Dihedral : 12.166 110.920 5570 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.26 % Allowed : 18.31 % Favored : 79.42 % 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: 1.39 (0.14), residues: 3812 helix: 1.99 (0.11), residues: 2416 sheet: 0.57 (0.35), residues: 230 loop : -1.36 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 94 TYR 0.021 0.001 TYR V 196 PHE 0.017 0.001 PHE W 252 TRP 0.006 0.001 TRP A 256 HIS 0.006 0.001 HIS W 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (33566) covalent geometry : angle 0.53405 / 0.27 (45022) hydrogen bonds : bond 0.03693 / 2.46 ( 1898) hydrogen bonds : angle 3.75445 / 2.65 ( 5574) Misc. bond : bond 0.00017 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4846.16 seconds wall clock time: 85 minutes 5.61 seconds (5105.61 seconds total)