Starting phenix.real_space_refine on Tue Aug 26 04:01:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7y_9945/08_2025/6k7y_9945.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7y_9945/08_2025/6k7y_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_9945/08_2025/6k7y_9945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7y_9945/08_2025/6k7y_9945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k7y_9945/08_2025/6k7y_9945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7y_9945/08_2025/6k7y_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-2.0-5787/lib/python3.9/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: 7.89, per 1000 atoms: 0.24 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: 3.10 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.97 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: 6.74 Time building geometry restraints manager: 4.04 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: 19963 34.30 - 68.60: 889 68.60 - 102.90: 58 102.90 - 137.20: 4 137.20 - 171.50: 10 Dihedral angle restraints: 20924 sinusoidal: 9538 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 20921 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: 4.140 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.690 Find NCS groups from input model: 0.810 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 17.851 171.500 13528 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 aren 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 covalent geometry : bond 0.00625 (33566) covalent geometry : angle 0.97380 (45022) hydrogen bonds : bond 0.12863 ( 1898) hydrogen bonds : angle 5.14451 ( 5574) Misc. bond : bond 0.90249 ( 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 : 1.255 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: 0.8435 (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: 0.2328 time to fit residues: 157.7678 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 : 1.086 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 185 GLN A 196 GLN A 298 GLN B 195 HIS 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 D 246 GLN H 95 HIS I 159 ASN I 245 GLN I 348 GLN I 352 HIS 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 Q 246 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 = 0.3417 r_free = 0.3417 target = 0.113526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090529 restraints weight = 57028.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092985 restraints weight = 34694.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.094613 restraints weight = 24843.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095646 restraints weight = 19843.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096382 restraints weight = 17128.621| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1292 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 : 0.531 8.404 45022 Z= 0.270 Chirality : 0.040 0.169 4926 Planarity : 0.004 0.042 5546 Dihedral : 16.616 137.186 5734 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.12 % Allowed : 9.20 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.14), residues: 3812 helix: 0.78 (0.11), residues: 2430 sheet: -0.51 (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 W 343 TYR 0.016 0.001 TYR I 196 PHE 0.015 0.001 PHE J 252 TRP 0.005 0.001 TRP A 256 HIS 0.005 0.001 HIS V 352 Details of bonding type rmsd covalent geometry : bond 0.00244 (33566) covalent geometry : angle 0.53084 (45022) hydrogen bonds : bond 0.04196 ( 1898) hydrogen bonds : angle 4.12528 ( 5574) Misc. bond : bond 0.00559 ( 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 397 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 359 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.7955 (tpt) cc_final: 0.7665 (tpp) REVERT: D 177 ASN cc_start: 0.8113 (t0) cc_final: 0.7711 (m-40) REVERT: D 242 TYR cc_start: 0.9014 (t80) cc_final: 0.8562 (t80) REVERT: D 284 MET cc_start: 0.8747 (mtp) cc_final: 0.8511 (mtp) REVERT: E 98 PHE cc_start: 0.8679 (t80) cc_final: 0.8440 (t80) REVERT: I 332 LEU cc_start: 0.9501 (tp) cc_final: 0.9203 (tt) REVERT: J 262 GLU cc_start: 0.8683 (tp30) cc_final: 0.8415 (tp30) REVERT: J 264 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: O 329 MET cc_start: 0.7956 (tpt) cc_final: 0.7667 (tpp) REVERT: Q 177 ASN cc_start: 0.8114 (t0) cc_final: 0.7712 (m-40) REVERT: Q 242 TYR cc_start: 0.9030 (t80) cc_final: 0.8555 (t80) REVERT: Q 284 MET cc_start: 0.8773 (mtp) cc_final: 0.8558 (mtp) REVERT: R 98 PHE cc_start: 0.8682 (t80) cc_final: 0.8443 (t80) REVERT: V 332 LEU cc_start: 0.9501 (tp) cc_final: 0.9212 (tt) REVERT: W 262 GLU cc_start: 0.8682 (tp30) cc_final: 0.8423 (tp30) REVERT: W 264 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7687 (mt0) outliers start: 38 outliers final: 19 residues processed: 377 average time/residue: 0.2128 time to fit residues: 129.9847 Evaluate side-chains 338 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 317 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 30 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 295 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 95 HIS I 159 ASN ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 GLN I 375 ASN ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 159 ASN ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 GLN V 375 ASN ** W 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.087895 restraints weight = 57538.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090364 restraints weight = 35241.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.091705 restraints weight = 25366.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092691 restraints weight = 20078.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092792 restraints weight = 18121.200| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33567 Z= 0.183 Angle : 0.555 7.560 45022 Z= 0.283 Chirality : 0.042 0.169 4926 Planarity : 0.004 0.044 5546 Dihedral : 15.357 125.086 5730 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.56 % Allowed : 12.23 % Favored : 86.21 % 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 aren not related in a simple way. whole: 0.26 (0.14), residues: 3812 helix: 1.12 (0.11), residues: 2438 sheet: -0.26 (0.32), residues: 230 loop : -1.80 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 52 TYR 0.017 0.001 TYR I 130 PHE 0.020 0.002 PHE J 252 TRP 0.007 0.001 TRP B 255 HIS 0.004 0.001 HIS W 248 Details of bonding type rmsd covalent geometry : bond 0.00441 (33566) covalent geometry : angle 0.55473 (45022) hydrogen bonds : bond 0.04569 ( 1898) hydrogen bonds : angle 4.03066 ( 5574) Misc. bond : bond 0.00102 ( 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 385 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 332 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.8025 (tpt) cc_final: 0.7737 (tpp) REVERT: D 177 ASN cc_start: 0.8044 (t0) cc_final: 0.7700 (m-40) REVERT: D 284 MET cc_start: 0.8864 (mtp) cc_final: 0.8603 (mtp) REVERT: I 332 LEU cc_start: 0.9501 (tp) cc_final: 0.9257 (tt) REVERT: J 264 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: O 329 MET cc_start: 0.8033 (tpt) cc_final: 0.7742 (tpp) REVERT: Q 177 ASN cc_start: 0.8048 (t0) cc_final: 0.7706 (m-40) REVERT: Q 284 MET cc_start: 0.8875 (mtp) cc_final: 0.8624 (mtp) REVERT: V 332 LEU cc_start: 0.9512 (tp) cc_final: 0.9232 (tt) REVERT: W 264 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7725 (mt0) outliers start: 53 outliers final: 38 residues processed: 363 average time/residue: 0.1942 time to fit residues: 114.5764 Evaluate side-chains 350 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 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 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 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 264 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 363 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 119 optimal weight: 0.0570 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 248 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.089379 restraints weight = 56996.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.091435 restraints weight = 35606.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093076 restraints weight = 25822.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.093694 restraints weight = 20412.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093929 restraints weight = 19148.613| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33567 Z= 0.124 Angle : 0.507 7.286 45022 Z= 0.260 Chirality : 0.040 0.163 4926 Planarity : 0.003 0.057 5546 Dihedral : 14.538 123.072 5730 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.85 % Allowed : 13.87 % Favored : 84.27 % 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 aren not related in a simple way. whole: 0.65 (0.14), residues: 3812 helix: 1.40 (0.11), residues: 2442 sheet: 0.06 (0.32), residues: 230 loop : -1.63 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 94 TYR 0.017 0.001 TYR V 196 PHE 0.022 0.001 PHE J 252 TRP 0.005 0.001 TRP A 256 HIS 0.016 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00288 (33566) covalent geometry : angle 0.50670 (45022) hydrogen bonds : bond 0.04030 ( 1898) hydrogen bonds : angle 3.89950 ( 5574) Misc. bond : bond 0.00060 ( 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 390 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 327 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.7995 (tpt) cc_final: 0.7736 (tpp) REVERT: D 177 ASN cc_start: 0.8008 (t0) cc_final: 0.7647 (m-40) REVERT: D 284 MET cc_start: 0.8835 (mtp) cc_final: 0.8595 (mtp) REVERT: E 98 PHE cc_start: 0.8808 (t80) cc_final: 0.8467 (t80) REVERT: I 300 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7919 (tp-100) REVERT: I 332 LEU cc_start: 0.9483 (tp) cc_final: 0.9205 (tt) REVERT: J 264 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: O 329 MET cc_start: 0.8005 (tpt) cc_final: 0.7734 (tpp) REVERT: Q 177 ASN cc_start: 0.8005 (t0) cc_final: 0.7650 (m-40) REVERT: Q 284 MET cc_start: 0.8847 (mtp) cc_final: 0.8618 (mtp) REVERT: R 98 PHE cc_start: 0.8808 (t80) cc_final: 0.8469 (t80) REVERT: V 300 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7900 (tp-100) REVERT: V 332 LEU cc_start: 0.9500 (tp) cc_final: 0.9231 (tt) REVERT: W 264 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7774 (mt0) outliers start: 63 outliers final: 37 residues processed: 365 average time/residue: 0.1816 time to fit residues: 110.2345 Evaluate side-chains 345 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain C residue 125 VAL 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 G residue 85 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 73 ILE 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 264 GLN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain P residue 125 VAL 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 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 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 264 GLN 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: 0.0770 chunk 184 optimal weight: 0.7980 chunk 237 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 355 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 159 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.090270 restraints weight = 57295.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092717 restraints weight = 34808.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094174 restraints weight = 25295.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.095009 restraints weight = 19839.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095159 restraints weight = 17837.307| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33567 Z= 0.115 Angle : 0.498 8.614 45022 Z= 0.254 Chirality : 0.039 0.158 4926 Planarity : 0.003 0.047 5546 Dihedral : 13.699 119.358 5730 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.09 % Allowed : 14.37 % Favored : 83.54 % 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 aren not related in a simple way. whole: 0.96 (0.14), residues: 3812 helix: 1.64 (0.11), residues: 2436 sheet: 0.34 (0.33), residues: 230 loop : -1.53 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 394 TYR 0.017 0.001 TYR V 209 PHE 0.020 0.001 PHE W 252 TRP 0.005 0.001 TRP A 256 HIS 0.004 0.001 HIS W 384 Details of bonding type rmsd covalent geometry : bond 0.00265 (33566) covalent geometry : angle 0.49809 (45022) hydrogen bonds : bond 0.03796 ( 1898) hydrogen bonds : angle 3.79733 ( 5574) Misc. bond : bond 0.00057 ( 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 411 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 340 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.7956 (tpt) cc_final: 0.7721 (tpp) REVERT: D 284 MET cc_start: 0.8850 (mtp) cc_final: 0.8626 (mtp) REVERT: E 98 PHE cc_start: 0.8823 (t80) cc_final: 0.8548 (t80) REVERT: I 300 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7897 (tp-100) REVERT: J 264 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: O 329 MET cc_start: 0.7965 (tpt) cc_final: 0.7720 (tpp) REVERT: Q 284 MET cc_start: 0.8872 (mtp) cc_final: 0.8646 (mtp) REVERT: R 98 PHE cc_start: 0.8814 (t80) cc_final: 0.8543 (t80) REVERT: V 300 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7876 (tp-100) REVERT: W 264 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7760 (mt0) outliers start: 71 outliers final: 47 residues processed: 389 average time/residue: 0.1968 time to fit residues: 125.0895 Evaluate side-chains 361 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 267 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 D residue 75 VAL 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 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 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 264 GLN 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 267 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 Q residue 75 VAL 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 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 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 264 GLN Chi-restraints excluded: chain W residue 326 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 7 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 296 optimal weight: 0.9990 chunk 337 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 252 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088844 restraints weight = 57102.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090779 restraints weight = 35729.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.092194 restraints weight = 26123.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093185 restraints weight = 21554.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093352 restraints weight = 19646.760| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33567 Z= 0.146 Angle : 0.524 8.674 45022 Z= 0.265 Chirality : 0.041 0.188 4926 Planarity : 0.004 0.062 5546 Dihedral : 13.620 117.393 5730 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.94 % Allowed : 15.49 % Favored : 82.57 % 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 aren not related in a simple way. whole: 1.07 (0.14), residues: 3812 helix: 1.73 (0.11), residues: 2432 sheet: 0.42 (0.34), residues: 230 loop : -1.49 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 94 TYR 0.017 0.001 TYR V 209 PHE 0.017 0.001 PHE J 252 TRP 0.004 0.001 TRP N 256 HIS 0.004 0.001 HIS W 384 Details of bonding type rmsd covalent geometry : bond 0.00348 (33566) covalent geometry : angle 0.52380 (45022) hydrogen bonds : bond 0.04029 ( 1898) hydrogen bonds : angle 3.80629 ( 5574) Misc. bond : bond 0.00063 ( 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 386 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 320 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8616 (mm) REVERT: B 329 MET cc_start: 0.7995 (tpt) cc_final: 0.7740 (tpp) REVERT: D 284 MET cc_start: 0.8878 (mtp) cc_final: 0.8632 (mtp) REVERT: E 98 PHE cc_start: 0.8797 (t80) cc_final: 0.8480 (t80) REVERT: I 300 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7912 (tp-100) REVERT: J 264 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7817 (mt0) REVERT: O 234 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8616 (mm) REVERT: O 329 MET cc_start: 0.7959 (tpt) cc_final: 0.7704 (tpp) REVERT: Q 284 MET cc_start: 0.8885 (mtp) cc_final: 0.8640 (mtp) REVERT: R 98 PHE cc_start: 0.8799 (t80) cc_final: 0.8488 (t80) REVERT: V 300 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7896 (tp-100) REVERT: W 264 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7813 (mt0) outliers start: 66 outliers final: 52 residues processed: 361 average time/residue: 0.1889 time to fit residues: 112.8638 Evaluate side-chains 367 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 309 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 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 75 VAL 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 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 G residue 91 LEU 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 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 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 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 75 VAL 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 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 85 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 73 ILE 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 326 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 327 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 294 optimal weight: 0.5980 chunk 307 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 chunk 192 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** 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 = 0.3414 r_free = 0.3414 target = 0.113208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.090305 restraints weight = 57231.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092919 restraints weight = 34811.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094076 restraints weight = 24994.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.094845 restraints weight = 19931.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.095101 restraints weight = 18351.696| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2114 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= 0.109 Angle : 0.492 8.724 45022 Z= 0.249 Chirality : 0.039 0.183 4926 Planarity : 0.003 0.060 5546 Dihedral : 13.307 113.346 5730 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.18 % Allowed : 15.76 % Favored : 82.07 % 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 aren not related in a simple way. whole: 1.32 (0.14), residues: 3812 helix: 1.94 (0.11), residues: 2418 sheet: 0.57 (0.34), residues: 230 loop : -1.40 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG W 394 TYR 0.018 0.001 TYR V 209 PHE 0.015 0.001 PHE J 252 TRP 0.005 0.001 TRP A 256 HIS 0.005 0.001 HIS W 384 Details of bonding type rmsd covalent geometry : bond 0.00248 (33566) covalent geometry : angle 0.49238 (45022) hydrogen bonds : bond 0.03679 ( 1898) hydrogen bonds : angle 3.70723 ( 5574) Misc. bond : bond 0.00025 ( 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 409 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 335 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8634 (mm) REVERT: B 329 MET cc_start: 0.7911 (tpt) cc_final: 0.7671 (tpp) REVERT: D 284 MET cc_start: 0.8839 (mtp) cc_final: 0.8613 (mtp) REVERT: E 98 PHE cc_start: 0.8743 (t80) cc_final: 0.8441 (t80) REVERT: I 300 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7872 (tp-100) REVERT: J 264 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: O 234 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8639 (mm) REVERT: O 329 MET cc_start: 0.7918 (tpt) cc_final: 0.7672 (tpp) REVERT: Q 284 MET cc_start: 0.8858 (mtp) cc_final: 0.8627 (mtp) REVERT: R 98 PHE cc_start: 0.8766 (t80) cc_final: 0.8474 (t80) REVERT: V 300 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7865 (tp-100) REVERT: W 264 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7800 (mt0) outliers start: 74 outliers final: 48 residues processed: 384 average time/residue: 0.1803 time to fit residues: 114.9436 Evaluate side-chains 368 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 314 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 148 ASP 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 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 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 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 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 148 ASP 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 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 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 85 SER 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 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 256 optimal weight: 1.9990 chunk 262 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 321 optimal weight: 0.0270 chunk 135 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 305 HIS I 397 GLN ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.090542 restraints weight = 56998.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.092636 restraints weight = 35546.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093956 restraints weight = 25702.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.094919 restraints weight = 20930.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095127 restraints weight = 19249.480| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2182 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= 0.118 Angle : 0.501 7.201 45022 Z= 0.253 Chirality : 0.040 0.185 4926 Planarity : 0.003 0.067 5546 Dihedral : 13.178 112.020 5730 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.03 % Allowed : 16.28 % Favored : 81.69 % 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 aren not related in a simple way. whole: 1.42 (0.14), residues: 3812 helix: 2.02 (0.11), residues: 2418 sheet: 0.55 (0.34), residues: 230 loop : -1.34 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG W 394 TYR 0.019 0.001 TYR I 209 PHE 0.014 0.001 PHE W 252 TRP 0.005 0.001 TRP A 256 HIS 0.006 0.001 HIS J 384 Details of bonding type rmsd covalent geometry : bond 0.00273 (33566) covalent geometry : angle 0.50091 (45022) hydrogen bonds : bond 0.03764 ( 1898) hydrogen bonds : angle 3.70377 ( 5574) Misc. bond : bond 0.00049 ( 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 393 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 324 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8657 (mm) REVERT: B 329 MET cc_start: 0.7873 (tpt) cc_final: 0.7635 (tpp) REVERT: D 284 MET cc_start: 0.8858 (mtp) cc_final: 0.8617 (mtp) REVERT: E 98 PHE cc_start: 0.8729 (t80) cc_final: 0.8430 (t80) REVERT: J 264 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7820 (mt0) REVERT: O 234 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8660 (mm) REVERT: O 329 MET cc_start: 0.7874 (tpt) cc_final: 0.7634 (tpp) REVERT: Q 284 MET cc_start: 0.8869 (mtp) cc_final: 0.8630 (mtp) REVERT: R 98 PHE cc_start: 0.8751 (t80) cc_final: 0.8482 (t80) REVERT: W 264 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7822 (mt0) outliers start: 69 outliers final: 48 residues processed: 370 average time/residue: 0.1793 time to fit residues: 109.8797 Evaluate side-chains 363 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 148 ASP Chi-restraints excluded: chain B residue 234 LEU 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 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 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 I residue 283 PHE 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 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 148 ASP Chi-restraints excluded: chain O residue 234 LEU 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 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 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 V residue 283 PHE 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 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: 0.6980 chunk 236 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** 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 = 0.3375 r_free = 0.3375 target = 0.110515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.087496 restraints weight = 57287.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089832 restraints weight = 35292.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.091394 restraints weight = 25600.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.092251 restraints weight = 19919.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092370 restraints weight = 18266.123| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33567 Z= 0.211 Angle : 0.576 11.015 45022 Z= 0.292 Chirality : 0.043 0.215 4926 Planarity : 0.004 0.073 5546 Dihedral : 13.573 116.412 5730 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.97 % Allowed : 16.52 % Favored : 81.51 % 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 aren not related in a simple way. whole: 1.24 (0.14), residues: 3812 helix: 1.84 (0.11), residues: 2422 sheet: 0.49 (0.34), residues: 230 loop : -1.34 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 394 TYR 0.019 0.001 TYR I 114 PHE 0.020 0.002 PHE I 296 TRP 0.006 0.001 TRP B 255 HIS 0.007 0.001 HIS J 384 Details of bonding type rmsd covalent geometry : bond 0.00515 (33566) covalent geometry : angle 0.57641 (45022) hydrogen bonds : bond 0.04503 ( 1898) hydrogen bonds : angle 3.86752 ( 5574) Misc. bond : bond 0.00108 ( 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 384 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 317 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.8008 (tpt) cc_final: 0.7728 (tpp) REVERT: D 284 MET cc_start: 0.8893 (mtp) cc_final: 0.8617 (mtp) REVERT: E 98 PHE cc_start: 0.8755 (t80) cc_final: 0.8484 (t80) REVERT: J 264 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7749 (mt0) REVERT: O 329 MET cc_start: 0.8009 (tpt) cc_final: 0.7726 (tpp) REVERT: Q 284 MET cc_start: 0.8895 (mtp) cc_final: 0.8612 (mtp) REVERT: R 98 PHE cc_start: 0.8771 (t80) cc_final: 0.8534 (t80) REVERT: W 264 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7779 (mt0) outliers start: 67 outliers final: 57 residues processed: 363 average time/residue: 0.1709 time to fit residues: 102.8129 Evaluate side-chains 374 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 234 LEU 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 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 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 I residue 283 PHE 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 104 MET Chi-restraints excluded: chain J residue 170 LEU 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 234 LEU 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 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 229 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 353 optimal weight: 2.9990 chunk 303 optimal weight: 0.0040 chunk 173 optimal weight: 0.8980 chunk 326 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 chunk 254 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** 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 = 0.111252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.088295 restraints weight = 57650.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.090355 restraints weight = 36256.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.091712 restraints weight = 26334.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093360 restraints weight = 21642.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093369 restraints weight = 18593.459| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33567 Z= 0.171 Angle : 0.556 10.466 45022 Z= 0.280 Chirality : 0.042 0.238 4926 Planarity : 0.003 0.071 5546 Dihedral : 13.485 114.611 5730 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.94 % Allowed : 16.61 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.14), residues: 3812 helix: 1.88 (0.11), residues: 2416 sheet: 0.53 (0.35), residues: 230 loop : -1.35 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 394 TYR 0.018 0.001 TYR I 209 PHE 0.017 0.001 PHE V 296 TRP 0.005 0.001 TRP C 255 HIS 0.007 0.001 HIS J 384 Details of bonding type rmsd covalent geometry : bond 0.00415 (33566) covalent geometry : angle 0.55633 (45022) hydrogen bonds : bond 0.04264 ( 1898) hydrogen bonds : angle 3.83725 ( 5574) Misc. bond : bond 0.00066 ( 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 384 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 318 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.8006 (tpt) cc_final: 0.7736 (tpp) REVERT: D 284 MET cc_start: 0.8877 (mtp) cc_final: 0.8620 (mtp) REVERT: E 98 PHE cc_start: 0.8755 (t80) cc_final: 0.8480 (t80) REVERT: J 264 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: O 329 MET cc_start: 0.8004 (tpt) cc_final: 0.7733 (tpp) REVERT: Q 284 MET cc_start: 0.8875 (mtp) cc_final: 0.8625 (mtp) REVERT: R 98 PHE cc_start: 0.8739 (t80) cc_final: 0.8493 (t80) REVERT: W 264 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7763 (mt0) outliers start: 66 outliers final: 58 residues processed: 362 average time/residue: 0.1659 time to fit residues: 100.1796 Evaluate side-chains 371 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 311 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 234 LEU 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 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 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 I residue 283 PHE 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 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 234 LEU 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 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 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 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 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 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: 0.9980 chunk 37 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 296 optimal weight: 0.2980 chunk 118 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090912 restraints weight = 57165.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092998 restraints weight = 35642.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094636 restraints weight = 25728.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095282 restraints weight = 20343.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095502 restraints weight = 19068.643| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33567 Z= 0.106 Angle : 0.520 11.445 45022 Z= 0.261 Chirality : 0.039 0.252 4926 Planarity : 0.003 0.046 5546 Dihedral : 13.015 110.205 5730 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.65 % Allowed : 16.87 % Favored : 81.48 % 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 aren not related in a simple way. whole: 1.53 (0.14), residues: 3812 helix: 2.08 (0.11), residues: 2418 sheet: 0.67 (0.35), residues: 230 loop : -1.27 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 52 TYR 0.020 0.001 TYR I 114 PHE 0.014 0.001 PHE J 252 TRP 0.009 0.001 TRP W 286 HIS 0.007 0.001 HIS J 384 Details of bonding type rmsd covalent geometry : bond 0.00236 (33566) covalent geometry : angle 0.51978 (45022) hydrogen bonds : bond 0.03711 ( 1898) hydrogen bonds : angle 3.72921 ( 5574) Misc. bond : bond 0.00028 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4350.76 seconds wall clock time: 76 minutes 30.29 seconds (4590.29 seconds total)