Starting phenix.real_space_refine on Sat Jun 28 15:09:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7y_9945/06_2025/6k7y_9945.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7y_9945/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7y_9945/06_2025/6k7y_9945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7y_9945/06_2025/6k7y_9945.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7y_9945/06_2025/6k7y_9945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7y_9945/06_2025/6k7y_9945.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 2, 'GLU:plan': 3, 'TRP:plan': 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: {'GLN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 2, 'GLU:plan': 3, 'TRP:plan': 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: 22.02, per 1000 atoms: 0.67 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: 8.14 Conformation dependent library (CDL) restraints added in 4.3 seconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7396 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 20 sheets defined 65.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 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: 10.99 Time building geometry restraints manager: 9.59 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 72.050 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.170 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP O 255 HIS 0.004 0.001 HIS J 248 PHE 0.018 0.002 PHE V 296 TYR 0.013 0.001 TYR I 196 ARG 0.041 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.12863 ( 1898) hydrogen bonds : angle 5.14451 ( 5574) covalent geometry : bond 0.00625 (33566) covalent geometry : angle 0.97380 (45022) 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 : 3.831 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: 0.5224 time to fit residues: 355.0901 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 : 3.722 ------------------------------------------------------------------------------- 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 319 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 158 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 296 optimal weight: 0.0370 chunk 114 optimal weight: 0.0000 chunk 180 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 343 optimal weight: 7.9990 overall best weight: 0.5802 ------------------------------------------------------------------------------- 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 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3414 r_free = 0.3414 target = 0.113307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090365 restraints weight = 56825.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092788 restraints weight = 34575.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094401 restraints weight = 24812.737| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33567 Z= 0.118 Angle : 0.536 8.618 45022 Z= 0.272 Chirality : 0.040 0.172 4926 Planarity : 0.004 0.042 5546 Dihedral : 16.610 136.959 5734 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.12 % Allowed : 9.26 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3812 helix: 0.77 (0.11), residues: 2430 sheet: -0.52 (0.31), residues: 230 loop : -2.03 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 256 HIS 0.005 0.001 HIS I 352 PHE 0.016 0.001 PHE J 252 TYR 0.016 0.001 TYR I 196 ARG 0.006 0.000 ARG S 52 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 1898) hydrogen bonds : angle 4.13720 ( 5574) covalent geometry : bond 0.00256 (33566) covalent geometry : angle 0.53576 (45022) Misc. bond : bond 0.00358 ( 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 : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.7964 (tpt) cc_final: 0.7673 (tpp) REVERT: D 177 ASN cc_start: 0.8134 (t0) cc_final: 0.7733 (m-40) REVERT: D 242 TYR cc_start: 0.9020 (t80) cc_final: 0.8561 (t80) REVERT: D 284 MET cc_start: 0.8748 (mtp) cc_final: 0.8512 (mtp) REVERT: E 98 PHE cc_start: 0.8700 (t80) cc_final: 0.8443 (t80) REVERT: I 332 LEU cc_start: 0.9499 (tp) cc_final: 0.9209 (tt) REVERT: J 262 GLU cc_start: 0.8689 (tp30) cc_final: 0.8348 (tp30) REVERT: J 264 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: O 329 MET cc_start: 0.7967 (tpt) cc_final: 0.7669 (tpp) REVERT: Q 177 ASN cc_start: 0.8136 (t0) cc_final: 0.7737 (m-40) REVERT: Q 242 TYR cc_start: 0.9036 (t80) cc_final: 0.8553 (t80) REVERT: Q 284 MET cc_start: 0.8770 (mtp) cc_final: 0.8554 (mtp) REVERT: R 98 PHE cc_start: 0.8705 (t80) cc_final: 0.8448 (t80) REVERT: V 332 LEU cc_start: 0.9502 (tp) cc_final: 0.9211 (tt) REVERT: W 262 GLU cc_start: 0.8694 (tp30) cc_final: 0.8341 (tp30) REVERT: W 264 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7688 (mt0) outliers start: 38 outliers final: 19 residues processed: 378 average time/residue: 0.4506 time to fit residues: 277.9421 Evaluate side-chains 336 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 315 time to evaluate : 3.780 ------------------------------------------------------------------------------- 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 207 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 305 optimal weight: 0.7980 chunk 349 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.088053 restraints weight = 57704.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.090474 restraints weight = 35337.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.091921 restraints weight = 25421.993| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33567 Z= 0.178 Angle : 0.552 7.521 45022 Z= 0.282 Chirality : 0.042 0.169 4926 Planarity : 0.004 0.044 5546 Dihedral : 15.393 124.902 5730 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.53 % Allowed : 11.85 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3812 helix: 1.14 (0.11), residues: 2438 sheet: -0.34 (0.31), residues: 236 loop : -1.80 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.004 0.001 HIS W 248 PHE 0.022 0.002 PHE J 252 TYR 0.019 0.001 TYR I 130 ARG 0.006 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 1898) hydrogen bonds : angle 4.02562 ( 5574) covalent geometry : bond 0.00430 (33566) covalent geometry : angle 0.55190 (45022) Misc. bond : bond 0.00188 ( 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 383 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.8736 (mtp) cc_final: 0.8499 (mtp) REVERT: B 329 MET cc_start: 0.8035 (tpt) cc_final: 0.7746 (tpp) REVERT: D 177 ASN cc_start: 0.8056 (t0) cc_final: 0.7716 (m-40) REVERT: D 284 MET cc_start: 0.8851 (mtp) cc_final: 0.8590 (mtp) REVERT: I 332 LEU cc_start: 0.9495 (tp) cc_final: 0.9254 (tt) REVERT: J 264 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7709 (mt0) REVERT: O 329 MET cc_start: 0.8038 (tpt) cc_final: 0.7746 (tpp) REVERT: Q 177 ASN cc_start: 0.8057 (t0) cc_final: 0.7721 (m-40) REVERT: Q 284 MET cc_start: 0.8863 (mtp) cc_final: 0.8610 (mtp) REVERT: V 332 LEU cc_start: 0.9506 (tp) cc_final: 0.9228 (tt) REVERT: W 264 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7710 (mt0) outliers start: 52 outliers final: 36 residues processed: 363 average time/residue: 0.4293 time to fit residues: 254.8363 Evaluate side-chains 346 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 3.526 ------------------------------------------------------------------------------- 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 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 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 180 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 233 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 281 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 357 optimal weight: 0.1980 chunk 283 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** J 248 HIS ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 248 HIS ** W 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.088549 restraints weight = 57308.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090960 restraints weight = 35185.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.092280 restraints weight = 25537.276| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33567 Z= 0.156 Angle : 0.529 7.785 45022 Z= 0.271 Chirality : 0.041 0.167 4926 Planarity : 0.004 0.045 5546 Dihedral : 14.592 122.875 5730 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.97 % Allowed : 14.32 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3812 helix: 1.37 (0.11), residues: 2440 sheet: 0.06 (0.32), residues: 230 loop : -1.65 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 256 HIS 0.003 0.001 HIS W 384 PHE 0.021 0.001 PHE W 252 TYR 0.019 0.001 TYR I 196 ARG 0.009 0.000 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 1898) hydrogen bonds : angle 3.94336 ( 5574) covalent geometry : bond 0.00374 (33566) covalent geometry : angle 0.52937 (45022) Misc. bond : bond 0.00092 ( 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 386 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 319 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.8024 (tpt) cc_final: 0.7742 (tpp) REVERT: D 177 ASN cc_start: 0.8027 (t0) cc_final: 0.7671 (m-40) REVERT: D 284 MET cc_start: 0.8859 (mtp) cc_final: 0.8606 (mtp) REVERT: E 98 PHE cc_start: 0.8813 (t80) cc_final: 0.8488 (t80) REVERT: I 332 LEU cc_start: 0.9507 (tp) cc_final: 0.9210 (tt) REVERT: J 264 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: O 329 MET cc_start: 0.8026 (tpt) cc_final: 0.7742 (tpp) REVERT: Q 177 ASN cc_start: 0.8022 (t0) cc_final: 0.7672 (m-40) REVERT: Q 284 MET cc_start: 0.8855 (mtp) cc_final: 0.8606 (mtp) REVERT: R 98 PHE cc_start: 0.8819 (t80) cc_final: 0.8494 (t80) REVERT: V 332 LEU cc_start: 0.9511 (tp) cc_final: 0.9240 (tt) REVERT: W 264 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7732 (mt0) outliers start: 67 outliers final: 43 residues processed: 362 average time/residue: 0.4122 time to fit residues: 248.9574 Evaluate side-chains 343 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 298 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 391 LEU Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 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 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 264 GLN Chi-restraints excluded: chain W residue 326 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 333 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 272 optimal weight: 0.7980 chunk 342 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 376 optimal weight: 0.9980 chunk 171 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 159 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.089844 restraints weight = 56735.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.092283 restraints weight = 34922.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093909 restraints weight = 25121.579| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1907 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= 0.111 Angle : 0.494 8.451 45022 Z= 0.252 Chirality : 0.039 0.158 4926 Planarity : 0.003 0.045 5546 Dihedral : 13.752 118.535 5730 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.94 % Allowed : 14.84 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3812 helix: 1.64 (0.11), residues: 2434 sheet: 0.35 (0.33), residues: 230 loop : -1.54 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 256 HIS 0.003 0.001 HIS W 384 PHE 0.021 0.001 PHE J 252 TYR 0.017 0.001 TYR V 209 ARG 0.007 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 1898) hydrogen bonds : angle 3.80465 ( 5574) covalent geometry : bond 0.00250 (33566) covalent geometry : angle 0.49355 (45022) Misc. bond : bond 0.00043 ( 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 403 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 337 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.7958 (tpt) cc_final: 0.7714 (tpp) REVERT: D 177 ASN cc_start: 0.7909 (t0) cc_final: 0.7597 (m-40) REVERT: D 284 MET cc_start: 0.8847 (mtp) cc_final: 0.8616 (mtp) REVERT: E 98 PHE cc_start: 0.8812 (t80) cc_final: 0.8562 (t80) REVERT: J 264 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7869 (mt0) REVERT: O 208 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7691 (mm-30) REVERT: O 329 MET cc_start: 0.7960 (tpt) cc_final: 0.7711 (tpp) REVERT: Q 177 ASN cc_start: 0.7901 (t0) cc_final: 0.7593 (m-40) REVERT: Q 284 MET cc_start: 0.8854 (mtp) cc_final: 0.8625 (mtp) REVERT: R 98 PHE cc_start: 0.8812 (t80) cc_final: 0.8563 (t80) REVERT: W 264 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7802 (mt0) outliers start: 66 outliers final: 44 residues processed: 379 average time/residue: 0.4205 time to fit residues: 262.9103 Evaluate side-chains 357 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 3.457 ------------------------------------------------------------------------------- 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 267 THR 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 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 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 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 267 THR 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 146 LEU Chi-restraints excluded: chain Q residue 148 ASP 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 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 317 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 324 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 240 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.087992 restraints weight = 57521.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.089970 restraints weight = 36291.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.091345 restraints weight = 26568.327| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 33567 Z= 0.175 Angle : 0.549 8.820 45022 Z= 0.278 Chirality : 0.042 0.164 4926 Planarity : 0.004 0.053 5546 Dihedral : 13.837 117.285 5730 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.09 % Allowed : 15.49 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3812 helix: 1.64 (0.11), residues: 2438 sheet: 0.38 (0.34), residues: 230 loop : -1.49 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 255 HIS 0.004 0.001 HIS W 384 PHE 0.017 0.002 PHE W 252 TYR 0.017 0.001 TYR V 209 ARG 0.013 0.000 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 1898) hydrogen bonds : angle 3.87158 ( 5574) covalent geometry : bond 0.00422 (33566) covalent geometry : angle 0.54924 (45022) Misc. bond : bond 0.00081 ( 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 395 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 324 time to evaluate : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.8011 (tpt) cc_final: 0.7734 (tpp) REVERT: D 284 MET cc_start: 0.8874 (mtp) cc_final: 0.8619 (mtp) REVERT: E 98 PHE cc_start: 0.8801 (t80) cc_final: 0.8545 (t80) REVERT: J 264 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: O 329 MET cc_start: 0.8014 (tpt) cc_final: 0.7736 (tpp) REVERT: Q 284 MET cc_start: 0.8858 (mtp) cc_final: 0.8597 (mtp) REVERT: R 98 PHE cc_start: 0.8799 (t80) cc_final: 0.8489 (t80) REVERT: U 79 TYR cc_start: 0.8920 (t80) cc_final: 0.8595 (t80) REVERT: W 264 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7735 (mt0) outliers start: 71 outliers final: 54 residues processed: 372 average time/residue: 0.4344 time to fit residues: 268.2352 Evaluate side-chains 365 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 3.877 ------------------------------------------------------------------------------- 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 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 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 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 243 MET 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 79 optimal weight: 4.9990 chunk 249 optimal weight: 0.0570 chunk 202 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 297 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090786 restraints weight = 57131.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092950 restraints weight = 35288.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094477 restraints weight = 25378.550| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33567 Z= 0.103 Angle : 0.496 8.761 45022 Z= 0.251 Chirality : 0.039 0.190 4926 Planarity : 0.003 0.046 5546 Dihedral : 13.346 112.758 5730 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.97 % Allowed : 16.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3812 helix: 1.91 (0.11), residues: 2418 sheet: 0.55 (0.34), residues: 230 loop : -1.39 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 256 HIS 0.006 0.001 HIS W 384 PHE 0.016 0.001 PHE J 252 TYR 0.018 0.001 TYR I 209 ARG 0.007 0.000 ARG S 52 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 1898) hydrogen bonds : angle 3.72683 ( 5574) covalent geometry : bond 0.00227 (33566) covalent geometry : angle 0.49556 (45022) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 337 time to evaluate : 3.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8613 (mm) REVERT: B 329 MET cc_start: 0.7881 (tpt) cc_final: 0.7641 (tpp) REVERT: D 284 MET cc_start: 0.8830 (mtp) cc_final: 0.8609 (mtp) REVERT: E 98 PHE cc_start: 0.8784 (t80) cc_final: 0.8528 (t80) REVERT: J 264 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: O 234 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8610 (mm) REVERT: O 329 MET cc_start: 0.7887 (tpt) cc_final: 0.7646 (tpp) REVERT: Q 284 MET cc_start: 0.8842 (mtp) cc_final: 0.8639 (mtp) REVERT: R 98 PHE cc_start: 0.8776 (t80) cc_final: 0.8507 (t80) REVERT: W 264 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7861 (mt0) outliers start: 67 outliers final: 50 residues processed: 380 average time/residue: 0.4233 time to fit residues: 265.6008 Evaluate side-chains 366 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 3.690 ------------------------------------------------------------------------------- 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 243 MET 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 F residue 95 HIS 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 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 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 146 LEU Chi-restraints excluded: chain Q residue 170 HIS Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain 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 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 326 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 0.0040 chunk 329 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 307 optimal weight: 0.0040 chunk 167 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5808 ------------------------------------------------------------------------------- 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** I 305 HIS ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 305 HIS V 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.091315 restraints weight = 57135.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093423 restraints weight = 35580.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095012 restraints weight = 25698.217| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2227 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= 0.102 Angle : 0.487 7.381 45022 Z= 0.247 Chirality : 0.039 0.181 4926 Planarity : 0.003 0.046 5546 Dihedral : 13.061 110.973 5730 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.97 % Allowed : 16.84 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.14), residues: 3812 helix: 2.06 (0.11), residues: 2418 sheet: 0.58 (0.34), residues: 230 loop : -1.31 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 256 HIS 0.006 0.000 HIS W 384 PHE 0.013 0.001 PHE W 252 TYR 0.018 0.001 TYR V 209 ARG 0.007 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 1898) hydrogen bonds : angle 3.66873 ( 5574) covalent geometry : bond 0.00228 (33566) covalent geometry : angle 0.48695 (45022) Misc. bond : bond 0.00034 ( 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 400 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 333 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8642 (mm) REVERT: B 329 MET cc_start: 0.7865 (tpt) cc_final: 0.7644 (tpp) REVERT: D 284 MET cc_start: 0.8827 (mtp) cc_final: 0.8612 (mtp) REVERT: J 264 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: O 234 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8665 (mm) REVERT: O 329 MET cc_start: 0.7874 (tpt) cc_final: 0.7648 (tpp) REVERT: Q 284 MET cc_start: 0.8839 (mtp) cc_final: 0.8618 (mtp) REVERT: W 264 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7848 (mt0) outliers start: 67 outliers final: 49 residues processed: 375 average time/residue: 0.4224 time to fit residues: 263.9782 Evaluate side-chains 365 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain 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 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 283 PHE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 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 170 HIS Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 234 LEU 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 318 VAL Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 326 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 97 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** 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** N 246 GLN ** V 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.085270 restraints weight = 58008.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.087582 restraints weight = 36157.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.089135 restraints weight = 26387.245| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 33567 Z= 0.293 Angle : 0.642 8.209 45022 Z= 0.326 Chirality : 0.046 0.191 4926 Planarity : 0.004 0.045 5546 Dihedral : 14.037 122.039 5730 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.35 % Allowed : 16.78 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3812 helix: 1.64 (0.11), residues: 2432 sheet: 0.37 (0.34), residues: 230 loop : -1.39 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 255 HIS 0.006 0.001 HIS W 384 PHE 0.024 0.002 PHE I 296 TYR 0.019 0.002 TYR I 114 ARG 0.007 0.001 ARG O 297 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 1898) hydrogen bonds : angle 4.02497 ( 5574) covalent geometry : bond 0.00711 (33566) covalent geometry : angle 0.64186 (45022) Misc. bond : bond 0.00148 ( 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 385 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 305 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 MET cc_start: 0.8034 (tpt) cc_final: 0.7628 (tpp) REVERT: D 284 MET cc_start: 0.8901 (mtp) cc_final: 0.8595 (mtp) REVERT: J 264 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: O 329 MET cc_start: 0.8027 (tpt) cc_final: 0.7584 (tpp) REVERT: Q 284 MET cc_start: 0.8912 (mtp) cc_final: 0.8607 (mtp) REVERT: W 264 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7822 (mt0) outliers start: 80 outliers final: 64 residues processed: 368 average time/residue: 0.4098 time to fit residues: 252.2313 Evaluate side-chains 365 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 299 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 283 PHE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain J residue 384 HIS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 276 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 233 THR 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 170 HIS Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain R residue 85 SER 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 61 VAL Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 283 PHE Chi-restraints excluded: chain V residue 318 VAL Chi-restraints excluded: chain V residue 391 LEU Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 298 ILE Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 384 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 34 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 372 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 168 optimal weight: 1.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** I 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 GLN N 246 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089665 restraints weight = 56812.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091752 restraints weight = 35688.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093136 restraints weight = 25879.252| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2227 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= 0.118 Angle : 0.526 10.915 45022 Z= 0.265 Chirality : 0.040 0.241 4926 Planarity : 0.003 0.046 5546 Dihedral : 13.349 111.933 5730 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.97 % Allowed : 17.31 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.14), residues: 3812 helix: 1.95 (0.11), residues: 2418 sheet: 0.57 (0.35), residues: 230 loop : -1.31 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 286 HIS 0.006 0.001 HIS W 384 PHE 0.015 0.001 PHE J 252 TYR 0.017 0.001 TYR I 209 ARG 0.007 0.000 ARG S 52 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 1898) hydrogen bonds : angle 3.79116 ( 5574) covalent geometry : bond 0.00271 (33566) covalent geometry : angle 0.52633 (45022) Misc. bond : bond 0.00029 ( 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 389 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 322 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8586 (mm) REVERT: B 329 MET cc_start: 0.7957 (tpt) cc_final: 0.7706 (tpp) REVERT: D 284 MET cc_start: 0.8821 (mtp) cc_final: 0.8599 (mtp) REVERT: J 264 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: O 329 MET cc_start: 0.7918 (tpt) cc_final: 0.7668 (tpp) REVERT: Q 284 MET cc_start: 0.8840 (mtp) cc_final: 0.8617 (mtp) REVERT: W 264 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7830 (mt0) outliers start: 67 outliers final: 52 residues processed: 367 average time/residue: 0.4315 time to fit residues: 262.0667 Evaluate side-chains 365 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 310 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 283 PHE Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 430 ASN Chi-restraints excluded: chain J residue 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 110 VAL 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 170 HIS Chi-restraints excluded: chain Q residue 191 CYS Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 283 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 391 LEU Chi-restraints excluded: chain V residue 409 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain W residue 298 ILE Chi-restraints excluded: chain W residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 152 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 279 optimal weight: 0.0670 chunk 68 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 chunk 317 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 160 optimal weight: 0.0470 overall best weight: 1.4220 ------------------------------------------------------------------------------- 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** ** W 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.088116 restraints weight = 57227.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090511 restraints weight = 35180.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.092118 restraints weight = 25383.132| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33567 Z= 0.166 Angle : 0.558 9.816 45022 Z= 0.282 Chirality : 0.042 0.204 4926 Planarity : 0.004 0.086 5546 Dihedral : 13.426 114.846 5730 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.91 % Allowed : 17.31 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.14), residues: 3812 helix: 1.89 (0.11), residues: 2432 sheet: 0.56 (0.35), residues: 230 loop : -1.31 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 286 HIS 0.006 0.001 HIS J 384 PHE 0.019 0.001 PHE I 296 TYR 0.022 0.001 TYR V 114 ARG 0.018 0.000 ARG J 394 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 1898) hydrogen bonds : angle 3.83334 ( 5574) covalent geometry : bond 0.00401 (33566) covalent geometry : angle 0.55830 (45022) Misc. bond : bond 0.00070 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9208.35 seconds wall clock time: 161 minutes 27.23 seconds (9687.23 seconds total)