Starting phenix.real_space_refine on Fri Jun 20 01:53:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7x_9944/06_2025/6k7x_9944.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7x_9944/06_2025/6k7x_9944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7x_9944/06_2025/6k7x_9944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7x_9944/06_2025/6k7x_9944.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7x_9944/06_2025/6k7x_9944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7x_9944/06_2025/6k7x_9944.cif" } resolution = 3.27 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= 0.064 sd= 1.605 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 6 9.91 5 P 32 5.49 5 S 72 5.16 5 C 15050 2.51 5 N 3688 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 226 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22944 Number of models: 1 Model: "" Number of chains: 24 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: "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: "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: "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: "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: "K" 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: "L" 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: "M" 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: "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: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "P" 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: "Q" 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: "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: "C" 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: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 189 Unusual residues: {' CA': 3, 'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: "D" 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: "K" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 188 Unusual residues: {' CA': 2, 'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Chain: "L" 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: "M" 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: "N" 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 Time building chain proxies: 16.05, per 1000 atoms: 0.70 Number of scatterers: 22944 At special positions: 0 Unit cell: (221.473, 101.463, 137.466, 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 6 19.99 S 72 16.00 P 32 15.00 O 4096 8.00 N 3688 7.00 C 15050 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=0, symmetry=0 Time building additional restraints: 5.68 Conformation dependent library (CDL) restraints added in 2.6 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5032 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 16 sheets defined 62.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.526A pdb=" N PHE C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 175 through 191 removed outlier: 4.044A pdb=" N VAL C 179 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 223 removed outlier: 3.820A pdb=" N ASN C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 200 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 4.168A pdb=" N LYS C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 256 removed outlier: 3.675A pdb=" N THR C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 Proline residue: C 265 - end of helix removed outlier: 3.934A pdb=" N TYR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 310 removed outlier: 3.762A pdb=" N LYS C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 334 removed outlier: 3.816A pdb=" N TYR C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.569A pdb=" N LEU C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.606A pdb=" N PHE A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.794A 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 171 through 190 removed outlier: 3.796A pdb=" N THR A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 213 removed outlier: 3.688A pdb=" N LEU A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 256 removed outlier: 4.166A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.811A 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: 3.563A pdb=" N MET A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 310 removed outlier: 3.633A pdb=" N LYS A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 333 removed outlier: 3.672A pdb=" N TYR A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 175 through 214 removed outlier: 3.593A pdb=" N VAL B 179 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 254 removed outlier: 4.053A pdb=" N LYS B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 286 Proline residue: B 265 - end of helix removed outlier: 3.776A pdb=" N TYR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 307 removed outlier: 3.771A pdb=" N ASP B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 341 removed outlier: 3.748A pdb=" N TYR B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Proline residue: B 337 - end of helix Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.709A pdb=" N PHE D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 171 through 190 removed outlier: 3.655A pdb=" N THR D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 184 " --> pdb=" O LYS D 180 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 188 " --> pdb=" O GLN D 184 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 211 Processing helix chain 'D' and resid 214 through 256 removed outlier: 3.812A pdb=" N LYS D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU D 234 " --> pdb=" O LYS D 230 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 286 Proline residue: D 265 - end of helix removed outlier: 3.700A pdb=" N THR D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 282 " --> pdb=" O MET D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 310 removed outlier: 3.916A pdb=" N ASP D 296 " --> pdb=" O PRO D 292 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 308 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 335 removed outlier: 3.741A pdb=" N ALA D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET D 329 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 75 removed outlier: 3.531A pdb=" N PHE H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 96 removed outlier: 3.516A pdb=" N GLY H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 95 removed outlier: 3.763A pdb=" N ILE E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE E 75 " --> pdb=" O PHE E 71 " (cutoff:3.500A) Proline residue: E 76 - end of helix removed outlier: 3.653A pdb=" N VAL E 80 " --> pdb=" O PRO E 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 95 removed outlier: 4.000A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.846A pdb=" N ILE G 73 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE G 75 " --> pdb=" O PHE G 71 " (cutoff:3.500A) Proline residue: G 76 - end of helix removed outlier: 3.718A pdb=" N VAL G 80 " --> pdb=" O PRO G 76 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 85 " --> pdb=" O GLY G 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 removed outlier: 3.525A pdb=" N PHE K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 Processing helix chain 'K' and resid 175 through 191 removed outlier: 4.043A pdb=" N VAL K 179 " --> pdb=" O THR K 175 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN K 184 " --> pdb=" O LYS K 180 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN K 185 " --> pdb=" O THR K 181 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 223 removed outlier: 3.820A pdb=" N ASN K 198 " --> pdb=" O GLN K 194 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU K 200 " --> pdb=" O GLN K 196 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU K 212 " --> pdb=" O GLU K 208 " (cutoff:3.500A) Proline residue: K 216 - end of helix removed outlier: 4.168A pdb=" N LYS K 219 " --> pdb=" O ALA K 215 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL K 220 " --> pdb=" O PRO K 216 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU K 223 " --> pdb=" O LYS K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 256 removed outlier: 3.675A pdb=" N THR K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL K 235 " --> pdb=" O ARG K 231 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU K 240 " --> pdb=" O LEU K 236 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP K 255 " --> pdb=" O ALA K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 286 Proline residue: K 265 - end of helix removed outlier: 3.934A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE K 282 " --> pdb=" O MET K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 310 removed outlier: 3.763A pdb=" N LYS K 305 " --> pdb=" O LEU K 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS K 308 " --> pdb=" O HIS K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 334 removed outlier: 3.815A pdb=" N TYR K 317 " --> pdb=" O ASP K 313 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA K 323 " --> pdb=" O GLN K 319 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE K 324 " --> pdb=" O LEU K 320 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA K 325 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU K 331 " --> pdb=" O ALA K 327 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS K 332 " --> pdb=" O GLU K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 340 removed outlier: 3.569A pdb=" N LEU K 338 " --> pdb=" O LEU K 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 120 removed outlier: 3.607A pdb=" N PHE L 111 " --> pdb=" O SER L 107 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG L 113 " --> pdb=" O GLY L 109 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP L 119 " --> pdb=" O LEU L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'L' and resid 171 through 190 removed outlier: 3.796A pdb=" N THR L 188 " --> pdb=" O GLN L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 213 removed outlier: 3.688A pdb=" N LEU L 207 " --> pdb=" O LEU L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 256 removed outlier: 4.166A pdb=" N VAL L 220 " --> pdb=" O PRO L 216 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU L 223 " --> pdb=" O LYS L 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS L 227 " --> pdb=" O GLU L 223 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU L 234 " --> pdb=" O LYS L 230 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU L 236 " --> pdb=" O THR L 232 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR L 254 " --> pdb=" O LEU L 250 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP L 255 " --> pdb=" O ALA L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 286 Proline residue: L 265 - end of helix removed outlier: 3.563A pdb=" N MET L 278 " --> pdb=" O SER L 274 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE L 282 " --> pdb=" O MET L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 310 removed outlier: 3.633A pdb=" N LYS L 305 " --> pdb=" O LEU L 301 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS L 308 " --> pdb=" O HIS L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 333 removed outlier: 3.672A pdb=" N TYR L 317 " --> pdb=" O ASP L 313 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA L 325 " --> pdb=" O LYS L 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 116 Processing helix chain 'M' and resid 140 through 145 Processing helix chain 'M' and resid 175 through 214 removed outlier: 3.592A pdb=" N VAL M 179 " --> pdb=" O THR M 175 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS M 191 " --> pdb=" O TYR M 187 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLU M 193 " --> pdb=" O THR M 189 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN M 198 " --> pdb=" O GLN M 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU M 202 " --> pdb=" O ASN M 198 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU M 205 " --> pdb=" O ARG M 201 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU M 208 " --> pdb=" O ILE M 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 254 removed outlier: 4.054A pdb=" N LYS M 219 " --> pdb=" O ALA M 215 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL M 220 " --> pdb=" O PRO M 216 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU M 223 " --> pdb=" O LYS M 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS M 227 " --> pdb=" O GLU M 223 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU M 229 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU M 234 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE M 247 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY M 248 " --> pdb=" O ALA M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 286 Proline residue: M 265 - end of helix removed outlier: 3.776A pdb=" N TYR M 279 " --> pdb=" O ALA M 275 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE M 282 " --> pdb=" O MET M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 307 removed outlier: 3.770A pdb=" N ASP M 296 " --> pdb=" O PRO M 292 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN M 298 " --> pdb=" O ALA M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 341 removed outlier: 3.748A pdb=" N TYR M 317 " --> pdb=" O ASP M 313 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN M 319 " --> pdb=" O GLU M 315 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP M 336 " --> pdb=" O LYS M 332 " (cutoff:3.500A) Proline residue: M 337 - end of helix Processing helix chain 'N' and resid 107 through 120 removed outlier: 3.708A pdb=" N PHE N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP N 119 " --> pdb=" O LEU N 115 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG N 120 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 145 Processing helix chain 'N' and resid 171 through 190 removed outlier: 3.655A pdb=" N THR N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN N 184 " --> pdb=" O LYS N 180 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN N 185 " --> pdb=" O THR N 181 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU N 186 " --> pdb=" O LEU N 182 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR N 188 " --> pdb=" O GLN N 184 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR N 189 " --> pdb=" O GLN N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 211 Processing helix chain 'N' and resid 214 through 256 removed outlier: 3.812A pdb=" N LYS N 219 " --> pdb=" O ALA N 215 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL N 220 " --> pdb=" O PRO N 216 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU N 223 " --> pdb=" O LYS N 219 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG N 231 " --> pdb=" O LYS N 227 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU N 234 " --> pdb=" O LYS N 230 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL N 235 " --> pdb=" O ARG N 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU N 253 " --> pdb=" O ILE N 249 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR N 254 " --> pdb=" O LEU N 250 " (cutoff:3.500A) removed outlier: 4.100A 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: 3.700A pdb=" N THR N 271 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR N 279 " --> pdb=" O ALA N 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE N 282 " --> pdb=" O MET N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 310 removed outlier: 3.916A pdb=" N ASP N 296 " --> pdb=" O PRO N 292 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS N 308 " --> pdb=" O HIS N 304 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 335 removed outlier: 3.741A pdb=" N ALA N 325 " --> pdb=" O LYS N 321 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET N 329 " --> pdb=" O ALA N 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 75 removed outlier: 3.531A pdb=" N PHE O 71 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE O 73 " --> pdb=" O ARG O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 96 removed outlier: 3.517A pdb=" N GLY O 81 " --> pdb=" O PHE O 77 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE O 88 " --> pdb=" O ILE O 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU O 94 " --> pdb=" O ALA O 90 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS O 95 " --> pdb=" O LEU O 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 95 removed outlier: 3.763A pdb=" N ILE P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE P 75 " --> pdb=" O PHE P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.653A pdb=" N VAL P 80 " --> pdb=" O PRO P 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER P 85 " --> pdb=" O GLY P 81 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 95 removed outlier: 4.000A pdb=" N ILE Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE Q 75 " --> pdb=" O PHE Q 71 " (cutoff:3.500A) Proline residue: Q 76 - end of helix Processing helix chain 'R' and resid 65 through 95 removed outlier: 3.846A pdb=" N ILE R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) Proline residue: R 76 - end of helix removed outlier: 3.718A pdb=" N VAL R 80 " --> pdb=" O PRO R 76 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER R 85 " --> pdb=" O GLY R 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS R 95 " --> pdb=" O LEU R 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 76 through 80 removed outlier: 3.643A pdb=" N THR C 76 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG C 96 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 126 through 128 removed outlier: 3.615A pdb=" N PHE C 149 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.735A pdb=" N GLU A 95 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 128 removed outlier: 3.803A pdb=" N LYS B 150 " --> pdb=" O TYR B 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA8, first strand: chain 'D' and resid 125 through 128 Processing sheet with id=AA9, first strand: chain 'K' and resid 76 through 80 removed outlier: 3.643A pdb=" N THR K 76 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ARG K 96 " --> pdb=" O ARG L 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 126 through 128 removed outlier: 3.615A pdb=" N PHE K 149 " --> pdb=" O VAL K 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 76 through 80 removed outlier: 3.735A pdb=" N GLU L 95 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 126 through 128 Processing sheet with id=AB4, first strand: chain 'M' and resid 77 through 80 Processing sheet with id=AB5, first strand: chain 'M' and resid 125 through 128 removed outlier: 3.802A pdb=" N LYS M 150 " --> pdb=" O TYR M 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 134 through 135 Processing sheet with id=AB7, first strand: chain 'N' and resid 125 through 128 1212 hydrogen bonds defined for protein. 3552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.86 Time building geometry restraints manager: 6.73 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: 3524 1.32 - 1.44: 5873 1.44 - 1.56: 13771 1.56 - 1.68: 66 1.68 - 1.81: 128 Bond restraints: 23362 Sorted by residual: bond pdb=" C1B PLX D 402 " pdb=" N1 PLX D 402 " ideal model delta sigma weight residual 1.501 1.429 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1B PLX N 402 " pdb=" N1 PLX N 402 " ideal model delta sigma weight residual 1.501 1.430 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1B PLX L 403 " pdb=" N1 PLX L 403 " ideal model delta sigma weight residual 1.501 1.431 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1B PLX A 405 " pdb=" N1 PLX A 405 " ideal model delta sigma weight residual 1.501 1.431 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1B PLX M 402 " pdb=" N1 PLX M 402 " ideal model delta sigma weight residual 1.501 1.432 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 23357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 30702 4.25 - 8.50: 576 8.50 - 12.75: 44 12.75 - 16.99: 4 16.99 - 21.24: 18 Bond angle restraints: 31344 Sorted by residual: angle pdb=" C51 CDL B 401 " pdb=" CB5 CDL B 401 " pdb=" OB6 CDL B 401 " ideal model delta sigma weight residual 111.33 128.68 -17.35 1.32e+00 5.72e-01 1.72e+02 angle pdb=" C51 CDL M 401 " pdb=" CB5 CDL M 401 " pdb=" OB6 CDL M 401 " ideal model delta sigma weight residual 111.33 128.65 -17.32 1.32e+00 5.72e-01 1.72e+02 angle pdb=" OB6 CDL B 401 " pdb=" CB5 CDL B 401 " pdb=" OB7 CDL B 401 " ideal model delta sigma weight residual 123.92 115.26 8.66 1.00e+00 9.92e-01 7.45e+01 angle pdb=" OB6 CDL M 401 " pdb=" CB5 CDL M 401 " pdb=" OB7 CDL M 401 " ideal model delta sigma weight residual 123.92 115.27 8.65 1.00e+00 9.92e-01 7.42e+01 angle pdb=" O2 PLX D 403 " pdb=" P1 PLX D 403 " pdb=" O3 PLX D 403 " ideal model delta sigma weight residual 121.72 100.48 21.24 3.00e+00 1.11e-01 5.01e+01 ... (remaining 31339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 13952 35.04 - 70.08: 800 70.08 - 105.12: 28 105.12 - 140.16: 12 140.16 - 175.20: 8 Dihedral angle restraints: 14800 sinusoidal: 7042 harmonic: 7758 Sorted by residual: dihedral pdb=" CA ASP D 155 " pdb=" C ASP D 155 " pdb=" N LEU D 156 " pdb=" CA LEU D 156 " ideal model delta harmonic sigma weight residual 180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ASP N 155 " pdb=" C ASP N 155 " pdb=" N LEU N 156 " pdb=" CA LEU N 156 " ideal model delta harmonic sigma weight residual -180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ILE M 153 " pdb=" C ILE M 153 " pdb=" N ASN M 154 " pdb=" CA ASN M 154 " ideal model delta harmonic sigma weight residual -180.00 -156.14 -23.86 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 14797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2780 0.075 - 0.150: 562 0.150 - 0.225: 62 0.225 - 0.300: 17 0.300 - 0.375: 17 Chirality restraints: 3438 Sorted by residual: chirality pdb=" CA4 CDL K 403 " pdb=" CA3 CDL K 403 " pdb=" CA6 CDL K 403 " pdb=" OA6 CDL K 403 " both_signs ideal model delta sigma weight residual False -2.57 -2.20 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA4 CDL C 401 " pdb=" CA3 CDL C 401 " pdb=" CA6 CDL C 401 " pdb=" OA6 CDL C 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.20 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C6 PLX B 403 " pdb=" C7 PLX B 403 " pdb=" O6 PLX B 403 " pdb=" O7 PLX B 403 " both_signs ideal model delta sigma weight residual False 2.01 2.37 -0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 3435 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 297 " -0.136 9.50e-02 1.11e+02 8.06e-02 3.67e+01 pdb=" NE ARG B 297 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 297 " -0.100 2.00e-02 2.50e+03 pdb=" NH1 ARG B 297 " 0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG B 297 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 297 " 0.137 9.50e-02 1.11e+02 8.05e-02 3.66e+01 pdb=" NE ARG M 297 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG M 297 " 0.100 2.00e-02 2.50e+03 pdb=" NH1 ARG M 297 " -0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG M 297 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 112 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C LEU A 112 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A 112 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 113 " -0.021 2.00e-02 2.50e+03 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5505 2.80 - 3.32: 18986 3.32 - 3.85: 35189 3.85 - 4.37: 40942 4.37 - 4.90: 72263 Nonbonded interactions: 172885 Sorted by model distance: nonbonded pdb=" NZ LYS G 62 " pdb=" OB3 CDL B 401 " model vdw 2.270 3.120 nonbonded pdb=" NZ LYS R 62 " pdb=" OB3 CDL M 401 " model vdw 2.275 3.120 nonbonded pdb=" OG SER B 225 " pdb=" OH TYR B 299 " model vdw 2.306 3.040 nonbonded pdb=" OG SER M 225 " pdb=" OH TYR M 299 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU N 264 " pdb="CA CA K 401 " model vdw 2.312 2.510 ... (remaining 172880 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 'K' and resid 73 through 345) selection = (chain 'L' and resid 73 through 345) selection = (chain 'M' and resid 73 through 345) selection = (chain 'N' and resid 73 through 345) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 51.460 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 0.099 23362 Z= 0.375 Angle : 1.333 21.242 31344 Z= 0.620 Chirality : 0.066 0.375 3438 Planarity : 0.008 0.081 3784 Dihedral : 19.737 175.196 9768 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.41 (0.12), residues: 2590 helix: -3.03 (0.09), residues: 1586 sheet: -1.14 (0.33), residues: 198 loop : -2.68 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 255 HIS 0.007 0.001 HIS K 170 PHE 0.023 0.003 PHE C 149 TYR 0.017 0.002 TYR C 268 ARG 0.102 0.002 ARG B 297 Details of bonding type rmsd hydrogen bonds : bond 0.12928 ( 1212) hydrogen bonds : angle 5.74855 ( 3552) covalent geometry : bond 0.00816 (23362) covalent geometry : angle 1.33275 (31344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 354 time to evaluate : 2.498 Fit side-chains REVERT: C 200 GLU cc_start: 0.7626 (tt0) cc_final: 0.7300 (tt0) REVERT: B 106 ASP cc_start: 0.7567 (m-30) cc_final: 0.7259 (m-30) REVERT: B 198 ASN cc_start: 0.8637 (t0) cc_final: 0.8320 (t0) REVERT: D 165 ARG cc_start: 0.7405 (mmp-170) cc_final: 0.6978 (mmp-170) REVERT: D 263 MET cc_start: 0.8606 (mmm) cc_final: 0.8394 (mmm) REVERT: G 99 VAL cc_start: 0.8467 (t) cc_final: 0.8207 (p) REVERT: K 200 GLU cc_start: 0.7593 (tt0) cc_final: 0.7256 (tt0) REVERT: M 106 ASP cc_start: 0.7571 (m-30) cc_final: 0.7261 (m-30) REVERT: M 198 ASN cc_start: 0.8709 (t0) cc_final: 0.8405 (t0) REVERT: N 165 ARG cc_start: 0.7400 (mmp-170) cc_final: 0.6973 (mmp-170) REVERT: N 202 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8106 (tm-30) REVERT: N 263 MET cc_start: 0.8573 (mmm) cc_final: 0.8330 (mmm) REVERT: R 99 VAL cc_start: 0.8448 (t) cc_final: 0.8186 (p) outliers start: 5 outliers final: 0 residues processed: 359 average time/residue: 0.3961 time to fit residues: 210.1866 Evaluate side-chains 249 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 232 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN C 185 GLN C 196 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN A 196 GLN A 246 GLN B 159 HIS B 177 ASN B 213 GLN D 114 GLN D 185 GLN D 194 GLN D 246 GLN D 318 ASN F 95 HIS K 116 GLN K 185 GLN K 196 GLN ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 177 ASN L 196 GLN L 246 GLN M 159 HIS M 177 ASN M 213 GLN M 246 GLN N 114 GLN N 185 GLN N 194 GLN N 246 GLN N 318 ASN Q 95 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.085224 restraints weight = 39350.123| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.91 r_work: 0.2915 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23362 Z= 0.140 Angle : 0.581 9.093 31344 Z= 0.296 Chirality : 0.043 0.176 3438 Planarity : 0.004 0.051 3784 Dihedral : 19.562 169.764 4398 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.53 % Allowed : 8.43 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.91 (0.16), residues: 2590 helix: -0.85 (0.13), residues: 1594 sheet: -0.57 (0.36), residues: 198 loop : -2.05 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 255 HIS 0.003 0.001 HIS A 304 PHE 0.015 0.002 PHE M 247 TYR 0.016 0.001 TYR K 268 ARG 0.005 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 1212) hydrogen bonds : angle 4.25532 ( 3552) covalent geometry : bond 0.00317 (23362) covalent geometry : angle 0.58092 (31344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 2.805 Fit side-chains REVERT: C 200 GLU cc_start: 0.8412 (tt0) cc_final: 0.8173 (tt0) REVERT: A 324 ILE cc_start: 0.8783 (pt) cc_final: 0.8518 (mt) REVERT: B 106 ASP cc_start: 0.8138 (m-30) cc_final: 0.7234 (m-30) REVERT: B 198 ASN cc_start: 0.8716 (t0) cc_final: 0.8383 (t0) REVERT: B 242 TYR cc_start: 0.8828 (t80) cc_final: 0.8595 (t80) REVERT: D 165 ARG cc_start: 0.7547 (mmp-170) cc_final: 0.7122 (mmp-170) REVERT: D 263 MET cc_start: 0.9096 (mmm) cc_final: 0.8762 (mmm) REVERT: K 200 GLU cc_start: 0.8409 (tt0) cc_final: 0.8162 (tt0) REVERT: M 106 ASP cc_start: 0.8137 (m-30) cc_final: 0.7236 (m-30) REVERT: M 198 ASN cc_start: 0.8788 (t0) cc_final: 0.8456 (t0) REVERT: M 293 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8245 (mm-30) REVERT: N 165 ARG cc_start: 0.7541 (mmp-170) cc_final: 0.7117 (mmp-170) REVERT: N 202 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8589 (tm-30) REVERT: N 263 MET cc_start: 0.9084 (mmm) cc_final: 0.8718 (mmm) REVERT: N 276 MET cc_start: 0.9322 (mtm) cc_final: 0.9011 (mtm) outliers start: 36 outliers final: 25 residues processed: 311 average time/residue: 0.3640 time to fit residues: 175.1016 Evaluate side-chains 273 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 274 SER Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 83 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 73 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 205 optimal weight: 0.0020 chunk 192 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.086563 restraints weight = 39360.717| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.91 r_work: 0.2940 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23362 Z= 0.109 Angle : 0.509 8.037 31344 Z= 0.260 Chirality : 0.041 0.163 3438 Planarity : 0.003 0.047 3784 Dihedral : 17.583 177.703 4398 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.53 % Allowed : 10.95 % Favored : 87.52 % 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: -0.68 (0.17), residues: 2590 helix: 0.24 (0.14), residues: 1602 sheet: -0.60 (0.34), residues: 222 loop : -1.73 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 255 HIS 0.003 0.001 HIS A 304 PHE 0.015 0.001 PHE R 88 TYR 0.015 0.001 TYR K 268 ARG 0.003 0.000 ARG L 165 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 1212) hydrogen bonds : angle 3.84315 ( 3552) covalent geometry : bond 0.00241 (23362) covalent geometry : angle 0.50857 (31344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 2.752 Fit side-chains REVERT: A 113 ARG cc_start: 0.8518 (ptp90) cc_final: 0.8173 (mtm-85) REVERT: B 198 ASN cc_start: 0.8529 (t0) cc_final: 0.8218 (t0) REVERT: B 242 TYR cc_start: 0.8824 (t80) cc_final: 0.8623 (t80) REVERT: D 165 ARG cc_start: 0.7503 (mmp-170) cc_final: 0.7140 (mmp-170) REVERT: D 263 MET cc_start: 0.9100 (mmm) cc_final: 0.8839 (mmm) REVERT: L 113 ARG cc_start: 0.8533 (ptp90) cc_final: 0.8192 (mtm-85) REVERT: L 324 ILE cc_start: 0.8733 (pt) cc_final: 0.8526 (mt) REVERT: M 198 ASN cc_start: 0.8573 (t0) cc_final: 0.8271 (t0) REVERT: N 165 ARG cc_start: 0.7501 (mmp-170) cc_final: 0.7135 (mmp-170) REVERT: N 202 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8539 (tm-30) outliers start: 36 outliers final: 30 residues processed: 303 average time/residue: 0.3849 time to fit residues: 182.7309 Evaluate side-chains 281 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 274 SER Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain R residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 237 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 99 optimal weight: 0.0570 chunk 36 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN G 95 HIS ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.080809 restraints weight = 40967.710| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.11 r_work: 0.2840 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23362 Z= 0.214 Angle : 0.596 8.517 31344 Z= 0.302 Chirality : 0.045 0.143 3438 Planarity : 0.004 0.044 3784 Dihedral : 17.432 172.559 4398 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.30 % Allowed : 12.86 % Favored : 84.84 % 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 (0.17), residues: 2590 helix: 0.55 (0.14), residues: 1600 sheet: -0.18 (0.35), residues: 196 loop : -1.56 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 255 HIS 0.004 0.001 HIS A 304 PHE 0.019 0.002 PHE M 247 TYR 0.012 0.001 TYR M 281 ARG 0.006 0.000 ARG R 52 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 1212) hydrogen bonds : angle 3.96101 ( 3552) covalent geometry : bond 0.00518 (23362) covalent geometry : angle 0.59595 (31344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 3.336 Fit side-chains REVERT: A 113 ARG cc_start: 0.8549 (ptp90) cc_final: 0.8193 (mtm-85) REVERT: B 172 ASN cc_start: 0.7910 (p0) cc_final: 0.7632 (p0) REVERT: B 198 ASN cc_start: 0.8524 (t0) cc_final: 0.8201 (t0) REVERT: D 165 ARG cc_start: 0.7655 (mmp-170) cc_final: 0.7204 (mmp-170) REVERT: D 263 MET cc_start: 0.9187 (mmm) cc_final: 0.8930 (mmm) REVERT: L 113 ARG cc_start: 0.8558 (ptp90) cc_final: 0.8200 (mtm-85) REVERT: L 324 ILE cc_start: 0.8688 (pt) cc_final: 0.8364 (mt) REVERT: M 172 ASN cc_start: 0.7914 (p0) cc_final: 0.7630 (p0) REVERT: M 198 ASN cc_start: 0.8579 (t0) cc_final: 0.8266 (t0) REVERT: N 165 ARG cc_start: 0.7657 (mmp-170) cc_final: 0.7203 (mmp-170) REVERT: N 202 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8526 (tm-30) outliers start: 54 outliers final: 44 residues processed: 279 average time/residue: 0.3793 time to fit residues: 168.0845 Evaluate side-chains 284 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 278 MET Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 235 VAL Chi-restraints excluded: chain N residue 274 SER Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain R residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 252 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.083799 restraints weight = 39436.824| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.93 r_work: 0.2897 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23362 Z= 0.134 Angle : 0.525 9.230 31344 Z= 0.266 Chirality : 0.042 0.133 3438 Planarity : 0.003 0.040 3784 Dihedral : 16.801 163.007 4398 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.96 % Allowed : 13.97 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.17), residues: 2590 helix: 0.89 (0.14), residues: 1598 sheet: -0.44 (0.33), residues: 220 loop : -1.50 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 255 HIS 0.003 0.001 HIS A 304 PHE 0.013 0.001 PHE D 149 TYR 0.014 0.001 TYR C 268 ARG 0.004 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 1212) hydrogen bonds : angle 3.79605 ( 3552) covalent geometry : bond 0.00318 (23362) covalent geometry : angle 0.52505 (31344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 2.921 Fit side-chains REVERT: C 200 GLU cc_start: 0.8479 (tt0) cc_final: 0.8252 (tt0) REVERT: A 113 ARG cc_start: 0.8471 (ptp90) cc_final: 0.8186 (mtm-85) REVERT: B 198 ASN cc_start: 0.8458 (t0) cc_final: 0.8193 (t0) REVERT: D 165 ARG cc_start: 0.7660 (mmp-170) cc_final: 0.7226 (mmp-170) REVERT: L 113 ARG cc_start: 0.8496 (ptp90) cc_final: 0.8210 (mtm-85) REVERT: M 198 ASN cc_start: 0.8542 (t0) cc_final: 0.8242 (t0) REVERT: N 165 ARG cc_start: 0.7630 (mmp-170) cc_final: 0.7300 (mmp-170) REVERT: N 202 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8560 (tm-30) outliers start: 46 outliers final: 33 residues processed: 280 average time/residue: 0.3365 time to fit residues: 148.4891 Evaluate side-chains 269 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 274 SER Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain R residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 146 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.082600 restraints weight = 39592.570| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.93 r_work: 0.2873 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23362 Z= 0.180 Angle : 0.561 9.328 31344 Z= 0.282 Chirality : 0.044 0.139 3438 Planarity : 0.003 0.039 3784 Dihedral : 16.587 155.868 4398 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.43 % Allowed : 14.27 % Favored : 83.30 % 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: 0.21 (0.17), residues: 2590 helix: 1.02 (0.14), residues: 1598 sheet: -0.39 (0.34), residues: 220 loop : -1.49 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 255 HIS 0.003 0.001 HIS A 304 PHE 0.016 0.002 PHE M 247 TYR 0.015 0.001 TYR C 268 ARG 0.004 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 1212) hydrogen bonds : angle 3.84238 ( 3552) covalent geometry : bond 0.00434 (23362) covalent geometry : angle 0.56059 (31344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 244 time to evaluate : 3.085 Fit side-chains REVERT: A 113 ARG cc_start: 0.8511 (ptp90) cc_final: 0.8229 (mtm-85) REVERT: B 198 ASN cc_start: 0.8544 (t0) cc_final: 0.8235 (t0) REVERT: D 165 ARG cc_start: 0.7725 (mmp-170) cc_final: 0.7366 (mmp-170) REVERT: L 113 ARG cc_start: 0.8526 (ptp90) cc_final: 0.8240 (mtm-85) REVERT: M 198 ASN cc_start: 0.8587 (t0) cc_final: 0.8270 (t0) REVERT: N 165 ARG cc_start: 0.7707 (mmp-170) cc_final: 0.7350 (mmp-170) REVERT: N 202 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8592 (tm-30) outliers start: 57 outliers final: 44 residues processed: 290 average time/residue: 0.4602 time to fit residues: 218.8677 Evaluate side-chains 281 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 319 GLN Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 274 SER Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 68 optimal weight: 0.9990 chunk 210 optimal weight: 0.1980 chunk 164 optimal weight: 0.0270 chunk 225 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.084981 restraints weight = 39101.842| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.92 r_work: 0.2918 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23362 Z= 0.108 Angle : 0.504 10.156 31344 Z= 0.255 Chirality : 0.041 0.129 3438 Planarity : 0.003 0.038 3784 Dihedral : 15.814 145.751 4398 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.92 % Allowed : 15.08 % Favored : 83.01 % 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: 0.58 (0.17), residues: 2590 helix: 1.35 (0.14), residues: 1600 sheet: -0.34 (0.35), residues: 200 loop : -1.39 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 255 HIS 0.003 0.001 HIS D 304 PHE 0.013 0.001 PHE R 88 TYR 0.016 0.001 TYR C 268 ARG 0.003 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 1212) hydrogen bonds : angle 3.66984 ( 3552) covalent geometry : bond 0.00245 (23362) covalent geometry : angle 0.50373 (31344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 2.916 Fit side-chains REVERT: A 113 ARG cc_start: 0.8431 (ptp90) cc_final: 0.8182 (mtm-85) REVERT: B 198 ASN cc_start: 0.8507 (t0) cc_final: 0.8221 (t0) REVERT: D 165 ARG cc_start: 0.7686 (mmp-170) cc_final: 0.7344 (mmp-170) REVERT: H 95 HIS cc_start: 0.7906 (m90) cc_final: 0.7645 (m90) REVERT: L 113 ARG cc_start: 0.8440 (ptp90) cc_final: 0.8191 (mtm-85) REVERT: M 198 ASN cc_start: 0.8564 (t0) cc_final: 0.8270 (t0) REVERT: N 165 ARG cc_start: 0.7679 (mmp-170) cc_final: 0.7337 (mmp-170) REVERT: N 202 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8541 (tm-30) REVERT: O 95 HIS cc_start: 0.7985 (m90) cc_final: 0.7712 (m90) outliers start: 45 outliers final: 33 residues processed: 287 average time/residue: 0.3919 time to fit residues: 175.8252 Evaluate side-chains 272 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 319 GLN Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 274 SER Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 83 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 172 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 103 optimal weight: 0.3980 chunk 160 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 231 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 254 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 191 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.104949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.085638 restraints weight = 39073.470| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.92 r_work: 0.2929 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23362 Z= 0.103 Angle : 0.508 9.157 31344 Z= 0.254 Chirality : 0.041 0.212 3438 Planarity : 0.003 0.036 3784 Dihedral : 15.234 137.028 4398 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.00 % Allowed : 15.46 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.17), residues: 2590 helix: 1.59 (0.14), residues: 1600 sheet: -0.13 (0.34), residues: 220 loop : -1.32 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 255 HIS 0.003 0.001 HIS L 304 PHE 0.013 0.001 PHE G 88 TYR 0.014 0.001 TYR C 268 ARG 0.007 0.000 ARG R 52 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 1212) hydrogen bonds : angle 3.60061 ( 3552) covalent geometry : bond 0.00232 (23362) covalent geometry : angle 0.50829 (31344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 2.864 Fit side-chains REVERT: A 113 ARG cc_start: 0.8407 (ptp90) cc_final: 0.8182 (mtm-85) REVERT: B 94 ARG cc_start: 0.7412 (mmm160) cc_final: 0.7211 (mmm160) REVERT: B 198 ASN cc_start: 0.8474 (t0) cc_final: 0.8189 (t0) REVERT: L 113 ARG cc_start: 0.8407 (ptp90) cc_final: 0.8183 (mtm-85) REVERT: M 198 ASN cc_start: 0.8543 (t0) cc_final: 0.8236 (t0) REVERT: N 202 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8550 (tm-30) REVERT: O 83 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8758 (tt) outliers start: 47 outliers final: 34 residues processed: 286 average time/residue: 0.3493 time to fit residues: 156.4393 Evaluate side-chains 277 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 319 GLN Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain R residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 44 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 192 optimal weight: 0.5980 chunk 227 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 211 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.085106 restraints weight = 39290.955| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.94 r_work: 0.2921 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23362 Z= 0.117 Angle : 0.524 8.894 31344 Z= 0.260 Chirality : 0.042 0.218 3438 Planarity : 0.003 0.036 3784 Dihedral : 14.982 132.536 4398 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.83 % Allowed : 15.72 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.17), residues: 2590 helix: 1.66 (0.14), residues: 1600 sheet: -0.08 (0.34), residues: 220 loop : -1.28 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 255 HIS 0.003 0.001 HIS L 304 PHE 0.013 0.001 PHE G 88 TYR 0.014 0.001 TYR C 268 ARG 0.007 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 1212) hydrogen bonds : angle 3.61501 ( 3552) covalent geometry : bond 0.00274 (23362) covalent geometry : angle 0.52432 (31344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 2.577 Fit side-chains REVERT: A 113 ARG cc_start: 0.8382 (ptp90) cc_final: 0.8161 (mtm-85) REVERT: B 94 ARG cc_start: 0.7394 (mmm160) cc_final: 0.7172 (mmm160) REVERT: B 198 ASN cc_start: 0.8465 (t0) cc_final: 0.8178 (t0) REVERT: L 113 ARG cc_start: 0.8401 (ptp90) cc_final: 0.8180 (mtm-85) REVERT: M 198 ASN cc_start: 0.8513 (t0) cc_final: 0.8204 (t0) REVERT: N 202 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8566 (tm-30) REVERT: O 83 LEU cc_start: 0.9019 (tp) cc_final: 0.8775 (tt) outliers start: 43 outliers final: 35 residues processed: 275 average time/residue: 0.3478 time to fit residues: 150.4626 Evaluate side-chains 275 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain K residue 328 GLU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 319 GLN Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 274 SER Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain R residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 61 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 205 optimal weight: 0.4980 chunk 193 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.084118 restraints weight = 39914.988| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.91 r_work: 0.2893 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23362 Z= 0.151 Angle : 0.562 10.693 31344 Z= 0.278 Chirality : 0.043 0.237 3438 Planarity : 0.003 0.036 3784 Dihedral : 14.932 128.850 4398 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.58 % Allowed : 15.97 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.17), residues: 2590 helix: 1.66 (0.14), residues: 1598 sheet: -0.12 (0.34), residues: 220 loop : -1.27 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 255 HIS 0.003 0.001 HIS L 304 PHE 0.014 0.001 PHE M 247 TYR 0.013 0.001 TYR K 268 ARG 0.007 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 1212) hydrogen bonds : angle 3.70698 ( 3552) covalent geometry : bond 0.00363 (23362) covalent geometry : angle 0.56212 (31344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 2.578 Fit side-chains REVERT: A 113 ARG cc_start: 0.8448 (ptp90) cc_final: 0.8219 (mtm-85) REVERT: B 94 ARG cc_start: 0.7438 (mmm160) cc_final: 0.7192 (mmm160) REVERT: B 198 ASN cc_start: 0.8475 (t0) cc_final: 0.8190 (t0) REVERT: L 113 ARG cc_start: 0.8461 (ptp90) cc_final: 0.8228 (mtm-85) REVERT: M 198 ASN cc_start: 0.8534 (t0) cc_final: 0.8169 (t0) REVERT: N 202 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8562 (tm-30) REVERT: O 83 LEU cc_start: 0.9078 (tp) cc_final: 0.8822 (tt) outliers start: 37 outliers final: 37 residues processed: 270 average time/residue: 0.3675 time to fit residues: 156.7992 Evaluate side-chains 278 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain K residue 328 GLU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 319 GLN Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 274 SER Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 28 optimal weight: 0.5980 chunk 219 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 239 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.084263 restraints weight = 39678.615| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.89 r_work: 0.2896 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23362 Z= 0.145 Angle : 0.559 11.986 31344 Z= 0.276 Chirality : 0.043 0.237 3438 Planarity : 0.003 0.036 3784 Dihedral : 14.788 125.978 4398 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.87 % Allowed : 15.80 % Favored : 82.33 % 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 (0.17), residues: 2590 helix: 1.70 (0.14), residues: 1598 sheet: -0.16 (0.34), residues: 220 loop : -1.28 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS A 304 PHE 0.014 0.001 PHE M 247 TYR 0.017 0.001 TYR K 258 ARG 0.007 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 1212) hydrogen bonds : angle 3.70432 ( 3552) covalent geometry : bond 0.00348 (23362) covalent geometry : angle 0.55875 (31344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11978.64 seconds wall clock time: 209 minutes 31.87 seconds (12571.87 seconds total)