Starting phenix.real_space_refine on Thu May 22 18:22:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7x_9944/05_2025/6k7x_9944.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7x_9944/05_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_9944/05_2025/6k7x_9944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7x_9944/05_2025/6k7x_9944.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7x_9944/05_2025/6k7x_9944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7x_9944/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.57, per 1000 atoms: 0.64 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: 6.34 Conformation dependent library (CDL) restraints added in 2.9 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: 1.97 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: 6.67 Time building geometry restraints manager: 7.24 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: 3.920 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: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 49.980 Find NCS groups from input model: 1.230 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.600 ------------------------------------------------------------------------------- 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 : 2.542 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: 0.3978 time to fit residues: 210.4345 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 : 2.593 ------------------------------------------------------------------------------- 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 = 39350.112| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.91 r_work: 0.2916 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- 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 : 2.735 Fit side-chains REVERT: C 200 GLU cc_start: 0.8413 (tt0) cc_final: 0.8175 (tt0) REVERT: A 324 ILE cc_start: 0.8783 (pt) cc_final: 0.8516 (mt) REVERT: B 106 ASP cc_start: 0.8137 (m-30) cc_final: 0.7230 (m-30) REVERT: B 198 ASN cc_start: 0.8711 (t0) cc_final: 0.8378 (t0) REVERT: B 242 TYR cc_start: 0.8825 (t80) cc_final: 0.8592 (t80) REVERT: D 165 ARG cc_start: 0.7540 (mmp-170) cc_final: 0.7114 (mmp-170) REVERT: D 263 MET cc_start: 0.9096 (mmm) cc_final: 0.8763 (mmm) REVERT: K 200 GLU cc_start: 0.8417 (tt0) cc_final: 0.8171 (tt0) REVERT: M 106 ASP cc_start: 0.8133 (m-30) cc_final: 0.7230 (m-30) REVERT: M 198 ASN cc_start: 0.8782 (t0) cc_final: 0.8450 (t0) REVERT: M 293 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8250 (mm-30) REVERT: N 165 ARG cc_start: 0.7538 (mmp-170) cc_final: 0.7111 (mmp-170) REVERT: N 202 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8592 (tm-30) REVERT: N 263 MET cc_start: 0.9085 (mmm) cc_final: 0.8721 (mmm) REVERT: N 276 MET cc_start: 0.9320 (mtm) cc_final: 0.9009 (mtm) outliers start: 36 outliers final: 25 residues processed: 311 average time/residue: 0.3444 time to fit residues: 165.3670 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 : 2.756 ------------------------------------------------------------------------------- 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: 0.9980 chunk 233 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 205 optimal weight: 0.2980 chunk 192 optimal weight: 0.9990 chunk 136 optimal weight: 0.0000 chunk 42 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.105890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.086136 restraints weight = 39393.349| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.91 r_work: 0.2934 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23362 Z= 0.114 Angle : 0.515 8.199 31344 Z= 0.263 Chirality : 0.042 0.159 3438 Planarity : 0.003 0.047 3784 Dihedral : 17.745 178.704 4398 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.58 % Allowed : 10.86 % Favored : 87.56 % 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: -0.73 (0.17), residues: 2590 helix: 0.20 (0.13), residues: 1602 sheet: -0.62 (0.34), residues: 222 loop : -1.73 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 255 HIS 0.003 0.001 HIS K 304 PHE 0.014 0.001 PHE R 88 TYR 0.016 0.001 TYR K 268 ARG 0.005 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 1212) hydrogen bonds : angle 3.87722 ( 3552) covalent geometry : bond 0.00258 (23362) covalent geometry : angle 0.51469 (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 312 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 2.827 Fit side-chains REVERT: A 113 ARG cc_start: 0.8531 (ptp90) cc_final: 0.8176 (mtm-85) REVERT: B 198 ASN cc_start: 0.8550 (t0) cc_final: 0.8236 (t0) REVERT: B 242 TYR cc_start: 0.8836 (t80) cc_final: 0.8636 (t80) REVERT: D 165 ARG cc_start: 0.7504 (mmp-170) cc_final: 0.7096 (mmp-170) REVERT: D 263 MET cc_start: 0.9093 (mmm) cc_final: 0.8818 (mmm) REVERT: L 113 ARG cc_start: 0.8541 (ptp90) cc_final: 0.8187 (mtm-85) REVERT: L 324 ILE cc_start: 0.8748 (pt) cc_final: 0.8521 (mt) REVERT: M 198 ASN cc_start: 0.8597 (t0) cc_final: 0.8292 (t0) REVERT: M 293 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8263 (mm-30) REVERT: N 165 ARG cc_start: 0.7503 (mmp-170) cc_final: 0.7089 (mmp-170) REVERT: N 202 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8536 (tm-30) outliers start: 37 outliers final: 29 residues processed: 302 average time/residue: 0.3504 time to fit residues: 163.8033 Evaluate side-chains 279 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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 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 85 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 68 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 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: 0.8980 chunk 190 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 36 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.100757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.080546 restraints weight = 41023.597| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.12 r_work: 0.2835 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23362 Z= 0.218 Angle : 0.597 8.662 31344 Z= 0.303 Chirality : 0.045 0.145 3438 Planarity : 0.004 0.048 3784 Dihedral : 17.549 173.506 4398 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.21 % Allowed : 13.20 % Favored : 84.58 % 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: -0.34 (0.17), residues: 2590 helix: 0.49 (0.14), residues: 1600 sheet: -0.22 (0.35), residues: 196 loop : -1.58 (0.21), residues: 794 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 0.019 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 0.04835 ( 1212) hydrogen bonds : angle 3.98474 ( 3552) covalent geometry : bond 0.00531 (23362) covalent geometry : angle 0.59677 (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 295 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 2.499 Fit side-chains REVERT: A 113 ARG cc_start: 0.8572 (ptp90) cc_final: 0.8208 (mtm-85) REVERT: B 172 ASN cc_start: 0.7913 (p0) cc_final: 0.7631 (p0) REVERT: B 198 ASN cc_start: 0.8539 (t0) cc_final: 0.8213 (t0) REVERT: D 165 ARG cc_start: 0.7663 (mmp-170) cc_final: 0.7209 (mmp-170) REVERT: D 263 MET cc_start: 0.9189 (mmm) cc_final: 0.8933 (mmm) REVERT: L 113 ARG cc_start: 0.8582 (ptp90) cc_final: 0.8220 (mtm-85) REVERT: M 172 ASN cc_start: 0.7912 (p0) cc_final: 0.7626 (p0) REVERT: M 198 ASN cc_start: 0.8596 (t0) cc_final: 0.8284 (t0) REVERT: N 165 ARG cc_start: 0.7664 (mmp-170) cc_final: 0.7208 (mmp-170) REVERT: N 202 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8557 (tm-30) outliers start: 52 outliers final: 43 residues processed: 274 average time/residue: 0.3379 time to fit residues: 145.5274 Evaluate side-chains 279 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 2.788 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 57 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 102 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 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 = 0.3330 r_free = 0.3330 target = 0.103322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.083792 restraints weight = 39399.346| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.95 r_work: 0.2893 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2048 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= 0.126 Angle : 0.521 9.372 31344 Z= 0.264 Chirality : 0.042 0.135 3438 Planarity : 0.003 0.043 3784 Dihedral : 16.904 164.628 4398 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.00 % Allowed : 13.80 % Favored : 84.20 % 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: 0.04 (0.17), residues: 2590 helix: 0.86 (0.14), residues: 1598 sheet: -0.44 (0.33), residues: 220 loop : -1.51 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 255 HIS 0.003 0.001 HIS A 304 PHE 0.013 0.001 PHE N 149 TYR 0.016 0.001 TYR K 268 ARG 0.005 0.000 ARG R 52 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 1212) hydrogen bonds : angle 3.79641 ( 3552) covalent geometry : bond 0.00297 (23362) covalent geometry : angle 0.52070 (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 300 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 2.496 Fit side-chains REVERT: A 113 ARG cc_start: 0.8488 (ptp90) cc_final: 0.8188 (mtm-85) REVERT: B 198 ASN cc_start: 0.8490 (t0) cc_final: 0.8188 (t0) REVERT: D 165 ARG cc_start: 0.7682 (mmp-170) cc_final: 0.7245 (mmp-170) REVERT: L 113 ARG cc_start: 0.8498 (ptp90) cc_final: 0.8198 (mtm-85) REVERT: M 198 ASN cc_start: 0.8554 (t0) cc_final: 0.8257 (t0) REVERT: N 165 ARG cc_start: 0.7671 (mmp-170) cc_final: 0.7237 (mmp-170) REVERT: N 202 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8532 (tm-30) outliers start: 47 outliers final: 36 residues processed: 283 average time/residue: 0.3340 time to fit residues: 148.5988 Evaluate side-chains 278 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 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 259 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 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 148 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 146 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 198 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.102494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.083061 restraints weight = 39283.022| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.94 r_work: 0.2885 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23362 Z= 0.151 Angle : 0.541 9.320 31344 Z= 0.271 Chirality : 0.043 0.134 3438 Planarity : 0.003 0.040 3784 Dihedral : 16.467 155.533 4398 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.39 % Allowed : 14.18 % Favored : 83.43 % 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: 0.29 (0.17), residues: 2590 helix: 1.09 (0.14), residues: 1598 sheet: -0.32 (0.34), residues: 220 loop : -1.48 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 255 HIS 0.003 0.001 HIS A 304 PHE 0.014 0.001 PHE G 88 TYR 0.016 0.001 TYR C 268 ARG 0.004 0.000 ARG R 52 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 1212) hydrogen bonds : angle 3.78495 ( 3552) covalent geometry : bond 0.00360 (23362) covalent geometry : angle 0.54093 (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 306 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 250 time to evaluate : 2.492 Fit side-chains REVERT: A 113 ARG cc_start: 0.8493 (ptp90) cc_final: 0.8213 (mtm-85) REVERT: B 198 ASN cc_start: 0.8504 (t0) cc_final: 0.8212 (t0) REVERT: D 165 ARG cc_start: 0.7726 (mmp-170) cc_final: 0.7377 (mmp-170) REVERT: L 113 ARG cc_start: 0.8505 (ptp90) cc_final: 0.8224 (mtm-85) REVERT: M 198 ASN cc_start: 0.8645 (t0) cc_final: 0.8335 (t0) REVERT: N 165 ARG cc_start: 0.7702 (mmp-170) cc_final: 0.7353 (mmp-170) REVERT: N 202 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8569 (tm-30) outliers start: 56 outliers final: 43 residues processed: 289 average time/residue: 0.3364 time to fit residues: 153.7890 Evaluate side-chains 283 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 86 ILE 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 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 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 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 L residue 148 ASP 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.6503 > 50: distance: 14 - 95: 16.649 distance: 17 - 92: 16.678 distance: 28 - 80: 12.932 distance: 31 - 77: 15.457 distance: 44 - 65: 28.907 distance: 47 - 62: 18.302 distance: 54 - 58: 8.495 distance: 58 - 59: 13.430 distance: 59 - 60: 11.077 distance: 60 - 61: 13.122 distance: 60 - 62: 24.534 distance: 62 - 63: 25.913 distance: 63 - 64: 20.320 distance: 63 - 66: 18.111 distance: 64 - 65: 13.109 distance: 64 - 70: 28.955 distance: 66 - 67: 22.175 distance: 67 - 68: 36.537 distance: 67 - 69: 40.840 distance: 70 - 71: 12.245 distance: 70 - 76: 16.906 distance: 71 - 72: 18.505 distance: 71 - 74: 17.379 distance: 72 - 73: 14.334 distance: 72 - 77: 27.101 distance: 74 - 75: 16.618 distance: 75 - 76: 13.228 distance: 77 - 78: 8.515 distance: 78 - 79: 15.712 distance: 78 - 81: 21.058 distance: 79 - 80: 8.984 distance: 79 - 84: 15.043 distance: 81 - 82: 10.763 distance: 81 - 83: 15.592 distance: 84 - 85: 20.788 distance: 84 - 185: 31.690 distance: 85 - 86: 6.664 distance: 85 - 88: 19.411 distance: 86 - 87: 22.611 distance: 86 - 92: 13.855 distance: 87 - 182: 31.465 distance: 88 - 89: 10.523 distance: 88 - 90: 7.378 distance: 89 - 91: 13.072 distance: 92 - 93: 7.157 distance: 93 - 94: 16.801 distance: 93 - 96: 9.252 distance: 94 - 95: 20.369 distance: 94 - 98: 10.501 distance: 96 - 97: 10.891 distance: 98 - 170: 9.423 distance: 99 - 100: 17.063 distance: 99 - 102: 6.865 distance: 100 - 101: 10.222 distance: 100 - 105: 14.379 distance: 101 - 167: 15.680 distance: 102 - 103: 15.141 distance: 102 - 104: 8.990 distance: 105 - 106: 9.366 distance: 106 - 107: 35.750 distance: 106 - 109: 21.359 distance: 107 - 108: 16.069 distance: 107 - 116: 30.040 distance: 109 - 110: 10.084 distance: 110 - 111: 13.542 distance: 111 - 112: 7.114 distance: 112 - 113: 10.070 distance: 113 - 114: 5.672 distance: 113 - 115: 3.746 distance: 116 - 117: 24.190 distance: 116 - 155: 26.526 distance: 117 - 118: 22.116 distance: 117 - 120: 38.002 distance: 118 - 119: 17.071 distance: 118 - 124: 13.540 distance: 120 - 121: 20.255 distance: 121 - 122: 16.968 distance: 121 - 123: 24.627 distance: 124 - 125: 13.274 distance: 124 - 130: 31.745 distance: 125 - 126: 36.727 distance: 125 - 128: 26.326 distance: 126 - 127: 23.157 distance: 126 - 131: 19.810 distance: 128 - 129: 35.295 distance: 129 - 130: 26.375