Starting phenix.real_space_refine on Wed Mar 4 04:32:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kan_22776/03_2026/7kan_22776_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kan_22776/03_2026/7kan_22776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kan_22776/03_2026/7kan_22776_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kan_22776/03_2026/7kan_22776_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kan_22776/03_2026/7kan_22776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kan_22776/03_2026/7kan_22776.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.058 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 49 5.16 5 C 6866 2.51 5 N 1790 2.21 5 O 1819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10526 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3331 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'HIS:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 245 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3612 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 31, 'TRANS': 438} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "E" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1355 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1454 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Time building chain proxies: 2.33, per 1000 atoms: 0.22 Number of scatterers: 10526 At special positions: 0 Unit cell: (107.16, 124.26, 136.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 2 15.00 O 1819 8.00 N 1790 7.00 C 6866 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: 0.71 Conformation dependent library (CDL) restraints added in 479.5 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 67.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 82 through 99 removed outlier: 3.510A pdb=" N SER A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 137 removed outlier: 3.944A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY A 137 " --> pdb=" O HIS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.845A pdb=" N GLY A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 173 removed outlier: 3.842A pdb=" N CYS A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 195 removed outlier: 3.811A pdb=" N ASN A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.516A pdb=" N LEU A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 4.029A pdb=" N GLN A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.535A pdb=" N MET A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.581A pdb=" N THR A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 4.290A pdb=" N LYS A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 439 removed outlier: 3.766A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 3.937A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 463 removed outlier: 3.608A pdb=" N ILE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 30 through 68 removed outlier: 3.706A pdb=" N PHE C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Proline residue: C 61 - end of helix removed outlier: 3.682A pdb=" N ALA C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 123 removed outlier: 3.815A pdb=" N VAL B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 33 Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 56 through 68 removed outlier: 3.739A pdb=" N ILE D 60 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 97 removed outlier: 4.283A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.637A pdb=" N ILE D 196 " --> pdb=" O PRO D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 228 removed outlier: 4.421A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 237 through 247 removed outlier: 3.807A pdb=" N ARG D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 4.030A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.891A pdb=" N GLU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 271 " --> pdb=" O TYR D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.536A pdb=" N ASP D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.775A pdb=" N ILE D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 323 Processing helix chain 'D' and resid 332 through 357 removed outlier: 4.185A pdb=" N GLU D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 374 Processing helix chain 'D' and resid 382 through 387 removed outlier: 3.850A pdb=" N LEU D 385 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 387 " --> pdb=" O LEU D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 382 through 387' Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.652A pdb=" N GLU D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 431 through 443 removed outlier: 4.106A pdb=" N SER D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 36 Proline residue: E 9 - end of helix Processing helix chain 'E' and resid 45 through 60 removed outlier: 3.841A pdb=" N ASP E 49 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 104 removed outlier: 4.410A pdb=" N GLN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 138 removed outlier: 3.739A pdb=" N GLN E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 167 removed outlier: 4.002A pdb=" N PHE E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'F' and resid 31 through 56 removed outlier: 4.066A pdb=" N ASP F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 87 removed outlier: 4.483A pdb=" N SER F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'F' and resid 113 through 134 removed outlier: 4.101A pdb=" N ALA F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 3.519A pdb=" N GLY F 141 " --> pdb=" O MET F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 171 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 192 through 203 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.752A pdb=" N GLU A 19 " --> pdb=" O VAL B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 201 through 204 removed outlier: 3.727A pdb=" N ASN D 7 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 190 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 284 removed outlier: 3.735A pdb=" N TYR A 281 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 267 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 265 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA5, first strand: chain 'D' and resid 452 through 457 removed outlier: 3.729A pdb=" N LYS D 452 " --> pdb=" O LYS D 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 558 through 565 removed outlier: 6.085A pdb=" N LEU D 550 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 548 " --> pdb=" O PHE D 563 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 617 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 14 669 hydrogen bonds defined for protein. 1989 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: 1.70 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1623 1.31 - 1.43: 2765 1.43 - 1.56: 6280 1.56 - 1.68: 4 1.68 - 1.81: 85 Bond restraints: 10757 Sorted by residual: bond pdb=" C21 PC1 A 502 " pdb=" O21 PC1 A 502 " ideal model delta sigma weight residual 1.331 1.404 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C31 PC1 A 501 " pdb=" O31 PC1 A 501 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C21 PC1 A 501 " pdb=" O21 PC1 A 501 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C31 PC1 A 502 " pdb=" O31 PC1 A 502 " ideal model delta sigma weight residual 1.330 1.396 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" N PC1 A 502 " pdb=" C12 PC1 A 502 " ideal model delta sigma weight residual 1.500 1.455 0.045 2.00e-02 2.50e+03 4.97e+00 ... (remaining 10752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 14521 3.69 - 7.38: 73 7.38 - 11.08: 8 11.08 - 14.77: 2 14.77 - 18.46: 2 Bond angle restraints: 14606 Sorted by residual: angle pdb=" N PRO D 29 " pdb=" CA PRO D 29 " pdb=" CB PRO D 29 " ideal model delta sigma weight residual 103.25 110.05 -6.80 1.05e+00 9.07e-01 4.19e+01 angle pdb=" C3D PC1 A 501 " pdb=" C3E PC1 A 501 " pdb=" C3F PC1 A 501 " ideal model delta sigma weight residual 113.44 131.90 -18.46 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C3B PC1 A 502 " pdb=" C3C PC1 A 502 " pdb=" C3D PC1 A 502 " ideal model delta sigma weight residual 113.66 131.20 -17.54 3.00e+00 1.11e-01 3.42e+01 angle pdb=" O12 PC1 A 502 " pdb=" P PC1 A 502 " pdb=" O14 PC1 A 502 " ideal model delta sigma weight residual 123.67 109.00 14.67 3.00e+00 1.11e-01 2.39e+01 angle pdb=" O12 PC1 A 501 " pdb=" P PC1 A 501 " pdb=" O14 PC1 A 501 " ideal model delta sigma weight residual 123.67 109.23 14.44 3.00e+00 1.11e-01 2.32e+01 ... (remaining 14601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5911 17.81 - 35.62: 452 35.62 - 53.43: 81 53.43 - 71.23: 11 71.23 - 89.04: 5 Dihedral angle restraints: 6460 sinusoidal: 2492 harmonic: 3968 Sorted by residual: dihedral pdb=" CA LEU A 80 " pdb=" C LEU A 80 " pdb=" N GLY A 81 " pdb=" CA GLY A 81 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CB GLU D 396 " pdb=" CG GLU D 396 " pdb=" CD GLU D 396 " pdb=" OE1 GLU D 396 " ideal model delta sinusoidal sigma weight residual 0.00 87.35 -87.35 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA THR A 288 " pdb=" C THR A 288 " pdb=" N SER A 289 " pdb=" CA SER A 289 " ideal model delta harmonic sigma weight residual -180.00 -164.63 -15.37 0 5.00e+00 4.00e-02 9.45e+00 ... (remaining 6457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1361 0.045 - 0.091: 278 0.091 - 0.136: 49 0.136 - 0.181: 3 0.181 - 0.227: 2 Chirality restraints: 1693 Sorted by residual: chirality pdb=" CA PRO D 29 " pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CB PRO D 29 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE D 473 " pdb=" CA ILE D 473 " pdb=" CG1 ILE D 473 " pdb=" CG2 ILE D 473 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ASP D 326 " pdb=" N ASP D 326 " pdb=" C ASP D 326 " pdb=" CB ASP D 326 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 1690 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 277 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" CD GLU D 277 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU D 277 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU D 277 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 56 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO F 57 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 292 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" CD GLU D 292 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU D 292 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU D 292 " -0.011 2.00e-02 2.50e+03 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 870 2.74 - 3.28: 10689 3.28 - 3.82: 16628 3.82 - 4.36: 17015 4.36 - 4.90: 30787 Nonbonded interactions: 75989 Sorted by model distance: nonbonded pdb=" OG1 THR A 419 " pdb=" OD2 ASP C 18 " model vdw 2.197 3.040 nonbonded pdb=" O THR D 464 " pdb=" OG SER D 467 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLU A 79 " pdb=" OH TYR A 139 " model vdw 2.257 3.040 nonbonded pdb=" NH1 ARG E 159 " pdb=" O ALA F 106 " model vdw 2.285 3.120 nonbonded pdb=" O SER E 37 " pdb=" OG SER E 37 " model vdw 2.299 3.040 ... (remaining 75984 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.004 0.073 10757 Z= 0.168 Angle : 0.716 18.459 14606 Z= 0.345 Chirality : 0.039 0.227 1693 Planarity : 0.004 0.051 1820 Dihedral : 12.943 89.043 3898 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1341 helix: -0.20 (0.17), residues: 865 sheet: -2.64 (0.57), residues: 68 loop : -2.69 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.013 0.001 TYR A 457 PHE 0.013 0.001 PHE D 15 TRP 0.028 0.001 TRP E 141 HIS 0.003 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00359 (10757) covalent geometry : angle 0.71622 (14606) hydrogen bonds : bond 0.12143 ( 669) hydrogen bonds : angle 4.73803 ( 1989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 162 MET cc_start: 0.7946 (tpp) cc_final: 0.7368 (tpp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1062 time to fit residues: 19.3496 Evaluate side-chains 78 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 220 HIS A 261 GLN D 61 GLN D 259 ASN D 386 GLN D 444 GLN D 470 GLN D 529 GLN E 95 GLN E 114 GLN F 14 HIS F 68 ASN F 83 ASN F 135 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.054389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.046411 restraints weight = 61785.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.047604 restraints weight = 31911.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048404 restraints weight = 20497.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048947 restraints weight = 15122.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049298 restraints weight = 12188.752| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10757 Z= 0.297 Angle : 0.726 9.529 14606 Z= 0.364 Chirality : 0.041 0.158 1693 Planarity : 0.005 0.056 1820 Dihedral : 7.878 71.653 1553 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.98 % Allowed : 12.38 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1341 helix: 0.77 (0.18), residues: 884 sheet: -2.12 (0.58), residues: 72 loop : -2.42 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 476 TYR 0.020 0.002 TYR A 287 PHE 0.016 0.002 PHE C 45 TRP 0.043 0.002 TRP E 141 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00675 (10757) covalent geometry : angle 0.72551 (14606) hydrogen bonds : bond 0.04856 ( 669) hydrogen bonds : angle 4.29357 ( 1989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.9304 (t0) cc_final: 0.9088 (t0) REVERT: C 20 MET cc_start: 0.8063 (tmm) cc_final: 0.7829 (tmm) REVERT: E 87 LYS cc_start: 0.9623 (ttmm) cc_final: 0.9328 (ttmm) REVERT: E 162 MET cc_start: 0.8428 (tpp) cc_final: 0.8074 (tpp) REVERT: F 174 ASP cc_start: 0.7945 (p0) cc_final: 0.6816 (p0) outliers start: 21 outliers final: 16 residues processed: 97 average time/residue: 0.0863 time to fit residues: 12.5932 Evaluate side-chains 88 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 123 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 chunk 113 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS C 64 ASN D 259 ASN F 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047937 restraints weight = 60588.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049223 restraints weight = 30091.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050082 restraints weight = 18924.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050618 restraints weight = 13646.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051040 restraints weight = 10942.033| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10757 Z= 0.126 Angle : 0.586 10.292 14606 Z= 0.288 Chirality : 0.037 0.162 1693 Planarity : 0.004 0.045 1820 Dihedral : 7.354 63.203 1553 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.51 % Allowed : 17.01 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1341 helix: 1.33 (0.18), residues: 882 sheet: -1.87 (0.58), residues: 72 loop : -2.08 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 162 TYR 0.012 0.001 TYR A 64 PHE 0.015 0.001 PHE D 15 TRP 0.022 0.001 TRP E 141 HIS 0.014 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00281 (10757) covalent geometry : angle 0.58600 (14606) hydrogen bonds : bond 0.04238 ( 669) hydrogen bonds : angle 3.82741 ( 1989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.9344 (t0) cc_final: 0.9021 (t0) REVERT: C 20 MET cc_start: 0.8029 (tmm) cc_final: 0.7775 (tmm) REVERT: E 87 LYS cc_start: 0.9667 (ttmm) cc_final: 0.9351 (ttmm) REVERT: E 162 MET cc_start: 0.8296 (tpp) cc_final: 0.7971 (tpp) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.0885 time to fit residues: 12.0585 Evaluate side-chains 85 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 20 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.055918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047916 restraints weight = 60383.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049201 restraints weight = 29865.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.050073 restraints weight = 18704.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050612 restraints weight = 13451.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051042 restraints weight = 10742.564| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10757 Z= 0.149 Angle : 0.579 12.566 14606 Z= 0.284 Chirality : 0.037 0.156 1693 Planarity : 0.004 0.045 1820 Dihedral : 7.039 56.882 1553 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.65 % Allowed : 17.49 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1341 helix: 1.62 (0.18), residues: 883 sheet: -1.59 (0.59), residues: 72 loop : -1.88 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 172 TYR 0.011 0.001 TYR A 287 PHE 0.013 0.001 PHE D 15 TRP 0.014 0.001 TRP E 141 HIS 0.002 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00340 (10757) covalent geometry : angle 0.57921 (14606) hydrogen bonds : bond 0.04066 ( 669) hydrogen bonds : angle 3.74856 ( 1989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.9387 (t0) cc_final: 0.9026 (t0) REVERT: C 20 MET cc_start: 0.8016 (tmm) cc_final: 0.7743 (tmm) REVERT: E 87 LYS cc_start: 0.9652 (ttmm) cc_final: 0.9334 (ttmm) REVERT: E 162 MET cc_start: 0.8268 (tpp) cc_final: 0.7897 (tpp) REVERT: F 174 ASP cc_start: 0.7626 (p0) cc_final: 0.7225 (p0) outliers start: 28 outliers final: 18 residues processed: 101 average time/residue: 0.0848 time to fit residues: 12.9857 Evaluate side-chains 91 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN D 604 HIS F 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046087 restraints weight = 60770.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047293 restraints weight = 31642.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048111 restraints weight = 20193.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048623 restraints weight = 14784.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049038 restraints weight = 11992.484| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10757 Z= 0.281 Angle : 0.714 11.950 14606 Z= 0.353 Chirality : 0.040 0.179 1693 Planarity : 0.004 0.047 1820 Dihedral : 7.279 59.511 1553 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.21 % Allowed : 19.47 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1341 helix: 1.63 (0.18), residues: 886 sheet: -1.63 (0.60), residues: 74 loop : -1.86 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 172 TYR 0.019 0.002 TYR A 287 PHE 0.018 0.002 PHE E 42 TRP 0.015 0.002 TRP E 141 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00634 (10757) covalent geometry : angle 0.71412 (14606) hydrogen bonds : bond 0.04920 ( 669) hydrogen bonds : angle 4.13853 ( 1989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.9468 (t0) cc_final: 0.9061 (t0) REVERT: A 287 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7963 (t80) REVERT: C 20 MET cc_start: 0.8043 (tmm) cc_final: 0.7772 (tmm) REVERT: D 415 MET cc_start: 0.8148 (ppp) cc_final: 0.7866 (ppp) REVERT: E 87 LYS cc_start: 0.9647 (ttmm) cc_final: 0.9315 (ttmm) REVERT: E 162 MET cc_start: 0.8365 (tpp) cc_final: 0.8024 (tpp) REVERT: F 174 ASP cc_start: 0.7707 (p0) cc_final: 0.7242 (p0) outliers start: 34 outliers final: 23 residues processed: 100 average time/residue: 0.0795 time to fit residues: 12.1644 Evaluate side-chains 94 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 154 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 118 optimal weight: 4.9990 chunk 4 optimal weight: 0.0060 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.055376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047446 restraints weight = 59874.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048680 restraints weight = 30730.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049491 restraints weight = 19586.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050078 restraints weight = 14375.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050425 restraints weight = 11470.901| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10757 Z= 0.139 Angle : 0.587 10.629 14606 Z= 0.287 Chirality : 0.037 0.169 1693 Planarity : 0.004 0.045 1820 Dihedral : 6.987 57.816 1553 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.27 % Allowed : 20.98 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1341 helix: 1.90 (0.18), residues: 885 sheet: -1.49 (0.61), residues: 74 loop : -1.73 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 162 TYR 0.012 0.001 TYR A 287 PHE 0.013 0.001 PHE D 15 TRP 0.013 0.001 TRP F 160 HIS 0.002 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00315 (10757) covalent geometry : angle 0.58689 (14606) hydrogen bonds : bond 0.04232 ( 669) hydrogen bonds : angle 3.72342 ( 1989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8919 (tmm) cc_final: 0.8472 (tmm) REVERT: A 168 ASP cc_start: 0.9455 (t0) cc_final: 0.9024 (t0) REVERT: C 20 MET cc_start: 0.8044 (tmm) cc_final: 0.7784 (tmm) REVERT: D 270 MET cc_start: 0.8665 (ttp) cc_final: 0.8402 (ppp) REVERT: E 87 LYS cc_start: 0.9605 (ttmm) cc_final: 0.9250 (ttmm) REVERT: E 162 MET cc_start: 0.8248 (tpp) cc_final: 0.7931 (tpp) REVERT: F 174 ASP cc_start: 0.7803 (p0) cc_final: 0.7375 (p0) outliers start: 24 outliers final: 18 residues processed: 100 average time/residue: 0.0907 time to fit residues: 13.6191 Evaluate side-chains 93 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 7 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 2 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.056551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048690 restraints weight = 58580.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.049942 restraints weight = 29870.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.050760 restraints weight = 18951.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.051340 restraints weight = 13847.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051645 restraints weight = 11031.847| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10757 Z= 0.122 Angle : 0.575 10.282 14606 Z= 0.280 Chirality : 0.037 0.166 1693 Planarity : 0.004 0.044 1820 Dihedral : 6.754 60.827 1553 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.46 % Allowed : 22.59 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1341 helix: 2.11 (0.18), residues: 877 sheet: -1.26 (0.62), residues: 73 loop : -1.55 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 93 TYR 0.011 0.001 TYR A 287 PHE 0.014 0.001 PHE D 15 TRP 0.014 0.001 TRP E 141 HIS 0.002 0.000 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00279 (10757) covalent geometry : angle 0.57523 (14606) hydrogen bonds : bond 0.03812 ( 669) hydrogen bonds : angle 3.55748 ( 1989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8926 (tmm) cc_final: 0.8461 (tmm) REVERT: A 168 ASP cc_start: 0.9447 (t0) cc_final: 0.8985 (t0) REVERT: C 20 MET cc_start: 0.8031 (tmm) cc_final: 0.7769 (tmm) REVERT: D 270 MET cc_start: 0.8598 (ttp) cc_final: 0.8398 (tmm) REVERT: D 415 MET cc_start: 0.8239 (ppp) cc_final: 0.7975 (pmm) REVERT: E 87 LYS cc_start: 0.9670 (ttmm) cc_final: 0.9278 (ttmm) REVERT: E 162 MET cc_start: 0.8286 (tpp) cc_final: 0.7887 (tpp) REVERT: F 174 ASP cc_start: 0.7939 (p0) cc_final: 0.7522 (p0) outliers start: 26 outliers final: 18 residues processed: 103 average time/residue: 0.0862 time to fit residues: 13.2786 Evaluate side-chains 93 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN F 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.056659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048807 restraints weight = 58698.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050052 restraints weight = 29863.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050842 restraints weight = 18923.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051430 restraints weight = 14014.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.051802 restraints weight = 11106.266| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10757 Z= 0.127 Angle : 0.582 9.925 14606 Z= 0.283 Chirality : 0.037 0.161 1693 Planarity : 0.004 0.045 1820 Dihedral : 6.662 59.517 1553 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.36 % Allowed : 22.78 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1341 helix: 2.18 (0.18), residues: 878 sheet: -1.14 (0.63), residues: 73 loop : -1.49 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 162 TYR 0.009 0.001 TYR A 287 PHE 0.013 0.001 PHE D 15 TRP 0.015 0.001 TRP E 141 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00294 (10757) covalent geometry : angle 0.58228 (14606) hydrogen bonds : bond 0.03746 ( 669) hydrogen bonds : angle 3.51939 ( 1989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8920 (tmm) cc_final: 0.8456 (tmm) REVERT: A 49 MET cc_start: 0.9005 (tpp) cc_final: 0.8799 (tpp) REVERT: A 168 ASP cc_start: 0.9440 (t0) cc_final: 0.8980 (t0) REVERT: C 20 MET cc_start: 0.8028 (tmm) cc_final: 0.7765 (tmm) REVERT: D 270 MET cc_start: 0.8608 (ttp) cc_final: 0.8353 (tmm) REVERT: D 415 MET cc_start: 0.8138 (ppp) cc_final: 0.7557 (ppp) REVERT: E 87 LYS cc_start: 0.9687 (ttmm) cc_final: 0.9369 (ttmm) REVERT: E 162 MET cc_start: 0.8271 (tpp) cc_final: 0.7890 (tpp) REVERT: E 164 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8842 (tm-30) REVERT: F 174 ASP cc_start: 0.7973 (p0) cc_final: 0.7561 (p0) outliers start: 25 outliers final: 21 residues processed: 96 average time/residue: 0.0871 time to fit residues: 12.6417 Evaluate side-chains 95 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 67 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.056909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049051 restraints weight = 58841.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050301 restraints weight = 29792.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051133 restraints weight = 18831.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051705 restraints weight = 13679.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052100 restraints weight = 10921.566| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10757 Z= 0.126 Angle : 0.581 9.848 14606 Z= 0.282 Chirality : 0.037 0.160 1693 Planarity : 0.004 0.045 1820 Dihedral : 6.572 59.867 1553 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.27 % Allowed : 22.97 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1341 helix: 2.23 (0.18), residues: 878 sheet: -1.00 (0.64), residues: 73 loop : -1.42 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 162 TYR 0.008 0.001 TYR A 287 PHE 0.013 0.001 PHE D 15 TRP 0.016 0.001 TRP E 141 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00291 (10757) covalent geometry : angle 0.58096 (14606) hydrogen bonds : bond 0.03682 ( 669) hydrogen bonds : angle 3.50840 ( 1989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8892 (tmm) cc_final: 0.8420 (tmm) REVERT: A 90 MET cc_start: 0.8538 (tmm) cc_final: 0.8083 (tmm) REVERT: A 168 ASP cc_start: 0.9438 (t0) cc_final: 0.8983 (t0) REVERT: A 287 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7746 (t80) REVERT: C 20 MET cc_start: 0.8018 (tmm) cc_final: 0.7751 (tmm) REVERT: D 270 MET cc_start: 0.8587 (ttp) cc_final: 0.8343 (tmm) REVERT: D 415 MET cc_start: 0.8069 (ppp) cc_final: 0.7686 (ppp) REVERT: E 87 LYS cc_start: 0.9672 (ttmm) cc_final: 0.9290 (ttmm) REVERT: E 162 MET cc_start: 0.8283 (tpp) cc_final: 0.7911 (tpp) REVERT: F 174 ASP cc_start: 0.7988 (p0) cc_final: 0.7580 (p0) outliers start: 24 outliers final: 20 residues processed: 96 average time/residue: 0.0872 time to fit residues: 12.8410 Evaluate side-chains 95 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.056099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048078 restraints weight = 58896.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049347 restraints weight = 29293.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050198 restraints weight = 18409.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050739 restraints weight = 13366.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051161 restraints weight = 10725.688| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10757 Z= 0.142 Angle : 0.602 11.253 14606 Z= 0.291 Chirality : 0.037 0.160 1693 Planarity : 0.004 0.044 1820 Dihedral : 6.548 60.571 1553 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.98 % Allowed : 22.87 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1341 helix: 2.22 (0.18), residues: 880 sheet: -0.90 (0.65), residues: 73 loop : -1.37 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 162 TYR 0.009 0.001 TYR A 287 PHE 0.012 0.001 PHE D 15 TRP 0.015 0.001 TRP E 141 HIS 0.006 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00329 (10757) covalent geometry : angle 0.60186 (14606) hydrogen bonds : bond 0.03786 ( 669) hydrogen bonds : angle 3.54780 ( 1989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8912 (tmm) cc_final: 0.8440 (tmm) REVERT: A 90 MET cc_start: 0.8570 (tmm) cc_final: 0.8100 (tmm) REVERT: A 168 ASP cc_start: 0.9443 (t0) cc_final: 0.8966 (t0) REVERT: A 287 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7693 (t80) REVERT: C 20 MET cc_start: 0.8038 (tmm) cc_final: 0.7771 (tmm) REVERT: D 270 MET cc_start: 0.8597 (ttp) cc_final: 0.8342 (tmm) REVERT: D 415 MET cc_start: 0.8022 (ppp) cc_final: 0.7740 (ppp) REVERT: E 87 LYS cc_start: 0.9677 (ttmm) cc_final: 0.9263 (ttmm) REVERT: E 162 MET cc_start: 0.8273 (tpp) cc_final: 0.7885 (tpp) REVERT: F 174 ASP cc_start: 0.7997 (p0) cc_final: 0.7581 (p0) outliers start: 21 outliers final: 20 residues processed: 95 average time/residue: 0.0858 time to fit residues: 12.3723 Evaluate side-chains 96 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.0040 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 0.0030 chunk 50 optimal weight: 7.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.056420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048389 restraints weight = 59405.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049648 restraints weight = 29596.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050511 restraints weight = 18671.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051053 restraints weight = 13547.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.051485 restraints weight = 10860.098| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10757 Z= 0.133 Angle : 0.603 10.489 14606 Z= 0.289 Chirality : 0.037 0.161 1693 Planarity : 0.004 0.045 1820 Dihedral : 6.492 60.047 1553 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.08 % Allowed : 22.78 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1341 helix: 2.25 (0.18), residues: 880 sheet: -0.85 (0.65), residues: 73 loop : -1.29 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 162 TYR 0.014 0.001 TYR F 100 PHE 0.013 0.001 PHE D 15 TRP 0.015 0.001 TRP E 141 HIS 0.006 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00307 (10757) covalent geometry : angle 0.60254 (14606) hydrogen bonds : bond 0.03713 ( 669) hydrogen bonds : angle 3.51552 ( 1989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1453.21 seconds wall clock time: 25 minutes 49.19 seconds (1549.19 seconds total)