Starting phenix.real_space_refine on Tue Jul 29 01:41:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kan_22776/07_2025/7kan_22776_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kan_22776/07_2025/7kan_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kan_22776/07_2025/7kan_22776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kan_22776/07_2025/7kan_22776.map" model { file = "/net/cci-nas-00/data/ceres_data/7kan_22776/07_2025/7kan_22776_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kan_22776/07_2025/7kan_22776_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'ASP:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, '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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 3} 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, 'ASN:plan1': 1, 'ASP:plan': 2} 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: 6.31, per 1000 atoms: 0.60 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: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.90 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: 2.86 Time building geometry restraints manager: 2.96 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: 0.770 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.360 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- 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 : 6.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (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 TRP 0.028 0.001 TRP E 141 HIS 0.003 0.001 HIS B 114 PHE 0.013 0.001 PHE D 15 TYR 0.013 0.001 TYR A 457 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.12143 ( 669) hydrogen bonds : angle 4.73803 ( 1989) covalent geometry : bond 0.00359 (10757) covalent geometry : angle 0.71622 (14606) *********************** 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 : 1.332 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: 0.2869 time to fit residues: 51.3433 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 : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 0.0070 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- 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 259 ASN D 444 GLN D 470 GLN D 529 GLN E 95 GLN E 114 GLN F 68 ASN F 83 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049135 restraints weight = 59749.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.050428 restraints weight = 29646.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051277 restraints weight = 18545.218| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1250 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= 0.139 Angle : 0.594 9.357 14606 Z= 0.292 Chirality : 0.037 0.156 1693 Planarity : 0.004 0.050 1820 Dihedral : 7.774 72.487 1553 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.42 % Allowed : 10.96 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1341 helix: 0.90 (0.18), residues: 882 sheet: -2.08 (0.57), residues: 72 loop : -2.27 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 141 HIS 0.002 0.001 HIS F 14 PHE 0.016 0.001 PHE C 45 TYR 0.013 0.001 TYR A 64 ARG 0.003 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 669) hydrogen bonds : angle 3.89186 ( 1989) covalent geometry : bond 0.00313 (10757) covalent geometry : angle 0.59404 (14606) *********************** 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 99 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 LYS cc_start: 0.9589 (ttmm) cc_final: 0.9292 (ttmm) REVERT: E 162 MET cc_start: 0.8314 (tpp) cc_final: 0.7977 (tpp) REVERT: F 174 ASP cc_start: 0.7975 (p0) cc_final: 0.6467 (p0) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.4864 time to fit residues: 67.6455 Evaluate side-chains 86 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 372 CYS 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 E residue 20 LEU 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 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 D 259 ASN D 386 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048339 restraints weight = 60390.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049633 restraints weight = 29810.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050496 restraints weight = 18582.121| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10757 Z= 0.160 Angle : 0.586 11.369 14606 Z= 0.289 Chirality : 0.037 0.159 1693 Planarity : 0.004 0.046 1820 Dihedral : 7.301 65.728 1553 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.08 % Allowed : 14.84 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1341 helix: 1.35 (0.18), residues: 882 sheet: -1.79 (0.58), residues: 74 loop : -2.02 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 141 HIS 0.008 0.001 HIS A 133 PHE 0.013 0.001 PHE D 15 TYR 0.012 0.001 TYR A 287 ARG 0.003 0.000 ARG F 162 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 669) hydrogen bonds : angle 3.79070 ( 1989) covalent geometry : bond 0.00365 (10757) covalent geometry : angle 0.58589 (14606) *********************** 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 99 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.7805 (tmm) cc_final: 0.7387 (tmm) REVERT: C 20 MET cc_start: 0.8069 (tmm) cc_final: 0.7826 (tpp) REVERT: E 87 LYS cc_start: 0.9627 (ttmm) cc_final: 0.9273 (ttmm) REVERT: E 162 MET cc_start: 0.8328 (tpp) cc_final: 0.7978 (tpp) outliers start: 22 outliers final: 16 residues processed: 93 average time/residue: 0.4123 time to fit residues: 58.3431 Evaluate side-chains 89 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 277 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 300 CYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS D 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.047314 restraints weight = 60169.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048581 restraints weight = 29964.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.049419 restraints weight = 18834.655| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10757 Z= 0.201 Angle : 0.619 12.238 14606 Z= 0.306 Chirality : 0.038 0.158 1693 Planarity : 0.004 0.047 1820 Dihedral : 7.098 57.568 1553 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.17 % Allowed : 17.67 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1341 helix: 1.57 (0.18), residues: 885 sheet: -1.63 (0.58), residues: 74 loop : -1.94 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 141 HIS 0.004 0.001 HIS B 114 PHE 0.013 0.001 PHE E 42 TYR 0.017 0.001 TYR A 287 ARG 0.003 0.000 ARG F 162 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 669) hydrogen bonds : angle 3.84885 ( 1989) covalent geometry : bond 0.00459 (10757) covalent geometry : angle 0.61919 (14606) *********************** 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 100 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8903 (tmm) cc_final: 0.8464 (tmm) REVERT: A 245 MET cc_start: 0.7910 (tmm) cc_final: 0.7377 (tmm) REVERT: E 87 LYS cc_start: 0.9626 (ttmm) cc_final: 0.9289 (ttmm) REVERT: E 162 MET cc_start: 0.8285 (tpp) cc_final: 0.7960 (tpp) outliers start: 23 outliers final: 15 residues processed: 94 average time/residue: 0.3189 time to fit residues: 46.0753 Evaluate side-chains 87 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 277 VAL Chi-restraints excluded: chain A residue 300 CYS 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 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 73 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.056941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048919 restraints weight = 58218.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050215 restraints weight = 28960.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051100 restraints weight = 17923.608| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1971 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= 0.128 Angle : 0.555 11.068 14606 Z= 0.273 Chirality : 0.037 0.161 1693 Planarity : 0.004 0.045 1820 Dihedral : 6.816 59.610 1553 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.46 % Allowed : 18.24 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1341 helix: 1.83 (0.18), residues: 886 sheet: -1.37 (0.60), residues: 74 loop : -1.78 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 141 HIS 0.003 0.001 HIS A 133 PHE 0.014 0.001 PHE D 15 TYR 0.012 0.001 TYR A 287 ARG 0.002 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 669) hydrogen bonds : angle 3.59519 ( 1989) covalent geometry : bond 0.00287 (10757) covalent geometry : angle 0.55518 (14606) *********************** 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 107 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8915 (tmm) cc_final: 0.8441 (tmm) REVERT: A 245 MET cc_start: 0.7931 (tmm) cc_final: 0.7675 (tmm) REVERT: D 369 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9022 (tp) REVERT: E 87 LYS cc_start: 0.9616 (ttmm) cc_final: 0.9290 (ttmm) REVERT: E 162 MET cc_start: 0.8217 (tpp) cc_final: 0.7913 (tpp) REVERT: F 174 ASP cc_start: 0.7749 (p0) cc_final: 0.7339 (p0) outliers start: 26 outliers final: 17 residues processed: 103 average time/residue: 0.1955 time to fit residues: 30.6449 Evaluate side-chains 92 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 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 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 D residue 369 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 165 TYR Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 6 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.057135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049313 restraints weight = 58439.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.050562 restraints weight = 29597.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051390 restraints weight = 18723.295| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 10757 Z= 0.120 Angle : 0.559 10.563 14606 Z= 0.273 Chirality : 0.037 0.168 1693 Planarity : 0.004 0.046 1820 Dihedral : 6.683 59.338 1553 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.89 % Allowed : 19.85 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1341 helix: 2.03 (0.18), residues: 878 sheet: -1.22 (0.61), residues: 74 loop : -1.61 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 141 HIS 0.004 0.001 HIS A 133 PHE 0.014 0.001 PHE D 15 TYR 0.009 0.001 TYR A 287 ARG 0.003 0.000 ARG F 172 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 669) hydrogen bonds : angle 3.50652 ( 1989) covalent geometry : bond 0.00277 (10757) covalent geometry : angle 0.55873 (14606) *********************** 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 96 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8894 (tmm) cc_final: 0.8402 (tmm) REVERT: A 90 MET cc_start: 0.8591 (tmm) cc_final: 0.8164 (tmm) REVERT: A 245 MET cc_start: 0.7961 (tmm) cc_final: 0.7666 (tmm) REVERT: D 369 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9009 (tp) REVERT: D 415 MET cc_start: 0.8244 (ppp) cc_final: 0.7890 (ppp) REVERT: E 87 LYS cc_start: 0.9648 (ttmm) cc_final: 0.9305 (ttmm) REVERT: E 162 MET cc_start: 0.8258 (tpp) cc_final: 0.7975 (tpp) REVERT: F 174 ASP cc_start: 0.7812 (p0) cc_final: 0.7397 (p0) outliers start: 20 outliers final: 13 residues processed: 94 average time/residue: 0.2713 time to fit residues: 38.3271 Evaluate side-chains 86 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 2.083 ------------------------------------------------------------------------------- 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 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 D residue 369 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.057381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049546 restraints weight = 59384.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.050810 restraints weight = 30053.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051605 restraints weight = 19017.837| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10757 Z= 0.112 Angle : 0.541 10.298 14606 Z= 0.264 Chirality : 0.036 0.165 1693 Planarity : 0.004 0.046 1820 Dihedral : 6.521 59.403 1553 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.80 % Allowed : 20.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1341 helix: 2.12 (0.18), residues: 881 sheet: -0.98 (0.63), residues: 73 loop : -1.56 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.004 0.000 HIS A 133 PHE 0.014 0.001 PHE D 15 TYR 0.009 0.001 TYR A 287 ARG 0.002 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 669) hydrogen bonds : angle 3.43905 ( 1989) covalent geometry : bond 0.00256 (10757) covalent geometry : angle 0.54141 (14606) *********************** 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 95 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8895 (tmm) cc_final: 0.8415 (tmm) REVERT: A 49 MET cc_start: 0.8940 (tpp) cc_final: 0.8369 (tpp) REVERT: A 90 MET cc_start: 0.8530 (tmm) cc_final: 0.8099 (tmm) REVERT: A 245 MET cc_start: 0.7886 (tmm) cc_final: 0.7592 (tmm) REVERT: D 369 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9027 (tp) REVERT: D 415 MET cc_start: 0.8127 (ppp) cc_final: 0.7921 (ppp) REVERT: E 87 LYS cc_start: 0.9679 (ttmm) cc_final: 0.9304 (ttmm) REVERT: E 162 MET cc_start: 0.8224 (tpp) cc_final: 0.7949 (tpp) REVERT: F 34 GLN cc_start: 0.8938 (mp10) cc_final: 0.8689 (mp10) REVERT: F 174 ASP cc_start: 0.7902 (p0) cc_final: 0.7469 (p0) outliers start: 19 outliers final: 14 residues processed: 93 average time/residue: 0.1931 time to fit residues: 27.2341 Evaluate side-chains 88 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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 54 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 145 ILE 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 27 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN F 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.055531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047638 restraints weight = 59456.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048870 restraints weight = 30342.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049557 restraints weight = 19252.533| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10757 Z= 0.207 Angle : 0.619 10.069 14606 Z= 0.306 Chirality : 0.038 0.163 1693 Planarity : 0.004 0.046 1820 Dihedral : 6.664 59.851 1553 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.17 % Allowed : 20.98 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1341 helix: 2.08 (0.18), residues: 886 sheet: -1.04 (0.64), residues: 74 loop : -1.62 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.006 0.001 HIS A 133 PHE 0.014 0.001 PHE E 42 TYR 0.014 0.001 TYR A 287 ARG 0.003 0.000 ARG F 162 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 669) hydrogen bonds : angle 3.70349 ( 1989) covalent geometry : bond 0.00475 (10757) covalent geometry : angle 0.61932 (14606) *********************** 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 97 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8944 (tmm) cc_final: 0.8465 (tmm) REVERT: A 90 MET cc_start: 0.8553 (tmm) cc_final: 0.8111 (tmm) REVERT: A 245 MET cc_start: 0.7995 (tmm) cc_final: 0.7324 (tmm) REVERT: A 287 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.8107 (t80) REVERT: E 162 MET cc_start: 0.8349 (tpp) cc_final: 0.8063 (tpp) REVERT: E 164 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8822 (tm-30) REVERT: F 174 ASP cc_start: 0.7925 (p0) cc_final: 0.7505 (p0) outliers start: 23 outliers final: 18 residues processed: 95 average time/residue: 0.2008 time to fit residues: 29.1389 Evaluate side-chains 91 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 295 LEU 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 F residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 134 optimal weight: 40.0000 chunk 102 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.057072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049098 restraints weight = 58663.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050405 restraints weight = 28645.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051277 restraints weight = 17774.660| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2348 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= 0.115 Angle : 0.576 9.973 14606 Z= 0.278 Chirality : 0.037 0.167 1693 Planarity : 0.004 0.044 1820 Dihedral : 6.486 59.589 1553 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.70 % Allowed : 21.17 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1341 helix: 2.24 (0.18), residues: 882 sheet: -0.86 (0.64), residues: 73 loop : -1.46 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.003 0.001 HIS A 133 PHE 0.016 0.001 PHE D 15 TYR 0.012 0.001 TYR A 287 ARG 0.002 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 669) hydrogen bonds : angle 3.45795 ( 1989) covalent geometry : bond 0.00255 (10757) covalent geometry : angle 0.57611 (14606) *********************** 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 92 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8914 (tmm) cc_final: 0.8419 (tmm) REVERT: A 90 MET cc_start: 0.8531 (tmm) cc_final: 0.8091 (tmm) REVERT: A 245 MET cc_start: 0.7885 (tmm) cc_final: 0.7558 (tmm) REVERT: E 162 MET cc_start: 0.8273 (tpp) cc_final: 0.8008 (tpp) REVERT: E 164 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8794 (tm-30) REVERT: F 34 GLN cc_start: 0.8944 (mp10) cc_final: 0.8715 (mp10) REVERT: F 174 ASP cc_start: 0.7939 (p0) cc_final: 0.7505 (p0) outliers start: 18 outliers final: 16 residues processed: 90 average time/residue: 0.1936 time to fit residues: 26.5401 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 : 1.135 ------------------------------------------------------------------------------- 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 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 295 LEU 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 54 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 20 LEU 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 131 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 32 optimal weight: 0.0170 chunk 60 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.055238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047347 restraints weight = 59416.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.048560 restraints weight = 30287.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049382 restraints weight = 19319.067| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 10757 Z= 0.226 Angle : 0.658 10.543 14606 Z= 0.322 Chirality : 0.039 0.162 1693 Planarity : 0.004 0.046 1820 Dihedral : 6.671 60.416 1553 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.70 % Allowed : 21.17 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1341 helix: 2.12 (0.18), residues: 888 sheet: -0.92 (0.66), residues: 74 loop : -1.56 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.006 0.001 HIS A 133 PHE 0.014 0.002 PHE E 42 TYR 0.013 0.001 TYR A 287 ARG 0.003 0.000 ARG D 476 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 669) hydrogen bonds : angle 3.75993 ( 1989) covalent geometry : bond 0.00519 (10757) covalent geometry : angle 0.65810 (14606) ********************** 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 90 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8938 (tmm) cc_final: 0.8451 (tmm) REVERT: A 90 MET cc_start: 0.8582 (tmm) cc_final: 0.8131 (tmm) REVERT: A 245 MET cc_start: 0.7943 (tmm) cc_final: 0.7226 (tmm) REVERT: E 162 MET cc_start: 0.8355 (tpp) cc_final: 0.8078 (tpp) REVERT: E 164 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8860 (tm-30) REVERT: F 174 ASP cc_start: 0.7929 (p0) cc_final: 0.7505 (p0) outliers start: 18 outliers final: 18 residues processed: 87 average time/residue: 0.2051 time to fit residues: 27.1280 Evaluate side-chains 90 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 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 295 LEU 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 A residue 460 MET 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 E residue 20 LEU 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 43 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.055773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047896 restraints weight = 59133.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.049132 restraints weight = 30059.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049900 restraints weight = 19078.323| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10757 Z= 0.163 Angle : 0.617 10.728 14606 Z= 0.299 Chirality : 0.037 0.164 1693 Planarity : 0.004 0.047 1820 Dihedral : 6.624 59.922 1553 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.70 % Allowed : 21.08 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1341 helix: 2.19 (0.18), residues: 887 sheet: -0.86 (0.66), residues: 74 loop : -1.51 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 141 HIS 0.005 0.001 HIS A 133 PHE 0.012 0.001 PHE D 15 TYR 0.013 0.001 TYR A 287 ARG 0.003 0.000 ARG F 162 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 669) hydrogen bonds : angle 3.64369 ( 1989) covalent geometry : bond 0.00377 (10757) covalent geometry : angle 0.61713 (14606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3500.63 seconds wall clock time: 66 minutes 24.01 seconds (3984.01 seconds total)