Starting phenix.real_space_refine on Fri Feb 14 16:14:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvf_41640/02_2025/8tvf_41640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvf_41640/02_2025/8tvf_41640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tvf_41640/02_2025/8tvf_41640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvf_41640/02_2025/8tvf_41640.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvf_41640/02_2025/8tvf_41640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvf_41640/02_2025/8tvf_41640.cif" } resolution = 2.8 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= -0.000 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6258 2.51 5 N 1647 2.21 5 O 2502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10461 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3246 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 188 Classifications: {'water': 188} Link IDs: {None: 187} Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 188 Classifications: {'water': 188} Link IDs: {None: 187} Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 188 Classifications: {'water': 188} Link IDs: {None: 187} Restraints were copied for chains: C, B, D, F Time building chain proxies: 6.98, per 1000 atoms: 0.67 Number of scatterers: 10461 At special positions: 0 Unit cell: (105.042, 98.0392, 101.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2502 8.00 N 1647 7.00 C 6258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.18 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.08 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 601 " - " ASN A 65 " " NAG B 601 " - " ASN B 65 " " NAG C 601 " - " ASN C 65 " " NAG D 1 " - " ASN B 459 " " NAG E 1 " - " ASN A 459 " " NAG F 1 " - " ASN C 459 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 15 sheets defined 41.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.844A pdb=" N LYS B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 94 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 120 through 132 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 142 through 148 Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.521A pdb=" N GLY B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 5.718A pdb=" N ASN B 183 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 209 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.524A pdb=" N LEU B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 323 through 326 Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.844A pdb=" N LYS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 94 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.521A pdb=" N GLY A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 5.719A pdb=" N ASN A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.523A pdb=" N LEU A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 323 through 326 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.845A pdb=" N LYS C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 94 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.521A pdb=" N GLY C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 5.719A pdb=" N ASN C 183 " --> pdb=" O PRO C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 209 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.524A pdb=" N LEU C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 247 Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 323 through 326 Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 447 through 461 Processing sheet with id=AA1, first strand: chain 'B' and resid 327 through 328 removed outlier: 7.811A pdb=" N VAL B 333 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS B 335 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS B 42 " --> pdb=" O CYS B 335 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE B 33 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU B 291 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LYS B 35 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N GLN B 289 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N LEU B 37 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N VAL B 287 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N TYR B 39 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N ASN B 285 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR B 41 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE B 310 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 321 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 157 removed outlier: 7.841A pdb=" N THR B 163 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU B 51 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR B 270 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL B 264 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.789A pdb=" N MET B 110 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AA6, first strand: chain 'B' and resid 405 through 407 Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 395 Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 328 removed outlier: 7.811A pdb=" N VAL A 333 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN A 40 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS A 335 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS A 42 " --> pdb=" O CYS A 335 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ILE A 33 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU A 291 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LYS A 35 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N GLN A 289 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N LEU A 37 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N VAL A 287 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N TYR A 39 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N ASN A 285 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR A 41 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE A 310 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 321 " --> pdb=" O PHE A 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 157 removed outlier: 7.841A pdb=" N THR A 163 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 51 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR A 270 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL A 264 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AB2, first strand: chain 'A' and resid 405 through 407 Processing sheet with id=AB3, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB4, first strand: chain 'C' and resid 327 through 328 removed outlier: 7.811A pdb=" N VAL C 333 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN C 40 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N CYS C 335 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS C 42 " --> pdb=" O CYS C 335 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ILE C 33 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU C 291 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LYS C 35 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N GLN C 289 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N LEU C 37 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N VAL C 287 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N TYR C 39 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N ASN C 285 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR C 41 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N PHE C 310 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE C 321 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 153 through 157 removed outlier: 7.841A pdb=" N THR C 163 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 51 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR C 270 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL C 264 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 298 496 hydrogen bonds defined for protein. 1317 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: 3.89 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1954 1.32 - 1.45: 2325 1.45 - 1.58: 5663 1.58 - 1.72: 3 1.72 - 1.85: 78 Bond restraints: 10023 Sorted by residual: bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.500 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sigma weight residual 1.417 1.500 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.500 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" NE ARG C 370 " pdb=" CZ ARG C 370 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.70e+01 bond pdb=" NE ARG B 370 " pdb=" CZ ARG B 370 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.69e+01 ... (remaining 10018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 12216 2.07 - 4.14: 1227 4.14 - 6.20: 165 6.20 - 8.27: 33 8.27 - 10.34: 6 Bond angle restraints: 13647 Sorted by residual: angle pdb=" C GLY C 441 " pdb=" N PRO C 442 " pdb=" CA PRO C 442 " ideal model delta sigma weight residual 119.66 125.54 -5.88 7.20e-01 1.93e+00 6.68e+01 angle pdb=" C GLY B 441 " pdb=" N PRO B 442 " pdb=" CA PRO B 442 " ideal model delta sigma weight residual 119.66 125.52 -5.86 7.20e-01 1.93e+00 6.62e+01 angle pdb=" C GLY A 441 " pdb=" N PRO A 442 " pdb=" CA PRO A 442 " ideal model delta sigma weight residual 119.66 125.51 -5.85 7.20e-01 1.93e+00 6.60e+01 angle pdb=" C SER A 46 " pdb=" N PRO A 47 " pdb=" CA PRO A 47 " ideal model delta sigma weight residual 120.31 127.85 -7.54 9.80e-01 1.04e+00 5.92e+01 angle pdb=" C SER C 46 " pdb=" N PRO C 47 " pdb=" CA PRO C 47 " ideal model delta sigma weight residual 120.31 127.84 -7.53 9.80e-01 1.04e+00 5.90e+01 ... (remaining 13642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 6062 21.32 - 42.64: 127 42.64 - 63.95: 42 63.95 - 85.27: 18 85.27 - 106.59: 18 Dihedral angle restraints: 6267 sinusoidal: 2508 harmonic: 3759 Sorted by residual: dihedral pdb=" CB CYS B 66 " pdb=" SG CYS B 66 " pdb=" SG CYS B 187 " pdb=" CB CYS B 187 " ideal model delta sinusoidal sigma weight residual -86.00 -40.03 -45.97 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.88 106.59 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.87 106.58 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 6264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1239 0.090 - 0.179: 395 0.179 - 0.269: 61 0.269 - 0.358: 24 0.358 - 0.448: 6 Chirality restraints: 1725 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.00e+01 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 3.94e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 3.92e+01 ... (remaining 1722 not shown) Planarity restraints: 1734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 459 " 0.022 2.00e-02 2.50e+03 2.36e-02 6.93e+00 pdb=" CG ASN A 459 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 459 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 459 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 459 " 0.022 2.00e-02 2.50e+03 2.35e-02 6.90e+00 pdb=" CG ASN B 459 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 459 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 459 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 459 " 0.022 2.00e-02 2.50e+03 2.35e-02 6.88e+00 pdb=" CG ASN C 459 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 459 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 459 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.029 2.00e-02 2.50e+03 ... (remaining 1731 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 22 2.60 - 3.17: 8982 3.17 - 3.75: 15539 3.75 - 4.32: 24469 4.32 - 4.90: 37641 Nonbonded interactions: 86653 Sorted by model distance: nonbonded pdb=" SG CYS A 350 " pdb=" SG CYS A 358 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS C 350 " pdb=" SG CYS C 358 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS A 389 " pdb=" SG CYS A 412 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 389 " pdb=" SG CYS C 412 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS A 326 " pdb=" SG CYS A 335 " model vdw 2.030 3.760 ... (remaining 86648 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.360 Find NCS groups from input model: 0.230 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:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.014 0.083 10023 Z= 0.924 Angle : 1.357 10.340 13647 Z= 0.927 Chirality : 0.092 0.448 1725 Planarity : 0.005 0.020 1728 Dihedral : 12.896 106.589 3834 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.36 % Rotamer: Outliers : 0.28 % Allowed : 0.84 % Favored : 98.89 % 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: 0.03 (0.21), residues: 1284 helix: 0.06 (0.22), residues: 447 sheet: 0.29 (0.30), residues: 261 loop : 0.05 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.005 TRP C 303 HIS 0.004 0.001 HIS A 253 PHE 0.011 0.004 PHE C 71 TYR 0.030 0.006 TYR B 41 ARG 0.004 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 1.196 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 116 average time/residue: 2.0755 time to fit residues: 252.8818 Evaluate side-chains 62 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 320 ASN B 454 GLN A 260 ASN C 260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.080377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.061446 restraints weight = 17971.591| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.76 r_work: 0.2524 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10023 Z= 0.213 Angle : 0.598 7.197 13647 Z= 0.318 Chirality : 0.046 0.139 1725 Planarity : 0.004 0.038 1728 Dihedral : 10.018 71.208 1623 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.09 % Favored : 98.68 % Rotamer: Outliers : 1.21 % Allowed : 5.57 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1284 helix: 1.29 (0.24), residues: 483 sheet: 0.31 (0.30), residues: 267 loop : 0.08 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 303 HIS 0.002 0.001 HIS B 130 PHE 0.014 0.002 PHE A 230 TYR 0.020 0.002 TYR C 249 ARG 0.009 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.276 Fit side-chains REVERT: B 200 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8578 (tm-30) REVERT: C 451 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8361 (mp) outliers start: 13 outliers final: 5 residues processed: 72 average time/residue: 1.6212 time to fit residues: 124.9735 Evaluate side-chains 62 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 451 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 454 GLN A 177 ASN C 162 GLN C 177 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.077776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.058897 restraints weight = 18208.171| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 2.76 r_work: 0.2463 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10023 Z= 0.241 Angle : 0.541 5.646 13647 Z= 0.288 Chirality : 0.045 0.157 1725 Planarity : 0.004 0.040 1728 Dihedral : 7.087 59.986 1623 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 0.93 % Favored : 98.83 % Rotamer: Outliers : 1.21 % Allowed : 5.94 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1284 helix: 1.54 (0.24), residues: 483 sheet: 0.41 (0.29), residues: 297 loop : 0.11 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 303 HIS 0.003 0.001 HIS B 130 PHE 0.011 0.002 PHE C 277 TYR 0.017 0.002 TYR A 249 ARG 0.004 0.001 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.277 Fit side-chains REVERT: B 200 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: A 309 ARG cc_start: 0.8789 (mtp180) cc_final: 0.8059 (ttt180) REVERT: C 142 MET cc_start: 0.8027 (mmp) cc_final: 0.7826 (mmm) REVERT: C 309 ARG cc_start: 0.8848 (ttp80) cc_final: 0.8530 (ttt180) outliers start: 13 outliers final: 6 residues processed: 62 average time/residue: 1.4881 time to fit residues: 99.7068 Evaluate side-chains 60 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN B 454 GLN C 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.076566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.057767 restraints weight = 18053.429| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 2.76 r_work: 0.2447 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10023 Z= 0.254 Angle : 0.508 5.219 13647 Z= 0.274 Chirality : 0.045 0.141 1725 Planarity : 0.003 0.034 1728 Dihedral : 5.471 45.322 1623 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.36 % Rotamer: Outliers : 1.86 % Allowed : 6.22 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1284 helix: 1.65 (0.24), residues: 483 sheet: 0.30 (0.30), residues: 297 loop : 0.07 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 303 HIS 0.003 0.001 HIS A 130 PHE 0.009 0.002 PHE A 277 TYR 0.018 0.002 TYR A 249 ARG 0.005 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 1.138 Fit side-chains REVERT: B 200 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8607 (tm-30) REVERT: A 309 ARG cc_start: 0.8786 (mtp180) cc_final: 0.8066 (ttt180) REVERT: C 142 MET cc_start: 0.8089 (mmp) cc_final: 0.7867 (mmm) REVERT: C 309 ARG cc_start: 0.8862 (ttp80) cc_final: 0.8541 (ttt180) REVERT: C 451 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8387 (mp) outliers start: 20 outliers final: 4 residues processed: 73 average time/residue: 1.4056 time to fit residues: 110.6437 Evaluate side-chains 59 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 451 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN A 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.077177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.058384 restraints weight = 17987.809| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.75 r_work: 0.2466 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10023 Z= 0.201 Angle : 0.490 5.168 13647 Z= 0.264 Chirality : 0.044 0.155 1725 Planarity : 0.003 0.034 1728 Dihedral : 5.006 31.781 1623 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.09 % Favored : 98.68 % Rotamer: Outliers : 1.76 % Allowed : 7.24 % Favored : 90.99 % 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: 1.02 (0.23), residues: 1284 helix: 1.68 (0.24), residues: 480 sheet: 0.27 (0.30), residues: 297 loop : 0.10 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS B 130 PHE 0.009 0.001 PHE C 277 TYR 0.015 0.001 TYR C 249 ARG 0.004 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 1.256 Fit side-chains REVERT: A 309 ARG cc_start: 0.8779 (mtp180) cc_final: 0.8127 (ttt180) REVERT: C 142 MET cc_start: 0.8106 (mmp) cc_final: 0.7896 (mmm) REVERT: C 200 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8776 (tm-30) REVERT: C 309 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8544 (ttt180) outliers start: 19 outliers final: 7 residues processed: 70 average time/residue: 1.5319 time to fit residues: 115.1500 Evaluate side-chains 62 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 100 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.078167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.059439 restraints weight = 17939.067| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 2.75 r_work: 0.2492 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10023 Z= 0.154 Angle : 0.474 6.577 13647 Z= 0.254 Chirality : 0.043 0.182 1725 Planarity : 0.003 0.033 1728 Dihedral : 4.647 19.498 1623 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.36 % Rotamer: Outliers : 1.58 % Allowed : 7.89 % Favored : 90.53 % 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: 1.07 (0.23), residues: 1284 helix: 1.78 (0.24), residues: 477 sheet: 0.34 (0.31), residues: 282 loop : 0.03 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 303 HIS 0.002 0.001 HIS A 130 PHE 0.009 0.001 PHE B 277 TYR 0.014 0.001 TYR C 249 ARG 0.004 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 1.158 Fit side-chains REVERT: A 309 ARG cc_start: 0.8760 (mtp180) cc_final: 0.8134 (ttt180) REVERT: C 142 MET cc_start: 0.8135 (mmp) cc_final: 0.7934 (mmm) REVERT: C 309 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8585 (ttt180) REVERT: C 451 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8309 (mm) outliers start: 17 outliers final: 6 residues processed: 70 average time/residue: 1.3854 time to fit residues: 104.8851 Evaluate side-chains 58 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 451 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 96 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.058472 restraints weight = 18382.303| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 2.78 r_work: 0.2475 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10023 Z= 0.212 Angle : 0.489 6.260 13647 Z= 0.261 Chirality : 0.044 0.170 1725 Planarity : 0.003 0.033 1728 Dihedral : 4.499 21.626 1623 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.71 % Favored : 98.05 % Rotamer: Outliers : 1.30 % Allowed : 8.64 % Favored : 90.06 % 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: 1.09 (0.23), residues: 1284 helix: 1.81 (0.24), residues: 477 sheet: 0.32 (0.31), residues: 282 loop : 0.05 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 303 HIS 0.002 0.000 HIS A 130 PHE 0.009 0.001 PHE B 277 TYR 0.014 0.001 TYR A 249 ARG 0.004 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.201 Fit side-chains REVERT: A 79 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8597 (ttmm) REVERT: A 309 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8151 (ttt180) REVERT: A 390 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8635 (mmt) REVERT: C 142 MET cc_start: 0.8189 (mmp) cc_final: 0.7944 (mmm) REVERT: C 309 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8563 (ttt180) REVERT: C 451 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8313 (mm) outliers start: 14 outliers final: 6 residues processed: 61 average time/residue: 1.4568 time to fit residues: 96.0391 Evaluate side-chains 61 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 451 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 109 optimal weight: 0.0000 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.078264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.059184 restraints weight = 17922.121| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 2.78 r_work: 0.2487 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10023 Z= 0.173 Angle : 0.469 5.329 13647 Z= 0.251 Chirality : 0.043 0.155 1725 Planarity : 0.003 0.031 1728 Dihedral : 4.348 20.327 1623 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.32 % Favored : 98.44 % Rotamer: Outliers : 1.30 % Allowed : 8.73 % Favored : 89.97 % 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: 1.17 (0.24), residues: 1284 helix: 1.83 (0.24), residues: 483 sheet: 0.37 (0.31), residues: 282 loop : 0.11 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 PHE 0.008 0.001 PHE B 277 TYR 0.013 0.001 TYR A 249 ARG 0.003 0.000 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 1.215 Fit side-chains REVERT: B 241 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8567 (mtt) REVERT: B 454 GLN cc_start: 0.8110 (mt0) cc_final: 0.7036 (mp10) REVERT: A 79 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8624 (ttmm) REVERT: A 309 ARG cc_start: 0.8748 (mtp180) cc_final: 0.8105 (ttt180) REVERT: C 309 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8599 (ttt180) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 1.3099 time to fit residues: 88.3560 Evaluate side-chains 61 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 0.0670 chunk 97 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.078024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.059533 restraints weight = 18307.003| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 2.74 r_work: 0.2490 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10023 Z= 0.167 Angle : 0.472 6.521 13647 Z= 0.252 Chirality : 0.043 0.148 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.268 19.626 1623 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.32 % Favored : 98.44 % Rotamer: Outliers : 1.02 % Allowed : 9.29 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1284 helix: 1.85 (0.24), residues: 483 sheet: 0.39 (0.31), residues: 282 loop : 0.13 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 PHE 0.009 0.001 PHE B 277 TYR 0.013 0.001 TYR C 249 ARG 0.003 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 1.187 Fit side-chains REVERT: B 241 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8532 (mtt) REVERT: A 79 LYS cc_start: 0.8845 (ttmm) cc_final: 0.8614 (ttmm) REVERT: A 274 GLU cc_start: 0.8995 (tt0) cc_final: 0.8748 (tt0) REVERT: A 309 ARG cc_start: 0.8743 (mtp180) cc_final: 0.8106 (ttt180) REVERT: C 309 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8603 (ttt180) outliers start: 11 outliers final: 5 residues processed: 62 average time/residue: 1.3590 time to fit residues: 91.5200 Evaluate side-chains 59 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.077664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.058688 restraints weight = 18011.805| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 2.76 r_work: 0.2477 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10023 Z= 0.196 Angle : 0.483 7.622 13647 Z= 0.258 Chirality : 0.044 0.152 1725 Planarity : 0.003 0.031 1728 Dihedral : 4.264 19.350 1623 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.64 % Favored : 98.13 % Rotamer: Outliers : 0.56 % Allowed : 10.12 % Favored : 89.32 % 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: 1.17 (0.24), residues: 1284 helix: 1.84 (0.24), residues: 483 sheet: 0.34 (0.31), residues: 282 loop : 0.14 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS C 130 PHE 0.009 0.001 PHE B 277 TYR 0.013 0.001 TYR A 249 ARG 0.003 0.000 ARG A 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: B 241 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8589 (mtt) REVERT: B 454 GLN cc_start: 0.8122 (mt0) cc_final: 0.7024 (mp10) REVERT: A 79 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8649 (ttmm) REVERT: A 274 GLU cc_start: 0.8994 (tt0) cc_final: 0.8741 (tt0) REVERT: A 309 ARG cc_start: 0.8762 (mtp180) cc_final: 0.8134 (ttt180) REVERT: C 309 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8627 (ttt180) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 1.4011 time to fit residues: 91.4234 Evaluate side-chains 59 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.078289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.059461 restraints weight = 17943.998| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 2.74 r_work: 0.2492 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10023 Z= 0.176 Angle : 0.491 10.872 13647 Z= 0.260 Chirality : 0.043 0.149 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.231 18.677 1623 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.25 % Favored : 98.52 % Rotamer: Outliers : 0.74 % Allowed : 9.94 % Favored : 89.32 % 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: 1.22 (0.24), residues: 1284 helix: 1.87 (0.24), residues: 483 sheet: 0.37 (0.31), residues: 282 loop : 0.16 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 PHE 0.009 0.001 PHE B 277 TYR 0.013 0.001 TYR A 249 ARG 0.004 0.000 ARG A 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4945.98 seconds wall clock time: 88 minutes 43.95 seconds (5323.95 seconds total)