Starting phenix.real_space_refine on Wed Feb 4 11:13:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvf_41640/02_2026/8tvf_41640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvf_41640/02_2026/8tvf_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_2026/8tvf_41640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvf_41640/02_2026/8tvf_41640.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvf_41640/02_2026/8tvf_41640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvf_41640/02_2026/8tvf_41640.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10461 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" 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: "D" 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: "B" 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: A, C, E, F Time building chain proxies: 2.81, per 1000 atoms: 0.27 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=15, 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 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.18 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.18 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.08 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.08 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 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: 0.94 Conformation dependent library (CDL) restraints added in 421.4 milliseconds 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: 0.44 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: 1.42 Time building geometry restraints manager: 1.22 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: 6084 21.32 - 42.64: 129 42.64 - 63.95: 48 63.95 - 85.27: 18 85.27 - 106.59: 18 Dihedral angle restraints: 6297 sinusoidal: 2538 harmonic: 3759 Sorted by residual: dihedral pdb=" CB CYS A 66 " pdb=" SG CYS A 66 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual -86.00 -40.01 -45.99 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 187 " pdb=" CB CYS C 187 " ideal model delta sinusoidal sigma weight residual -86.00 -40.01 -45.99 1 1.00e+01 1.00e-02 2.93e+01 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 ... (remaining 6294 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: 2.37 - 2.88: 3548 2.88 - 3.38: 9629 3.38 - 3.89: 18208 3.89 - 4.39: 21164 4.39 - 4.90: 34074 Nonbonded interactions: 86623 Sorted by model distance: nonbonded pdb=" OD1 ASP C 61 " pdb=" NE ARG C 64 " model vdw 2.371 3.120 nonbonded pdb=" OD1 ASP A 61 " pdb=" NE ARG A 64 " model vdw 2.371 3.120 nonbonded pdb=" OD1 ASP B 61 " pdb=" NE ARG B 64 " model vdw 2.372 3.120 nonbonded pdb=" N VAL B 368 " pdb=" O VAL B 368 " model vdw 2.498 2.496 nonbonded pdb=" N VAL A 368 " pdb=" O VAL A 368 " model vdw 2.498 2.496 ... (remaining 86618 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 1.800 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- 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 0.153 10050 Z= 0.776 Angle : 1.379 10.340 13713 Z= 0.931 Chirality : 0.092 0.448 1725 Planarity : 0.005 0.020 1728 Dihedral : 12.896 106.589 3834 Min Nonbonded Distance : 2.371 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (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 ARG 0.004 0.001 ARG A 258 TYR 0.030 0.006 TYR B 41 PHE 0.011 0.004 PHE C 71 TRP 0.006 0.005 TRP C 303 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.01404 (10023) covalent geometry : angle 1.35705 (13647) SS BOND : bond 0.07138 ( 15) SS BOND : angle 3.84434 ( 30) hydrogen bonds : bond 0.18699 ( 496) hydrogen bonds : angle 6.73440 ( 1317) link_BETA1-4 : bond 0.06517 ( 6) link_BETA1-4 : angle 4.56883 ( 18) link_NAG-ASN : bond 0.06705 ( 6) link_NAG-ASN : angle 2.72023 ( 18) *********************** 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 : 0.420 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 116 average time/residue: 0.9875 time to fit residues: 119.8826 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 : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN B 454 GLN A 260 ASN C 260 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.080219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.061339 restraints weight = 17770.051| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 2.69 r_work: 0.2521 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10050 Z= 0.152 Angle : 0.630 8.959 13713 Z= 0.329 Chirality : 0.046 0.136 1725 Planarity : 0.004 0.043 1728 Dihedral : 9.973 71.155 1623 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.37 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1284 helix: 1.29 (0.24), residues: 483 sheet: 0.27 (0.30), residues: 267 loop : 0.10 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 64 TYR 0.020 0.002 TYR C 249 PHE 0.016 0.002 PHE A 230 TRP 0.003 0.001 TRP C 303 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00341 (10023) covalent geometry : angle 0.60508 (13647) SS BOND : bond 0.00479 ( 15) SS BOND : angle 1.53895 ( 30) hydrogen bonds : bond 0.05238 ( 496) hydrogen bonds : angle 4.65999 ( 1317) link_BETA1-4 : bond 0.00745 ( 6) link_BETA1-4 : angle 4.18310 ( 18) link_NAG-ASN : bond 0.00916 ( 6) link_NAG-ASN : angle 1.81734 ( 18) *********************** 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 80 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.429 Fit side-chains REVERT: B 200 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8733 (tm-30) outliers start: 13 outliers final: 4 residues processed: 71 average time/residue: 0.7648 time to fit residues: 57.9434 Evaluate side-chains 59 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 A 320 ASN C 177 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.078783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.059911 restraints weight = 18010.386| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 2.73 r_work: 0.2488 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10050 Z= 0.131 Angle : 0.552 8.297 13713 Z= 0.286 Chirality : 0.045 0.162 1725 Planarity : 0.003 0.038 1728 Dihedral : 6.966 59.336 1623 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 0.62 % Favored : 99.14 % Rotamer: Outliers : 0.93 % Allowed : 6.50 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.23), residues: 1284 helix: 1.55 (0.24), residues: 483 sheet: 0.50 (0.29), residues: 297 loop : 0.17 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 64 TYR 0.016 0.001 TYR A 249 PHE 0.011 0.002 PHE C 277 TRP 0.001 0.000 TRP B 303 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00302 (10023) covalent geometry : angle 0.53013 (13647) SS BOND : bond 0.00375 ( 15) SS BOND : angle 1.37808 ( 30) hydrogen bonds : bond 0.04364 ( 496) hydrogen bonds : angle 4.19290 ( 1317) link_BETA1-4 : bond 0.00630 ( 6) link_BETA1-4 : angle 3.72210 ( 18) link_NAG-ASN : bond 0.00637 ( 6) link_NAG-ASN : angle 1.32105 ( 18) *********************** 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 69 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.436 Fit side-chains REVERT: B 200 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8624 (tm-30) REVERT: A 309 ARG cc_start: 0.8770 (mtp180) cc_final: 0.8045 (ttt180) REVERT: C 142 MET cc_start: 0.8046 (mmp) cc_final: 0.7844 (mmm) REVERT: C 309 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8546 (ttt180) REVERT: C 454 GLN cc_start: 0.8371 (mt0) cc_final: 0.8085 (mt0) outliers start: 10 outliers final: 4 residues processed: 61 average time/residue: 0.6991 time to fit residues: 45.6914 Evaluate side-chains 57 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 367 TYR 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 8 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 A 157 GLN C 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.057871 restraints weight = 18032.888| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 2.74 r_work: 0.2457 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2306 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10050 Z= 0.153 Angle : 0.525 6.479 13713 Z= 0.278 Chirality : 0.045 0.171 1725 Planarity : 0.003 0.035 1728 Dihedral : 5.400 43.569 1623 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.32 % Favored : 98.44 % Rotamer: Outliers : 2.14 % Allowed : 5.85 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.23), residues: 1284 helix: 1.68 (0.24), residues: 483 sheet: 0.44 (0.30), residues: 297 loop : 0.12 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 64 TYR 0.017 0.002 TYR A 249 PHE 0.009 0.002 PHE A 277 TRP 0.001 0.000 TRP B 303 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00367 (10023) covalent geometry : angle 0.50905 (13647) SS BOND : bond 0.00335 ( 15) SS BOND : angle 1.42589 ( 30) hydrogen bonds : bond 0.04446 ( 496) hydrogen bonds : angle 4.15433 ( 1317) link_BETA1-4 : bond 0.00271 ( 6) link_BETA1-4 : angle 2.89253 ( 18) link_NAG-ASN : bond 0.00455 ( 6) link_NAG-ASN : angle 1.23372 ( 18) *********************** 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 85 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.433 Fit side-chains REVERT: B 200 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8762 (tm-30) REVERT: A 309 ARG cc_start: 0.8977 (mtp180) cc_final: 0.8297 (ttt180) REVERT: C 142 MET cc_start: 0.8280 (mmp) cc_final: 0.8059 (mmm) REVERT: C 309 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8757 (ttt180) REVERT: C 451 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8281 (mp) outliers start: 23 outliers final: 3 residues processed: 74 average time/residue: 0.6949 time to fit residues: 54.9141 Evaluate side-chains 58 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 121 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.2963 r_free = 0.2963 target = 0.075573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.056803 restraints weight = 17925.883| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 2.72 r_work: 0.2425 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10050 Z= 0.202 Angle : 0.546 5.522 13713 Z= 0.291 Chirality : 0.046 0.166 1725 Planarity : 0.003 0.034 1728 Dihedral : 5.024 29.434 1623 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.64 % Favored : 98.13 % Rotamer: Outliers : 1.49 % Allowed : 6.87 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.23), residues: 1284 helix: 1.73 (0.24), residues: 477 sheet: 0.28 (0.30), residues: 297 loop : 0.02 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.016 0.002 TYR A 249 PHE 0.010 0.002 PHE A 234 TRP 0.002 0.001 TRP B 303 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00499 (10023) covalent geometry : angle 0.53231 (13647) SS BOND : bond 0.00580 ( 15) SS BOND : angle 1.54119 ( 30) hydrogen bonds : bond 0.04834 ( 496) hydrogen bonds : angle 4.21287 ( 1317) link_BETA1-4 : bond 0.00433 ( 6) link_BETA1-4 : angle 2.56770 ( 18) link_NAG-ASN : bond 0.00408 ( 6) link_NAG-ASN : angle 1.39960 ( 18) *********************** 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 74 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.302 Fit side-chains REVERT: B 200 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8798 (tm-30) REVERT: C 142 MET cc_start: 0.8348 (mmp) cc_final: 0.8135 (mmm) REVERT: C 309 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8805 (ttt180) outliers start: 16 outliers final: 6 residues processed: 64 average time/residue: 0.7162 time to fit residues: 49.2473 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 : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 68 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 48 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.2989 r_free = 0.2989 target = 0.077064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.058247 restraints weight = 17942.135| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 2.73 r_work: 0.2460 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10050 Z= 0.118 Angle : 0.501 7.676 13713 Z= 0.266 Chirality : 0.044 0.199 1725 Planarity : 0.003 0.033 1728 Dihedral : 4.684 19.257 1623 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.32 % Favored : 98.44 % Rotamer: Outliers : 1.30 % Allowed : 7.80 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1284 helix: 1.79 (0.24), residues: 477 sheet: 0.31 (0.30), residues: 297 loop : 0.06 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 64 TYR 0.014 0.001 TYR A 249 PHE 0.009 0.001 PHE A 277 TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00273 (10023) covalent geometry : angle 0.48677 (13647) SS BOND : bond 0.00489 ( 15) SS BOND : angle 1.62513 ( 30) hydrogen bonds : bond 0.03992 ( 496) hydrogen bonds : angle 4.07441 ( 1317) link_BETA1-4 : bond 0.00460 ( 6) link_BETA1-4 : angle 2.31668 ( 18) link_NAG-ASN : bond 0.00405 ( 6) link_NAG-ASN : angle 1.43230 ( 18) *********************** 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 73 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.411 Fit side-chains REVERT: B 200 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8835 (tm-30) REVERT: A 309 ARG cc_start: 0.8968 (mtp180) cc_final: 0.8358 (ttt180) REVERT: C 309 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8799 (ttt180) REVERT: C 451 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8267 (mm) outliers start: 14 outliers final: 5 residues processed: 64 average time/residue: 0.7357 time to fit residues: 50.4695 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 367 TYR 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 451 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.2994 r_free = 0.2994 target = 0.077323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.058416 restraints weight = 17858.596| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.73 r_work: 0.2465 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2315 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10050 Z= 0.120 Angle : 0.498 6.108 13713 Z= 0.264 Chirality : 0.044 0.170 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.535 22.371 1623 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.64 % Favored : 98.13 % Rotamer: Outliers : 1.58 % Allowed : 7.80 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.23), residues: 1284 helix: 1.83 (0.24), residues: 477 sheet: 0.37 (0.31), residues: 282 loop : -0.04 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.014 0.001 TYR A 249 PHE 0.009 0.001 PHE A 277 TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00282 (10023) covalent geometry : angle 0.48190 (13647) SS BOND : bond 0.00309 ( 15) SS BOND : angle 1.71003 ( 30) hydrogen bonds : bond 0.03894 ( 496) hydrogen bonds : angle 4.02144 ( 1317) link_BETA1-4 : bond 0.00430 ( 6) link_BETA1-4 : angle 2.20381 ( 18) link_NAG-ASN : bond 0.00399 ( 6) link_NAG-ASN : angle 1.66536 ( 18) *********************** 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 70 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.443 Fit side-chains REVERT: B 200 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8775 (tm-30) REVERT: A 309 ARG cc_start: 0.8955 (mtp180) cc_final: 0.8339 (ttt180) REVERT: C 309 ARG cc_start: 0.9035 (ttp80) cc_final: 0.8764 (ttt180) REVERT: C 451 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8231 (mm) outliers start: 17 outliers final: 7 residues processed: 62 average time/residue: 0.6943 time to fit residues: 46.3893 Evaluate side-chains 60 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLN 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 68 GLN 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 451 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.2993 r_free = 0.2993 target = 0.077007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.058588 restraints weight = 17975.523| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.71 r_work: 0.2466 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2317 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10050 Z= 0.127 Angle : 0.498 6.545 13713 Z= 0.264 Chirality : 0.044 0.152 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.477 22.543 1623 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.71 % Favored : 98.05 % Rotamer: Outliers : 1.11 % Allowed : 8.64 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.23), residues: 1284 helix: 1.76 (0.24), residues: 483 sheet: 0.37 (0.31), residues: 282 loop : -0.04 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.013 0.001 TYR A 249 PHE 0.009 0.001 PHE A 277 TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00302 (10023) covalent geometry : angle 0.48477 (13647) SS BOND : bond 0.00309 ( 15) SS BOND : angle 1.49376 ( 30) hydrogen bonds : bond 0.03931 ( 496) hydrogen bonds : angle 4.01608 ( 1317) link_BETA1-4 : bond 0.00378 ( 6) link_BETA1-4 : angle 2.14006 ( 18) link_NAG-ASN : bond 0.00399 ( 6) link_NAG-ASN : angle 1.51352 ( 18) *********************** 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 64 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.447 Fit side-chains REVERT: B 200 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8724 (tm-30) REVERT: A 309 ARG cc_start: 0.8940 (mtp180) cc_final: 0.8312 (ttt180) REVERT: C 309 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8785 (ttt180) REVERT: C 451 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8231 (mm) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 0.6935 time to fit residues: 42.6378 Evaluate side-chains 62 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 GLN 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 221 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 451 ILE 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 15 optimal weight: 0.0470 chunk 126 optimal weight: 0.0370 chunk 103 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 0.0470 overall best weight: 0.2854 ------------------------------------------------------------------------------- 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 = 0.3042 r_free = 0.3042 target = 0.079879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.061354 restraints weight = 17826.142| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.72 r_work: 0.2527 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10050 Z= 0.086 Angle : 0.468 6.957 13713 Z= 0.248 Chirality : 0.043 0.166 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.291 19.852 1623 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 0.78 % Favored : 98.99 % Rotamer: Outliers : 0.65 % Allowed : 9.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.24), residues: 1284 helix: 1.83 (0.24), residues: 483 sheet: 0.49 (0.31), residues: 282 loop : 0.05 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 131 TYR 0.012 0.001 TYR A 249 PHE 0.010 0.001 PHE B 277 TRP 0.001 0.000 TRP C 303 HIS 0.001 0.000 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00185 (10023) covalent geometry : angle 0.45655 (13647) SS BOND : bond 0.00219 ( 15) SS BOND : angle 1.19414 ( 30) hydrogen bonds : bond 0.03148 ( 496) hydrogen bonds : angle 3.83703 ( 1317) link_BETA1-4 : bond 0.00417 ( 6) link_BETA1-4 : angle 2.01825 ( 18) link_NAG-ASN : bond 0.00504 ( 6) link_NAG-ASN : angle 1.43636 ( 18) *********************** 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 63 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.425 Fit side-chains REVERT: B 454 GLN cc_start: 0.8182 (mt0) cc_final: 0.7168 (mp10) REVERT: A 274 GLU cc_start: 0.8981 (tt0) cc_final: 0.8749 (tt0) REVERT: A 309 ARG cc_start: 0.8726 (mtp180) cc_final: 0.8111 (ttt180) REVERT: C 309 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8616 (ttt180) outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 0.6854 time to fit residues: 44.3271 Evaluate side-chains 53 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain A residue 221 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.0000 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3022 r_free = 0.3022 target = 0.078973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.060076 restraints weight = 17808.561| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.76 r_work: 0.2491 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10050 Z= 0.110 Angle : 0.487 10.432 13713 Z= 0.257 Chirality : 0.043 0.146 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.262 20.152 1623 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.36 % Rotamer: Outliers : 0.46 % Allowed : 9.66 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1284 helix: 1.85 (0.24), residues: 483 sheet: 0.49 (0.31), residues: 282 loop : 0.09 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.013 0.001 TYR A 249 PHE 0.009 0.001 PHE B 277 TRP 0.001 0.000 TRP B 303 HIS 0.002 0.000 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00258 (10023) covalent geometry : angle 0.47713 (13647) SS BOND : bond 0.00301 ( 15) SS BOND : angle 1.11388 ( 30) hydrogen bonds : bond 0.03558 ( 496) hydrogen bonds : angle 3.87982 ( 1317) link_BETA1-4 : bond 0.00391 ( 6) link_BETA1-4 : angle 2.01041 ( 18) link_NAG-ASN : bond 0.00437 ( 6) link_NAG-ASN : angle 1.40256 ( 18) ********************** 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 59 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 454 GLN cc_start: 0.8005 (mt0) cc_final: 0.6863 (mp10) REVERT: A 274 GLU cc_start: 0.9001 (tt0) cc_final: 0.8758 (tt0) REVERT: A 309 ARG cc_start: 0.8732 (mtp180) cc_final: 0.8099 (ttt180) REVERT: C 274 GLU cc_start: 0.8946 (tt0) cc_final: 0.8706 (tt0) REVERT: C 309 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8628 (ttt180) outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 0.6970 time to fit residues: 43.5878 Evaluate side-chains 55 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain A residue 221 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3001 r_free = 0.3001 target = 0.077733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.058743 restraints weight = 17920.287| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 2.75 r_work: 0.2477 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10050 Z= 0.126 Angle : 0.492 6.299 13713 Z= 0.262 Chirality : 0.044 0.142 1725 Planarity : 0.003 0.032 1728 Dihedral : 4.291 19.940 1623 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.64 % Favored : 98.13 % Rotamer: Outliers : 0.37 % Allowed : 9.75 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.24), residues: 1284 helix: 1.84 (0.24), residues: 483 sheet: 0.45 (0.31), residues: 282 loop : 0.09 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.013 0.001 TYR A 249 PHE 0.008 0.001 PHE B 277 TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00301 (10023) covalent geometry : angle 0.48283 (13647) SS BOND : bond 0.00343 ( 15) SS BOND : angle 1.13385 ( 30) hydrogen bonds : bond 0.03829 ( 496) hydrogen bonds : angle 3.94131 ( 1317) link_BETA1-4 : bond 0.00423 ( 6) link_BETA1-4 : angle 1.99398 ( 18) link_NAG-ASN : bond 0.00440 ( 6) link_NAG-ASN : angle 1.36133 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.18 seconds wall clock time: 52 minutes 32.91 seconds (3152.91 seconds total)