Starting phenix.real_space_refine on Sun Jun 15 02:27:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsp_29421/06_2025/8fsp_29421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsp_29421/06_2025/8fsp_29421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fsp_29421/06_2025/8fsp_29421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsp_29421/06_2025/8fsp_29421.map" model { file = "/net/cci-nas-00/data/ceres_data/8fsp_29421/06_2025/8fsp_29421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsp_29421/06_2025/8fsp_29421_neut.cif" } resolution = 3.79 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= 0.002 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 45 5.16 5 C 10985 2.51 5 N 2710 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16685 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 11.02, per 1000 atoms: 0.66 Number of scatterers: 16685 At special positions: 0 Unit cell: (103.4, 101.2, 169.4, 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 45 16.00 O 2945 8.00 N 2710 7.00 C 10985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 135 " distance=0.00 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 149 " distance=0.00 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 243 " distance=0.00 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 290 " distance=0.00 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " 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 NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG A 502 " - " ASN A 148 " " NAG A 503 " - " ASN A 164 " " NAG B 501 " - " ASN B 82 " " NAG B 502 " - " ASN B 148 " " NAG B 503 " - " ASN B 164 " " NAG C 501 " - " ASN C 82 " " NAG C 502 " - " ASN C 148 " " NAG C 503 " - " ASN C 164 " " NAG D 501 " - " ASN D 82 " " NAG D 502 " - " ASN D 148 " " NAG D 503 " - " ASN D 164 " " NAG E 502 " - " ASN E 82 " " NAG E 503 " - " ASN E 148 " " NAG E 504 " - " ASN E 164 " Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 1.9 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 45.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.558A pdb=" N ALA A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.730A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 removed outlier: 4.048A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 247 through 273 removed outlier: 3.975A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 310 removed outlier: 3.835A pdb=" N VAL A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'A' and resid 398 through 426 removed outlier: 3.541A pdb=" N SER A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 Processing helix chain 'A' and resid 433 through 463 Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.558A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.730A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 removed outlier: 4.049A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 247 through 273 removed outlier: 3.974A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 310 removed outlier: 3.835A pdb=" N VAL B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 332 Processing helix chain 'B' and resid 398 through 426 removed outlier: 3.540A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 433 through 463 Processing helix chain 'C' and resid 10 through 21 removed outlier: 3.559A pdb=" N ALA C 21 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.730A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 235 removed outlier: 4.048A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 247 through 273 removed outlier: 3.975A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 269 " --> pdb=" O PHE C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 310 removed outlier: 3.836A pdb=" N VAL C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 398 through 426 removed outlier: 3.540A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 433 through 463 Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.558A pdb=" N ALA D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.730A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 235 removed outlier: 4.048A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 247 through 273 removed outlier: 3.974A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 310 removed outlier: 3.835A pdb=" N VAL D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'D' and resid 398 through 426 removed outlier: 3.540A pdb=" N SER D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 432 Processing helix chain 'D' and resid 433 through 463 Processing helix chain 'E' and resid 10 through 21 removed outlier: 3.558A pdb=" N ALA E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.730A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 235 removed outlier: 4.048A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 236 through 241 Processing helix chain 'E' and resid 247 through 273 removed outlier: 3.974A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 310 removed outlier: 3.836A pdb=" N VAL E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 332 Processing helix chain 'E' and resid 398 through 426 removed outlier: 3.540A pdb=" N SER E 407 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS E 411 " --> pdb=" O SER E 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 433 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 7.069A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.102A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 209 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 197 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 88 removed outlier: 7.069A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.102A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B 209 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 197 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 88 removed outlier: 7.069A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.102A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 209 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 197 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 87 through 88 removed outlier: 7.069A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.102A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 209 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 197 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 88 removed outlier: 7.069A pdb=" N VAL E 57 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN E 50 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.103A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU E 209 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS E 197 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2415 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: 4.85 Time building geometry restraints manager: 4.57 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: 2580 1.32 - 1.44: 4915 1.44 - 1.57: 9590 1.57 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 17155 Sorted by residual: bond pdb=" CA ALA D 208 " pdb=" CB ALA D 208 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.54e-02 4.22e+03 3.18e+01 bond pdb=" CA ALA C 208 " pdb=" CB ALA C 208 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.54e-02 4.22e+03 3.17e+01 bond pdb=" CA ALA E 208 " pdb=" CB ALA E 208 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.54e-02 4.22e+03 3.17e+01 bond pdb=" CA ALA A 208 " pdb=" CB ALA A 208 " ideal model delta sigma weight residual 1.528 1.442 0.086 1.54e-02 4.22e+03 3.15e+01 bond pdb=" CA ALA B 208 " pdb=" CB ALA B 208 " ideal model delta sigma weight residual 1.528 1.442 0.086 1.54e-02 4.22e+03 3.15e+01 ... (remaining 17150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 22548 2.25 - 4.50: 710 4.50 - 6.76: 137 6.76 - 9.01: 36 9.01 - 11.26: 24 Bond angle restraints: 23455 Sorted by residual: angle pdb=" N ASP A 202 " pdb=" CA ASP A 202 " pdb=" C ASP A 202 " ideal model delta sigma weight residual 110.61 121.73 -11.12 1.25e+00 6.40e-01 7.92e+01 angle pdb=" N ASP B 202 " pdb=" CA ASP B 202 " pdb=" C ASP B 202 " ideal model delta sigma weight residual 110.61 121.73 -11.12 1.25e+00 6.40e-01 7.91e+01 angle pdb=" N ASP C 202 " pdb=" CA ASP C 202 " pdb=" C ASP C 202 " ideal model delta sigma weight residual 110.61 121.72 -11.11 1.25e+00 6.40e-01 7.90e+01 angle pdb=" N ASP D 202 " pdb=" CA ASP D 202 " pdb=" C ASP D 202 " ideal model delta sigma weight residual 110.61 121.68 -11.07 1.25e+00 6.40e-01 7.84e+01 angle pdb=" N ASP E 202 " pdb=" CA ASP E 202 " pdb=" C ASP E 202 " ideal model delta sigma weight residual 110.61 121.66 -11.05 1.25e+00 6.40e-01 7.82e+01 ... (remaining 23450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 10151 34.00 - 68.00: 199 68.00 - 102.00: 30 102.00 - 136.01: 0 136.01 - 170.01: 15 Dihedral angle restraints: 10395 sinusoidal: 4500 harmonic: 5895 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 131.99 -38.99 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 131.98 -38.98 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 131.98 -38.98 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 10392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2362 0.077 - 0.153: 348 0.153 - 0.230: 25 0.230 - 0.306: 10 0.306 - 0.383: 5 Chirality restraints: 2750 Sorted by residual: chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 82 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG E 502 " pdb=" ND2 ASN E 82 " pdb=" C2 NAG E 502 " pdb=" O5 NAG E 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 2747 not shown) Planarity restraints: 2865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " 0.078 2.00e-02 2.50e+03 6.45e-02 5.21e+01 pdb=" C7 NAG B 501 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " 0.059 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.078 2.00e-02 2.50e+03 6.45e-02 5.21e+01 pdb=" C7 NAG D 501 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.059 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 501 " 0.078 2.00e-02 2.50e+03 6.44e-02 5.19e+01 pdb=" C7 NAG C 501 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG C 501 " 0.059 2.00e-02 2.50e+03 pdb=" N2 NAG C 501 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG C 501 " -0.013 2.00e-02 2.50e+03 ... (remaining 2862 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 65 2.61 - 3.18: 14000 3.18 - 3.75: 25098 3.75 - 4.33: 32468 4.33 - 4.90: 53371 Nonbonded interactions: 125002 Sorted by model distance: nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 149 " model vdw 2.034 3.760 nonbonded pdb=" NE ARG D 65 " pdb=" C5 Y82 D 504 " model vdw 2.428 3.420 nonbonded pdb=" NE ARG C 65 " pdb=" C5 Y82 C 504 " model vdw 2.429 3.420 nonbonded pdb=" NE ARG B 65 " pdb=" C5 Y82 B 504 " model vdw 2.430 3.420 nonbonded pdb=" NH2 ARG A 410 " pdb=" O GLU B 405 " model vdw 2.453 3.120 ... (remaining 124997 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'B' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'C' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'D' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'E' and (resid 7 through 465 or resid 502 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.120 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.006 0.087 17174 Z= 0.373 Angle : 0.993 11.259 23512 Z= 0.544 Chirality : 0.056 0.383 2750 Planarity : 0.006 0.065 2850 Dihedral : 15.982 170.008 6535 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -1.60 (0.19), residues: 1955 helix: 0.24 (0.19), residues: 740 sheet: -1.06 (0.25), residues: 430 loop : -2.30 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 63 HIS 0.003 0.001 HIS A 118 PHE 0.038 0.002 PHE D 287 TYR 0.010 0.002 TYR E 207 ARG 0.012 0.001 ARG B 424 Details of bonding type rmsd link_NAG-ASN : bond 0.01347 ( 15) link_NAG-ASN : angle 2.69475 ( 45) hydrogen bonds : bond 0.12878 ( 815) hydrogen bonds : angle 6.29894 ( 2415) SS BOND : bond 0.00332 ( 4) SS BOND : angle 1.96346 ( 12) covalent geometry : bond 0.00598 (17155) covalent geometry : angle 0.98666 (23455) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.903 Fit side-chains REVERT: A 254 PHE cc_start: 0.7595 (m-10) cc_final: 0.7328 (t80) REVERT: B 254 PHE cc_start: 0.7747 (m-10) cc_final: 0.7227 (t80) REVERT: C 254 PHE cc_start: 0.7735 (m-10) cc_final: 0.7278 (t80) REVERT: D 254 PHE cc_start: 0.8015 (m-10) cc_final: 0.7421 (t80) REVERT: E 254 PHE cc_start: 0.7806 (m-10) cc_final: 0.7212 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2287 time to fit residues: 33.1653 Evaluate side-chains 55 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0570 chunk 147 optimal weight: 0.0270 chunk 82 optimal weight: 0.0570 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 124 GLN C 124 GLN D 124 GLN E 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.098982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.066264 restraints weight = 55480.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.067617 restraints weight = 32594.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.068453 restraints weight = 23706.490| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17174 Z= 0.136 Angle : 0.630 7.676 23512 Z= 0.313 Chirality : 0.042 0.172 2750 Planarity : 0.004 0.050 2850 Dihedral : 13.371 156.407 2645 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.05 % Allowed : 6.94 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.19), residues: 1955 helix: 1.19 (0.19), residues: 785 sheet: -1.19 (0.25), residues: 415 loop : -1.72 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 68 HIS 0.002 0.000 HIS B 158 PHE 0.019 0.001 PHE C 287 TYR 0.013 0.001 TYR D 441 ARG 0.004 0.000 ARG C 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 15) link_NAG-ASN : angle 1.57806 ( 45) hydrogen bonds : bond 0.04973 ( 815) hydrogen bonds : angle 5.02465 ( 2415) SS BOND : bond 0.00014 ( 4) SS BOND : angle 0.89591 ( 12) covalent geometry : bond 0.00312 (17155) covalent geometry : angle 0.62622 (23455) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 1.971 Fit side-chains REVERT: B 254 PHE cc_start: 0.7477 (m-10) cc_final: 0.7128 (t80) REVERT: C 254 PHE cc_start: 0.7403 (m-10) cc_final: 0.7015 (t80) REVERT: D 254 PHE cc_start: 0.7835 (m-10) cc_final: 0.7327 (t80) REVERT: E 254 PHE cc_start: 0.7503 (m-10) cc_final: 0.7012 (t80) REVERT: E 411 HIS cc_start: 0.5760 (p90) cc_final: 0.5418 (p90) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.2394 time to fit residues: 29.1635 Evaluate side-chains 57 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 140 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 179 optimal weight: 40.0000 chunk 69 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS B 118 HIS C 118 HIS D 118 HIS E 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.093044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059751 restraints weight = 55574.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061036 restraints weight = 32807.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061783 restraints weight = 24150.639| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 17174 Z= 0.380 Angle : 0.832 11.595 23512 Z= 0.410 Chirality : 0.046 0.162 2750 Planarity : 0.005 0.048 2850 Dihedral : 13.465 155.093 2645 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.25 % Allowed : 10.46 % Favored : 88.29 % 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: -0.86 (0.19), residues: 1955 helix: 1.12 (0.18), residues: 785 sheet: -1.27 (0.23), residues: 475 loop : -1.98 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 75 HIS 0.006 0.001 HIS D 118 PHE 0.021 0.003 PHE B 142 TYR 0.023 0.002 TYR D 64 ARG 0.003 0.001 ARG E 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 15) link_NAG-ASN : angle 2.08067 ( 45) hydrogen bonds : bond 0.05785 ( 815) hydrogen bonds : angle 5.33384 ( 2415) SS BOND : bond 0.00584 ( 4) SS BOND : angle 0.84432 ( 12) covalent geometry : bond 0.00897 (17155) covalent geometry : angle 0.82753 (23455) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 2.002 Fit side-chains REVERT: A 411 HIS cc_start: 0.5933 (p90) cc_final: 0.5559 (p90) REVERT: B 116 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8279 (m-10) REVERT: B 411 HIS cc_start: 0.5691 (p90) cc_final: 0.5483 (p90) REVERT: C 103 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7150 (m-10) REVERT: C 411 HIS cc_start: 0.5924 (p90) cc_final: 0.5627 (p90) REVERT: D 411 HIS cc_start: 0.5760 (p90) cc_final: 0.5554 (p90) REVERT: E 411 HIS cc_start: 0.5684 (p90) cc_final: 0.5443 (p90) outliers start: 23 outliers final: 13 residues processed: 87 average time/residue: 0.2276 time to fit residues: 34.7862 Evaluate side-chains 74 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 111 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.095128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061538 restraints weight = 55316.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.062875 restraints weight = 32519.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063715 restraints weight = 23775.940| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17174 Z= 0.159 Angle : 0.633 10.220 23512 Z= 0.311 Chirality : 0.042 0.148 2750 Planarity : 0.004 0.044 2850 Dihedral : 13.289 156.419 2645 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.36 % Allowed : 12.63 % Favored : 86.02 % 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: -0.46 (0.19), residues: 1955 helix: 1.62 (0.19), residues: 775 sheet: -1.21 (0.23), residues: 425 loop : -1.82 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.002 0.001 HIS D 118 PHE 0.020 0.001 PHE C 287 TYR 0.016 0.001 TYR B 64 ARG 0.003 0.000 ARG C 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 15) link_NAG-ASN : angle 1.67981 ( 45) hydrogen bonds : bond 0.04786 ( 815) hydrogen bonds : angle 4.92317 ( 2415) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.33157 ( 12) covalent geometry : bond 0.00366 (17155) covalent geometry : angle 0.62936 (23455) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 2.031 Fit side-chains REVERT: A 411 HIS cc_start: 0.5799 (p90) cc_final: 0.5444 (p90) REVERT: A 442 LEU cc_start: 0.7523 (mt) cc_final: 0.7229 (pp) REVERT: C 411 HIS cc_start: 0.5958 (p90) cc_final: 0.5743 (p90) outliers start: 25 outliers final: 14 residues processed: 85 average time/residue: 0.2237 time to fit residues: 33.4501 Evaluate side-chains 76 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 15 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.094287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060760 restraints weight = 55893.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.062024 restraints weight = 32658.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062849 restraints weight = 23909.373| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17174 Z= 0.197 Angle : 0.652 10.928 23512 Z= 0.319 Chirality : 0.042 0.151 2750 Planarity : 0.004 0.042 2850 Dihedral : 13.197 155.936 2645 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.46 % Allowed : 13.66 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1955 helix: 1.73 (0.18), residues: 775 sheet: -1.24 (0.22), residues: 500 loop : -1.68 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 320 HIS 0.002 0.001 HIS C 158 PHE 0.018 0.002 PHE C 287 TYR 0.017 0.001 TYR B 64 ARG 0.003 0.000 ARG D 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 15) link_NAG-ASN : angle 1.71668 ( 45) hydrogen bonds : bond 0.04789 ( 815) hydrogen bonds : angle 4.87857 ( 2415) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.35386 ( 12) covalent geometry : bond 0.00460 (17155) covalent geometry : angle 0.64840 (23455) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 1.760 Fit side-chains REVERT: A 411 HIS cc_start: 0.5883 (p90) cc_final: 0.5629 (p90) REVERT: B 116 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8445 (m-10) REVERT: D 442 LEU cc_start: 0.7563 (mt) cc_final: 0.7209 (pp) outliers start: 27 outliers final: 20 residues processed: 87 average time/residue: 0.2121 time to fit residues: 32.3843 Evaluate side-chains 84 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 121 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 148 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.095417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.062087 restraints weight = 55451.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063428 restraints weight = 32331.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.064285 restraints weight = 23467.391| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17174 Z= 0.128 Angle : 0.595 10.045 23512 Z= 0.291 Chirality : 0.042 0.176 2750 Planarity : 0.004 0.042 2850 Dihedral : 13.150 156.407 2645 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.41 % Allowed : 14.25 % Favored : 84.34 % 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: -0.18 (0.20), residues: 1955 helix: 1.86 (0.18), residues: 775 sheet: -1.15 (0.22), residues: 495 loop : -1.58 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 68 HIS 0.002 0.001 HIS D 411 PHE 0.018 0.001 PHE D 287 TYR 0.015 0.001 TYR A 67 ARG 0.003 0.000 ARG C 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 15) link_NAG-ASN : angle 1.49981 ( 45) hydrogen bonds : bond 0.04393 ( 815) hydrogen bonds : angle 4.67646 ( 2415) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.35034 ( 12) covalent geometry : bond 0.00293 (17155) covalent geometry : angle 0.59188 (23455) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 1.792 Fit side-chains REVERT: A 411 HIS cc_start: 0.5795 (p90) cc_final: 0.5566 (p-80) REVERT: B 442 LEU cc_start: 0.7500 (mt) cc_final: 0.7163 (pp) REVERT: C 442 LEU cc_start: 0.7584 (mt) cc_final: 0.7240 (pp) REVERT: E 442 LEU cc_start: 0.7700 (mt) cc_final: 0.7303 (pp) REVERT: E 465 LEU cc_start: 0.5264 (OUTLIER) cc_final: 0.4296 (tp) outliers start: 26 outliers final: 7 residues processed: 88 average time/residue: 0.2432 time to fit residues: 36.3011 Evaluate side-chains 72 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 461 TYR Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 53 optimal weight: 7.9990 chunk 183 optimal weight: 0.0370 chunk 131 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.094754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.061246 restraints weight = 55240.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.062560 restraints weight = 32431.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.063406 restraints weight = 23577.504| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17174 Z= 0.145 Angle : 0.614 10.178 23512 Z= 0.300 Chirality : 0.042 0.186 2750 Planarity : 0.004 0.042 2850 Dihedral : 13.109 156.211 2645 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.79 % Allowed : 14.47 % Favored : 83.74 % 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: -0.12 (0.20), residues: 1955 helix: 1.84 (0.18), residues: 780 sheet: -1.16 (0.22), residues: 490 loop : -1.47 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.002 0.001 HIS E 411 PHE 0.018 0.001 PHE E 287 TYR 0.015 0.001 TYR D 67 ARG 0.007 0.000 ARG D 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 15) link_NAG-ASN : angle 1.52027 ( 45) hydrogen bonds : bond 0.04394 ( 815) hydrogen bonds : angle 4.64989 ( 2415) SS BOND : bond 0.00444 ( 4) SS BOND : angle 1.81040 ( 12) covalent geometry : bond 0.00337 (17155) covalent geometry : angle 0.61002 (23455) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 1.944 Fit side-chains REVERT: A 411 HIS cc_start: 0.5804 (p90) cc_final: 0.5422 (p-80) REVERT: B 442 LEU cc_start: 0.7556 (mt) cc_final: 0.7210 (pp) REVERT: B 465 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5612 (pp) REVERT: C 103 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6908 (m-10) REVERT: C 442 LEU cc_start: 0.7687 (mt) cc_final: 0.7404 (pp) REVERT: D 442 LEU cc_start: 0.7568 (mt) cc_final: 0.7245 (pp) REVERT: D 465 LEU cc_start: 0.5342 (OUTLIER) cc_final: 0.4359 (tp) REVERT: E 442 LEU cc_start: 0.7792 (mt) cc_final: 0.7423 (pp) REVERT: E 465 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4921 (pp) outliers start: 33 outliers final: 9 residues processed: 91 average time/residue: 0.2371 time to fit residues: 36.7899 Evaluate side-chains 75 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 461 TYR Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 130 optimal weight: 0.7980 chunk 17 optimal weight: 0.0030 chunk 138 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 13 optimal weight: 0.0670 chunk 178 optimal weight: 0.0670 chunk 140 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 overall best weight: 0.3868 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.096071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.062861 restraints weight = 56308.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064311 restraints weight = 31905.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.065220 restraints weight = 22680.551| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 17174 Z= 0.111 Angle : 0.591 9.156 23512 Z= 0.287 Chirality : 0.042 0.167 2750 Planarity : 0.004 0.040 2850 Dihedral : 13.061 156.557 2645 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.19 % Allowed : 15.12 % Favored : 83.69 % 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: -0.17 (0.19), residues: 1955 helix: 1.59 (0.18), residues: 815 sheet: -1.04 (0.24), residues: 420 loop : -1.50 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 68 HIS 0.002 0.001 HIS E 119 PHE 0.017 0.001 PHE E 287 TYR 0.015 0.001 TYR D 67 ARG 0.008 0.000 ARG D 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 15) link_NAG-ASN : angle 1.31185 ( 45) hydrogen bonds : bond 0.04062 ( 815) hydrogen bonds : angle 4.50103 ( 2415) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.72253 ( 12) covalent geometry : bond 0.00247 (17155) covalent geometry : angle 0.58877 (23455) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.848 Fit side-chains REVERT: A 131 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9149 (mm) REVERT: A 411 HIS cc_start: 0.5677 (p90) cc_final: 0.5473 (p90) REVERT: B 442 LEU cc_start: 0.7672 (mt) cc_final: 0.7383 (pp) REVERT: B 465 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5682 (pp) REVERT: C 442 LEU cc_start: 0.7649 (mt) cc_final: 0.7408 (pp) REVERT: D 442 LEU cc_start: 0.7456 (mt) cc_final: 0.7216 (pp) REVERT: E 442 LEU cc_start: 0.7734 (mt) cc_final: 0.7451 (pp) REVERT: E 465 LEU cc_start: 0.5108 (OUTLIER) cc_final: 0.4899 (pp) outliers start: 22 outliers final: 8 residues processed: 90 average time/residue: 0.2641 time to fit residues: 38.3693 Evaluate side-chains 76 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 178 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.093297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059814 restraints weight = 56310.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061172 restraints weight = 32251.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062035 restraints weight = 23259.746| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17174 Z= 0.228 Angle : 0.671 10.752 23512 Z= 0.325 Chirality : 0.043 0.196 2750 Planarity : 0.004 0.044 2850 Dihedral : 13.161 156.091 2645 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.25 % Allowed : 15.66 % Favored : 83.09 % 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: -0.24 (0.20), residues: 1955 helix: 1.60 (0.18), residues: 815 sheet: -1.32 (0.22), residues: 475 loop : -1.41 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 320 HIS 0.003 0.001 HIS E 411 PHE 0.022 0.002 PHE A 254 TYR 0.020 0.002 TYR B 64 ARG 0.007 0.000 ARG A 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 15) link_NAG-ASN : angle 1.62205 ( 45) hydrogen bonds : bond 0.04524 ( 815) hydrogen bonds : angle 4.74390 ( 2415) SS BOND : bond 0.00279 ( 4) SS BOND : angle 1.02544 ( 12) covalent geometry : bond 0.00536 (17155) covalent geometry : angle 0.66739 (23455) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 1.953 Fit side-chains REVERT: A 411 HIS cc_start: 0.5759 (p90) cc_final: 0.5432 (p90) REVERT: B 465 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5968 (pp) REVERT: C 103 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7117 (m-10) REVERT: C 131 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8915 (mm) REVERT: D 442 LEU cc_start: 0.7645 (mt) cc_final: 0.7317 (pp) REVERT: E 465 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.5431 (pp) outliers start: 23 outliers final: 11 residues processed: 83 average time/residue: 0.2217 time to fit residues: 32.3146 Evaluate side-chains 76 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 461 TYR Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 36 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 178 optimal weight: 0.0570 chunk 28 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.8080 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.093946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.060917 restraints weight = 55612.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.062255 restraints weight = 32457.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063067 restraints weight = 23538.189| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17174 Z= 0.160 Angle : 0.655 10.418 23512 Z= 0.313 Chirality : 0.043 0.253 2750 Planarity : 0.004 0.042 2850 Dihedral : 13.161 156.243 2645 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.98 % Allowed : 16.31 % Favored : 82.71 % 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: -0.18 (0.20), residues: 1955 helix: 1.68 (0.18), residues: 815 sheet: -1.24 (0.23), residues: 475 loop : -1.48 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 320 HIS 0.002 0.001 HIS C 158 PHE 0.022 0.002 PHE A 254 TYR 0.015 0.001 TYR B 64 ARG 0.006 0.000 ARG E 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 15) link_NAG-ASN : angle 1.53677 ( 45) hydrogen bonds : bond 0.04365 ( 815) hydrogen bonds : angle 4.72514 ( 2415) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.83161 ( 12) covalent geometry : bond 0.00371 (17155) covalent geometry : angle 0.65222 (23455) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 2.049 Fit side-chains REVERT: A 411 HIS cc_start: 0.5680 (p90) cc_final: 0.5361 (p90) REVERT: B 465 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.6031 (pp) REVERT: C 103 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7114 (m-10) REVERT: C 131 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8909 (mm) REVERT: D 442 LEU cc_start: 0.7635 (mt) cc_final: 0.7340 (pp) REVERT: E 465 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5517 (pp) outliers start: 18 outliers final: 12 residues processed: 77 average time/residue: 0.2262 time to fit residues: 30.9306 Evaluate side-chains 79 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 461 TYR Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 92 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.094075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.060995 restraints weight = 55532.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062371 restraints weight = 31626.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063242 restraints weight = 22644.132| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17174 Z= 0.152 Angle : 0.654 10.923 23512 Z= 0.310 Chirality : 0.044 0.356 2750 Planarity : 0.004 0.042 2850 Dihedral : 13.125 156.207 2645 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.30 % Allowed : 16.21 % Favored : 82.49 % 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: -0.16 (0.20), residues: 1955 helix: 1.72 (0.18), residues: 815 sheet: -1.30 (0.24), residues: 415 loop : -1.46 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 320 HIS 0.002 0.001 HIS E 158 PHE 0.019 0.002 PHE A 254 TYR 0.015 0.001 TYR D 67 ARG 0.006 0.000 ARG E 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 15) link_NAG-ASN : angle 1.43733 ( 45) hydrogen bonds : bond 0.04274 ( 815) hydrogen bonds : angle 4.70333 ( 2415) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.76639 ( 12) covalent geometry : bond 0.00353 (17155) covalent geometry : angle 0.65121 (23455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4826.77 seconds wall clock time: 84 minutes 34.24 seconds (5074.24 seconds total)