Starting phenix.real_space_refine on Sun Aug 24 03:58:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsp_29421/08_2025/8fsp_29421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsp_29421/08_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_29421/08_2025/8fsp_29421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsp_29421/08_2025/8fsp_29421.map" model { file = "/net/cci-nas-00/data/ceres_data/8fsp_29421/08_2025/8fsp_29421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsp_29421/08_2025/8fsp_29421_neut.cif" } resolution = 3.79 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= 0.002 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.20, per 1000 atoms: 0.25 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: 1.51 Conformation dependent library (CDL) restraints added in 757.1 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.59 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: 2.96 Time building geometry restraints manager: 2.02 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: 0.05 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: 2.810 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.750 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG B 424 TYR 0.010 0.002 TYR E 207 PHE 0.038 0.002 PHE D 287 TRP 0.009 0.001 TRP E 63 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00598 (17155) covalent geometry : angle 0.98666 (23455) SS BOND : bond 0.00332 ( 4) SS BOND : angle 1.96346 ( 12) hydrogen bonds : bond 0.12878 ( 815) hydrogen bonds : angle 6.29894 ( 2415) link_NAG-ASN : bond 0.01347 ( 15) link_NAG-ASN : angle 2.69475 ( 45) *********************** 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 : 0.659 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: 0.1077 time to fit residues: 15.5147 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 : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7838 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.099493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067161 restraints weight = 54746.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.068505 restraints weight = 32243.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069405 restraints weight = 23493.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.069930 restraints weight = 19385.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.070044 restraints weight = 17356.969| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17174 Z= 0.129 Angle : 0.624 7.586 23512 Z= 0.309 Chirality : 0.042 0.183 2750 Planarity : 0.004 0.052 2850 Dihedral : 13.298 155.386 2645 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.05 % Allowed : 6.67 % Favored : 93.28 % 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 aren not related in a simple way. whole: -0.66 (0.19), residues: 1955 helix: 1.19 (0.19), residues: 785 sheet: -1.20 (0.25), residues: 415 loop : -1.71 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 410 TYR 0.013 0.001 TYR D 441 PHE 0.018 0.001 PHE A 287 TRP 0.005 0.001 TRP D 459 HIS 0.002 0.000 HIS D 158 Details of bonding type rmsd covalent geometry : bond 0.00295 (17155) covalent geometry : angle 0.62106 (23455) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.64272 ( 12) hydrogen bonds : bond 0.04822 ( 815) hydrogen bonds : angle 4.97961 ( 2415) link_NAG-ASN : bond 0.00249 ( 15) link_NAG-ASN : angle 1.54616 ( 45) *********************** 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 76 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.599 Fit side-chains REVERT: B 254 PHE cc_start: 0.7429 (m-10) cc_final: 0.7112 (t80) REVERT: C 254 PHE cc_start: 0.7324 (m-10) cc_final: 0.6972 (t80) REVERT: D 254 PHE cc_start: 0.7802 (m-10) cc_final: 0.7318 (t80) REVERT: E 254 PHE cc_start: 0.7469 (m-10) cc_final: 0.7005 (t80) REVERT: E 411 HIS cc_start: 0.5738 (p90) cc_final: 0.5401 (p90) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1028 time to fit residues: 13.6124 Evaluate side-chains 56 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 4 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.095777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062941 restraints weight = 56112.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.064270 restraints weight = 32341.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065113 restraints weight = 23486.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.065590 restraints weight = 19567.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065845 restraints weight = 17706.617| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17174 Z= 0.196 Angle : 0.668 8.886 23512 Z= 0.333 Chirality : 0.043 0.151 2750 Planarity : 0.004 0.046 2850 Dihedral : 13.122 155.631 2645 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.03 % Allowed : 10.73 % Favored : 88.24 % 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 aren not related in a simple way. whole: -0.50 (0.19), residues: 1955 helix: 1.41 (0.18), residues: 780 sheet: -1.17 (0.23), residues: 435 loop : -1.68 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 410 TYR 0.013 0.001 TYR D 64 PHE 0.020 0.002 PHE B 287 TRP 0.008 0.001 TRP E 75 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00457 (17155) covalent geometry : angle 0.66488 (23455) SS BOND : bond 0.00439 ( 4) SS BOND : angle 0.69502 ( 12) hydrogen bonds : bond 0.04947 ( 815) hydrogen bonds : angle 4.89924 ( 2415) link_NAG-ASN : bond 0.00263 ( 15) link_NAG-ASN : angle 1.62953 ( 45) *********************** 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 100 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 411 HIS cc_start: 0.5973 (p90) cc_final: 0.5729 (p90) REVERT: B 116 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8362 (m-10) REVERT: B 411 HIS cc_start: 0.5484 (p90) cc_final: 0.5199 (p90) REVERT: D 116 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8431 (m-10) REVERT: E 411 HIS cc_start: 0.5804 (p90) cc_final: 0.5503 (p90) outliers start: 19 outliers final: 9 residues processed: 93 average time/residue: 0.1098 time to fit residues: 17.0770 Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 132 VAL Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 293 LEU 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 293 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.095771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.063000 restraints weight = 55542.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064338 restraints weight = 32072.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065189 restraints weight = 23339.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065692 restraints weight = 19396.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065865 restraints weight = 17496.173| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17174 Z= 0.170 Angle : 0.626 9.323 23512 Z= 0.307 Chirality : 0.042 0.148 2750 Planarity : 0.004 0.045 2850 Dihedral : 13.146 156.228 2645 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.41 % Allowed : 11.60 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.19), residues: 1955 helix: 1.59 (0.18), residues: 790 sheet: -0.96 (0.24), residues: 420 loop : -1.61 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 410 TYR 0.015 0.001 TYR B 64 PHE 0.018 0.002 PHE C 287 TRP 0.008 0.001 TRP B 68 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00399 (17155) covalent geometry : angle 0.62248 (23455) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.32036 ( 12) hydrogen bonds : bond 0.04604 ( 815) hydrogen bonds : angle 4.79058 ( 2415) link_NAG-ASN : bond 0.00130 ( 15) link_NAG-ASN : angle 1.61177 ( 45) *********************** 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 96 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 442 LEU cc_start: 0.7468 (mt) cc_final: 0.7199 (pp) REVERT: B 411 HIS cc_start: 0.5561 (p90) cc_final: 0.5332 (p90) REVERT: C 411 HIS cc_start: 0.5787 (p90) cc_final: 0.5493 (p90) REVERT: C 442 LEU cc_start: 0.7426 (mt) cc_final: 0.7108 (pp) REVERT: D 411 HIS cc_start: 0.5709 (p90) cc_final: 0.5290 (p90) REVERT: D 442 LEU cc_start: 0.7474 (mt) cc_final: 0.7143 (pp) REVERT: E 411 HIS cc_start: 0.5502 (p90) cc_final: 0.5268 (p90) outliers start: 26 outliers final: 14 residues processed: 84 average time/residue: 0.1090 time to fit residues: 15.6469 Evaluate side-chains 79 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 235 MET 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 461 TYR Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 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 129 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 140 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.093289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059606 restraints weight = 56213.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060905 restraints weight = 33118.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061699 restraints weight = 24292.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.062127 restraints weight = 20436.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062461 restraints weight = 18601.213| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 17174 Z= 0.286 Angle : 0.743 11.726 23512 Z= 0.364 Chirality : 0.045 0.182 2750 Planarity : 0.005 0.043 2850 Dihedral : 13.362 155.937 2645 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.01 % Allowed : 12.95 % Favored : 85.04 % 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 aren not related in a simple way. whole: -0.53 (0.19), residues: 1955 helix: 1.45 (0.18), residues: 785 sheet: -1.25 (0.21), residues: 500 loop : -1.76 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 439 TYR 0.021 0.002 TYR D 64 PHE 0.018 0.002 PHE B 142 TRP 0.014 0.002 TRP B 320 HIS 0.005 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00669 (17155) covalent geometry : angle 0.73817 (23455) SS BOND : bond 0.00406 ( 4) SS BOND : angle 0.53372 ( 12) hydrogen bonds : bond 0.05234 ( 815) hydrogen bonds : angle 5.11119 ( 2415) link_NAG-ASN : bond 0.00308 ( 15) link_NAG-ASN : angle 2.02642 ( 45) *********************** 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 102 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.651 Fit side-chains REVERT: B 116 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8564 (m-10) REVERT: C 103 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7099 (m-10) REVERT: C 411 HIS cc_start: 0.6158 (p90) cc_final: 0.5754 (p90) REVERT: D 116 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8449 (m-10) REVERT: E 411 HIS cc_start: 0.5777 (p90) cc_final: 0.5547 (p90) outliers start: 37 outliers final: 20 residues processed: 92 average time/residue: 0.1086 time to fit residues: 17.1698 Evaluate side-chains 81 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 235 MET 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 442 LEU 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 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 235 MET 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 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 133 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 121 optimal weight: 0.0470 chunk 155 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.096159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.062582 restraints weight = 55697.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063949 restraints weight = 32348.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.064742 restraints weight = 23463.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065314 restraints weight = 19639.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065600 restraints weight = 17640.305| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17174 Z= 0.121 Angle : 0.604 9.769 23512 Z= 0.296 Chirality : 0.043 0.206 2750 Planarity : 0.004 0.042 2850 Dihedral : 13.202 156.537 2645 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.46 % Allowed : 14.04 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.19), residues: 1955 helix: 1.74 (0.18), residues: 785 sheet: -1.12 (0.23), residues: 470 loop : -1.67 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 410 TYR 0.015 0.001 TYR A 67 PHE 0.019 0.001 PHE D 287 TRP 0.010 0.001 TRP C 68 HIS 0.004 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00267 (17155) covalent geometry : angle 0.60160 (23455) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.50842 ( 12) hydrogen bonds : bond 0.04391 ( 815) hydrogen bonds : angle 4.70179 ( 2415) link_NAG-ASN : bond 0.00176 ( 15) link_NAG-ASN : angle 1.48191 ( 45) *********************** 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 95 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.662 Fit side-chains REVERT: A 310 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7502 (tptt) REVERT: A 442 LEU cc_start: 0.7538 (mt) cc_final: 0.7285 (pp) REVERT: B 465 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5681 (pp) REVERT: C 103 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.6940 (m-10) REVERT: C 411 HIS cc_start: 0.5911 (p90) cc_final: 0.5621 (p90) REVERT: D 411 HIS cc_start: 0.5430 (p90) cc_final: 0.5147 (p90) REVERT: D 442 LEU cc_start: 0.7351 (mt) cc_final: 0.7095 (pp) REVERT: E 442 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7352 (pp) outliers start: 27 outliers final: 12 residues processed: 86 average time/residue: 0.1403 time to fit residues: 18.9148 Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 442 LEU 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 116 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 34 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.093896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.060664 restraints weight = 55562.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.062003 restraints weight = 32520.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.062832 restraints weight = 23612.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063332 restraints weight = 19688.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063501 restraints weight = 17754.038| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17174 Z= 0.206 Angle : 0.667 10.938 23512 Z= 0.324 Chirality : 0.043 0.254 2750 Planarity : 0.004 0.043 2850 Dihedral : 13.177 155.980 2645 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.73 % Allowed : 14.20 % Favored : 84.07 % 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 aren not related in a simple way. whole: -0.24 (0.19), residues: 1955 helix: 1.78 (0.18), residues: 785 sheet: -1.28 (0.22), residues: 490 loop : -1.55 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 410 TYR 0.018 0.001 TYR B 64 PHE 0.016 0.002 PHE C 287 TRP 0.010 0.001 TRP B 320 HIS 0.003 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00482 (17155) covalent geometry : angle 0.66205 (23455) SS BOND : bond 0.00481 ( 4) SS BOND : angle 1.98883 ( 12) hydrogen bonds : bond 0.04654 ( 815) hydrogen bonds : angle 4.82742 ( 2415) link_NAG-ASN : bond 0.00178 ( 15) link_NAG-ASN : angle 1.69659 ( 45) *********************** 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: 32 poor density : 66 time to evaluate : 0.644 Fit side-chains REVERT: A 310 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7465 (tptt) REVERT: A 465 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5420 (pp) REVERT: B 116 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8649 (m-10) REVERT: B 465 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5786 (pp) REVERT: C 103 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7072 (m-10) REVERT: C 411 HIS cc_start: 0.5946 (p90) cc_final: 0.5716 (p90) REVERT: D 411 HIS cc_start: 0.5797 (p90) cc_final: 0.5376 (p90) outliers start: 32 outliers final: 16 residues processed: 86 average time/residue: 0.1048 time to fit residues: 15.5505 Evaluate side-chains 86 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 442 LEU 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 116 TYR 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 235 MET 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 442 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 78 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.095332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.062443 restraints weight = 55846.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063812 restraints weight = 32248.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.064699 restraints weight = 23258.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065104 restraints weight = 19245.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.065484 restraints weight = 17444.871| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17174 Z= 0.127 Angle : 0.619 10.052 23512 Z= 0.298 Chirality : 0.042 0.245 2750 Planarity : 0.004 0.041 2850 Dihedral : 13.141 156.423 2645 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.30 % Allowed : 14.47 % Favored : 84.23 % 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 aren not related in a simple way. whole: -0.10 (0.19), residues: 1955 helix: 1.90 (0.18), residues: 785 sheet: -1.19 (0.24), residues: 410 loop : -1.53 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 410 TYR 0.015 0.001 TYR D 67 PHE 0.018 0.001 PHE E 287 TRP 0.009 0.001 TRP C 68 HIS 0.002 0.000 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00289 (17155) covalent geometry : angle 0.61643 (23455) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.74902 ( 12) hydrogen bonds : bond 0.04285 ( 815) hydrogen bonds : angle 4.67342 ( 2415) link_NAG-ASN : bond 0.00147 ( 15) link_NAG-ASN : angle 1.48299 ( 45) *********************** 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 93 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.657 Fit side-chains REVERT: A 310 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7474 (tptt) REVERT: B 131 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8967 (mm) REVERT: B 465 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5688 (pp) REVERT: C 103 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7039 (m-10) REVERT: C 254 PHE cc_start: 0.8153 (m-10) cc_final: 0.7405 (t80) REVERT: C 442 LEU cc_start: 0.7512 (mt) cc_final: 0.7271 (pp) REVERT: D 411 HIS cc_start: 0.5794 (p90) cc_final: 0.5480 (p90) REVERT: D 442 LEU cc_start: 0.7342 (mt) cc_final: 0.7093 (pp) outliers start: 24 outliers final: 15 residues processed: 82 average time/residue: 0.1173 time to fit residues: 16.0657 Evaluate side-chains 84 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 442 LEU 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 116 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 235 MET 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 442 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 194 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 145 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 0.0270 chunk 75 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.095932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063224 restraints weight = 55695.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064593 restraints weight = 32052.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065467 restraints weight = 23166.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.066033 restraints weight = 19116.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066296 restraints weight = 17111.047| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17174 Z= 0.116 Angle : 0.616 10.126 23512 Z= 0.294 Chirality : 0.043 0.252 2750 Planarity : 0.004 0.040 2850 Dihedral : 13.034 156.463 2645 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.25 % Allowed : 14.69 % Favored : 84.07 % 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 aren not related in a simple way. whole: -0.14 (0.19), residues: 1955 helix: 1.73 (0.18), residues: 815 sheet: -1.10 (0.25), residues: 420 loop : -1.59 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 410 TYR 0.016 0.001 TYR D 67 PHE 0.017 0.001 PHE D 287 TRP 0.008 0.001 TRP C 68 HIS 0.002 0.001 HIS E 411 Details of bonding type rmsd covalent geometry : bond 0.00260 (17155) covalent geometry : angle 0.61407 (23455) SS BOND : bond 0.00081 ( 4) SS BOND : angle 0.66559 ( 12) hydrogen bonds : bond 0.04074 ( 815) hydrogen bonds : angle 4.55841 ( 2415) link_NAG-ASN : bond 0.00128 ( 15) link_NAG-ASN : angle 1.26067 ( 45) *********************** 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 92 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.699 Fit side-chains REVERT: A 442 LEU cc_start: 0.7722 (mm) cc_final: 0.7479 (pp) REVERT: B 131 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8939 (mm) REVERT: C 103 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6973 (m-10) REVERT: C 254 PHE cc_start: 0.8124 (m-10) cc_final: 0.7436 (t80) REVERT: C 442 LEU cc_start: 0.7528 (mt) cc_final: 0.7326 (pp) REVERT: D 411 HIS cc_start: 0.5729 (p90) cc_final: 0.5445 (p90) outliers start: 23 outliers final: 16 residues processed: 81 average time/residue: 0.1097 time to fit residues: 15.0832 Evaluate side-chains 82 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 235 MET 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 283 ILE Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 89 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 113 optimal weight: 0.0170 overall best weight: 1.0422 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.095510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063398 restraints weight = 55569.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.064648 restraints weight = 34024.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.064778 restraints weight = 23807.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065186 restraints weight = 21744.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065214 restraints weight = 19493.723| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17174 Z= 0.125 Angle : 0.614 9.562 23512 Z= 0.296 Chirality : 0.043 0.288 2750 Planarity : 0.004 0.041 2850 Dihedral : 13.027 156.511 2645 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.03 % Allowed : 15.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.19), residues: 1955 helix: 1.76 (0.18), residues: 815 sheet: -1.12 (0.25), residues: 420 loop : -1.55 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 410 TYR 0.016 0.001 TYR D 67 PHE 0.018 0.001 PHE A 438 TRP 0.008 0.001 TRP C 68 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00285 (17155) covalent geometry : angle 0.61210 (23455) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.74281 ( 12) hydrogen bonds : bond 0.04058 ( 815) hydrogen bonds : angle 4.55261 ( 2415) link_NAG-ASN : bond 0.00117 ( 15) link_NAG-ASN : angle 1.32201 ( 45) ********************** 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 84 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.652 Fit side-chains REVERT: A 442 LEU cc_start: 0.7873 (mm) cc_final: 0.7568 (pp) REVERT: B 131 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8948 (mm) REVERT: C 103 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6997 (m-10) REVERT: C 254 PHE cc_start: 0.8136 (m-10) cc_final: 0.7438 (t80) REVERT: D 411 HIS cc_start: 0.5672 (p90) cc_final: 0.5190 (p90) outliers start: 19 outliers final: 16 residues processed: 73 average time/residue: 0.1026 time to fit residues: 13.2521 Evaluate side-chains 82 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 235 MET 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 283 ILE Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 153 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 140 optimal weight: 0.0060 chunk 17 optimal weight: 0.0170 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.096316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064258 restraints weight = 55727.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.065539 restraints weight = 34122.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065669 restraints weight = 23764.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066061 restraints weight = 21821.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.066107 restraints weight = 19427.404| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 17174 Z= 0.111 Angle : 0.606 10.613 23512 Z= 0.290 Chirality : 0.042 0.277 2750 Planarity : 0.004 0.040 2850 Dihedral : 12.991 156.698 2645 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.19 % Allowed : 15.34 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.19), residues: 1955 helix: 1.77 (0.18), residues: 815 sheet: -1.07 (0.25), residues: 420 loop : -1.55 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 410 TYR 0.016 0.001 TYR D 67 PHE 0.017 0.001 PHE A 438 TRP 0.008 0.001 TRP C 68 HIS 0.002 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00248 (17155) covalent geometry : angle 0.60391 (23455) SS BOND : bond 0.00058 ( 4) SS BOND : angle 0.59667 ( 12) hydrogen bonds : bond 0.03859 ( 815) hydrogen bonds : angle 4.44158 ( 2415) link_NAG-ASN : bond 0.00133 ( 15) link_NAG-ASN : angle 1.20855 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2627.36 seconds wall clock time: 46 minutes 33.39 seconds (2793.39 seconds total)