Starting phenix.real_space_refine on Mon Nov 18 15:47:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/11_2024/8fsp_29421_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/11_2024/8fsp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/11_2024/8fsp_29421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/11_2024/8fsp_29421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/11_2024/8fsp_29421_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/11_2024/8fsp_29421_neut.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10985 2.51 5 N 2710 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16685 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 9.10, per 1000 atoms: 0.55 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=2, 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 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: 4.41 Conformation dependent library (CDL) restraints added in 2.2 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 45.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 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: 6.42 Time building geometry restraints manager: 5.11 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: 10139 34.00 - 68.00: 197 68.00 - 102.00: 30 102.00 - 136.01: 0 136.01 - 170.01: 15 Dihedral angle restraints: 10381 sinusoidal: 4486 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 B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 131.94 -38.94 1 1.00e+01 1.00e-02 2.13e+01 dihedral pdb=" C7 Y82 C 504 " pdb=" C10 Y82 C 504 " pdb=" C9 Y82 C 504 " pdb=" N3 Y82 C 504 " ideal model delta sinusoidal sigma weight residual 78.34 -91.67 170.01 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 10378 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: 67 2.61 - 3.18: 13997 3.18 - 3.75: 25100 3.75 - 4.33: 32466 4.33 - 4.90: 53378 Nonbonded interactions: 125008 Sorted by model distance: nonbonded pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 149 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " model vdw 2.035 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 ... (remaining 125003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.980 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: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 39.200 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- 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 17155 Z= 0.384 Angle : 0.987 11.259 23455 Z= 0.543 Chirality : 0.056 0.383 2750 Planarity : 0.006 0.065 2850 Dihedral : 15.982 170.008 6535 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1955 helix: 0.24 (0.19), residues: 740 sheet: -1.06 (0.25), residues: 430 loop : -2.30 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 63 HIS 0.003 0.001 HIS A 118 PHE 0.038 0.002 PHE D 287 TYR 0.010 0.002 TYR E 207 ARG 0.012 0.001 ARG B 424 *********************** 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 : 2.026 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: 0.2338 time to fit residues: 33.9034 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 : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0570 chunk 147 optimal weight: 0.0270 chunk 82 optimal weight: 0.0570 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 124 GLN C 124 GLN D 124 GLN E 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17155 Z= 0.210 Angle : 0.621 7.518 23455 Z= 0.309 Chirality : 0.042 0.164 2750 Planarity : 0.004 0.051 2850 Dihedral : 13.235 154.919 2645 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.05 % Allowed : 6.78 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1955 helix: 1.23 (0.19), residues: 785 sheet: -1.26 (0.24), residues: 440 loop : -1.70 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 156 HIS 0.002 0.000 HIS B 158 PHE 0.017 0.001 PHE A 287 TYR 0.013 0.001 TYR D 441 ARG 0.003 0.000 ARG D 410 *********************** 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 78 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 2.020 Fit side-chains REVERT: A 411 HIS cc_start: 0.5455 (p90) cc_final: 0.5144 (p90) REVERT: B 235 MET cc_start: 0.7275 (ttp) cc_final: 0.7072 (ptm) REVERT: B 254 PHE cc_start: 0.7508 (m-10) cc_final: 0.7154 (t80) REVERT: C 254 PHE cc_start: 0.7380 (m-10) cc_final: 0.6988 (t80) REVERT: D 254 PHE cc_start: 0.7799 (m-10) cc_final: 0.7300 (t80) REVERT: E 254 PHE cc_start: 0.7479 (m-10) cc_final: 0.6999 (t80) REVERT: E 411 HIS cc_start: 0.5194 (p90) cc_final: 0.4818 (p90) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.2476 time to fit residues: 33.7327 Evaluate side-chains 63 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 191 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 0.0670 chunk 60 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17155 Z= 0.254 Angle : 0.627 8.387 23455 Z= 0.314 Chirality : 0.042 0.151 2750 Planarity : 0.004 0.044 2850 Dihedral : 13.117 156.311 2645 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.98 % Allowed : 10.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1955 helix: 1.52 (0.18), residues: 780 sheet: -1.11 (0.24), residues: 435 loop : -1.64 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 156 HIS 0.002 0.001 HIS C 18 PHE 0.018 0.002 PHE C 287 TYR 0.013 0.001 TYR B 64 ARG 0.003 0.000 ARG E 410 *********************** 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 99 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.951 Fit side-chains REVERT: A 411 HIS cc_start: 0.5454 (p90) cc_final: 0.5224 (p90) REVERT: B 116 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8422 (m-10) REVERT: B 411 HIS cc_start: 0.4908 (p90) cc_final: 0.4631 (p90) REVERT: D 116 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: D 411 HIS cc_start: 0.5255 (p90) cc_final: 0.4970 (p90) REVERT: E 411 HIS cc_start: 0.5245 (p90) cc_final: 0.4956 (p90) outliers start: 18 outliers final: 5 residues processed: 92 average time/residue: 0.2370 time to fit residues: 36.5858 Evaluate side-chains 67 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 116 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.0770 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17155 Z= 0.230 Angle : 0.599 8.660 23455 Z= 0.296 Chirality : 0.042 0.147 2750 Planarity : 0.004 0.044 2850 Dihedral : 13.072 155.858 2645 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.36 % Allowed : 11.38 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 1955 helix: 1.65 (0.18), residues: 790 sheet: -0.88 (0.24), residues: 420 loop : -1.57 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.002 0.001 HIS C 158 PHE 0.017 0.001 PHE A 287 TYR 0.014 0.001 TYR A 67 ARG 0.002 0.000 ARG E 410 *********************** 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: 25 poor density : 71 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: A 411 HIS cc_start: 0.5526 (p90) cc_final: 0.5306 (p90) REVERT: A 442 LEU cc_start: 0.7449 (mt) cc_final: 0.7152 (pp) REVERT: B 310 LYS cc_start: 0.6414 (mmtp) cc_final: 0.6046 (pttt) REVERT: B 411 HIS cc_start: 0.4969 (p90) cc_final: 0.4741 (p90) REVERT: C 411 HIS cc_start: 0.5243 (p90) cc_final: 0.4946 (p90) REVERT: C 442 LEU cc_start: 0.7354 (mt) cc_final: 0.7059 (pp) REVERT: D 411 HIS cc_start: 0.5015 (p90) cc_final: 0.4759 (p90) REVERT: D 442 LEU cc_start: 0.7459 (mt) cc_final: 0.7107 (pp) REVERT: E 411 HIS cc_start: 0.5159 (p90) cc_final: 0.4888 (p90) REVERT: E 442 LEU cc_start: 0.7330 (mt) cc_final: 0.6872 (pp) outliers start: 25 outliers final: 13 residues processed: 90 average time/residue: 0.2680 time to fit residues: 40.2765 Evaluate side-chains 80 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 160 optimal weight: 0.0270 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17155 Z= 0.179 Angle : 0.571 8.130 23455 Z= 0.282 Chirality : 0.041 0.216 2750 Planarity : 0.004 0.041 2850 Dihedral : 13.025 156.598 2645 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.14 % Allowed : 12.85 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1955 helix: 1.74 (0.18), residues: 790 sheet: -0.76 (0.24), residues: 420 loop : -1.45 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.002 0.000 HIS C 158 PHE 0.021 0.001 PHE B 438 TYR 0.014 0.001 TYR A 67 ARG 0.002 0.000 ARG E 410 *********************** 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 100 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 310 LYS cc_start: 0.6231 (mmtp) cc_final: 0.5961 (pttt) REVERT: C 411 HIS cc_start: 0.5268 (p90) cc_final: 0.4923 (p90) REVERT: C 442 LEU cc_start: 0.7428 (mt) cc_final: 0.7183 (pp) REVERT: E 310 LYS cc_start: 0.6507 (mmtp) cc_final: 0.6228 (pttp) outliers start: 21 outliers final: 15 residues processed: 90 average time/residue: 0.3365 time to fit residues: 45.9360 Evaluate side-chains 80 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 461 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 156 optimal weight: 0.0270 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 99 optimal weight: 8.9990 overall best weight: 1.1450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17155 Z= 0.197 Angle : 0.577 8.326 23455 Z= 0.285 Chirality : 0.041 0.244 2750 Planarity : 0.004 0.041 2850 Dihedral : 12.999 156.394 2645 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.68 % Allowed : 13.17 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1955 helix: 1.79 (0.18), residues: 790 sheet: -0.68 (0.24), residues: 420 loop : -1.52 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 156 HIS 0.002 0.000 HIS C 158 PHE 0.017 0.001 PHE C 287 TYR 0.014 0.001 TYR D 67 ARG 0.007 0.000 ARG B 410 *********************** 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 101 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 2.122 Fit side-chains revert: symmetry clash REVERT: A 442 LEU cc_start: 0.7448 (mt) cc_final: 0.7167 (pp) REVERT: C 411 HIS cc_start: 0.5456 (p90) cc_final: 0.5144 (p90) REVERT: D 442 LEU cc_start: 0.7268 (mt) cc_final: 0.7004 (pp) REVERT: E 442 LEU cc_start: 0.7702 (mt) cc_final: 0.7295 (pp) outliers start: 31 outliers final: 20 residues processed: 90 average time/residue: 0.2479 time to fit residues: 37.8976 Evaluate side-chains 84 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 235 MET 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 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 43 VAL Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 118 HIS E 118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17155 Z= 0.227 Angle : 0.596 8.950 23455 Z= 0.294 Chirality : 0.042 0.234 2750 Planarity : 0.004 0.041 2850 Dihedral : 13.035 156.359 2645 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.41 % Allowed : 13.66 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 1955 helix: 1.78 (0.18), residues: 790 sheet: -0.67 (0.24), residues: 420 loop : -1.49 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 156 HIS 0.004 0.001 HIS E 411 PHE 0.027 0.002 PHE C 254 TYR 0.013 0.001 TYR B 64 ARG 0.006 0.000 ARG B 410 *********************** 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 94 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.7448 (mt) cc_final: 0.7142 (pp) REVERT: B 116 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.8429 (m-10) REVERT: C 103 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: C 411 HIS cc_start: 0.5280 (p90) cc_final: 0.4969 (p90) outliers start: 26 outliers final: 14 residues processed: 83 average time/residue: 0.2638 time to fit residues: 36.8640 Evaluate side-chains 81 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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 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 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 461 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 147 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17155 Z= 0.219 Angle : 0.596 9.560 23455 Z= 0.293 Chirality : 0.042 0.236 2750 Planarity : 0.004 0.040 2850 Dihedral : 13.054 156.395 2645 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.46 % Allowed : 14.25 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1955 helix: 1.61 (0.18), residues: 815 sheet: -0.83 (0.22), residues: 495 loop : -1.61 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 68 HIS 0.002 0.001 HIS E 411 PHE 0.017 0.001 PHE A 287 TYR 0.014 0.001 TYR D 67 ARG 0.005 0.000 ARG A 410 *********************** 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 97 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.7364 (mt) cc_final: 0.7145 (pp) REVERT: B 116 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8461 (m-10) REVERT: C 103 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.6945 (m-10) REVERT: C 411 HIS cc_start: 0.5439 (p90) cc_final: 0.5212 (p90) REVERT: C 442 LEU cc_start: 0.7406 (mt) cc_final: 0.7123 (pp) outliers start: 27 outliers final: 16 residues processed: 86 average time/residue: 0.2637 time to fit residues: 37.5444 Evaluate side-chains 83 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 461 TYR 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 461 TYR Chi-restraints excluded: chain D residue 191 GLU 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 461 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 0.4980 chunk 165 optimal weight: 0.1980 chunk 174 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 17155 Z= 0.166 Angle : 0.575 9.281 23455 Z= 0.282 Chirality : 0.042 0.233 2750 Planarity : 0.003 0.040 2850 Dihedral : 13.006 156.599 2645 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.19 % Allowed : 14.47 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1955 helix: 1.66 (0.18), residues: 820 sheet: -0.82 (0.24), residues: 410 loop : -1.58 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.002 0.000 HIS E 119 PHE 0.017 0.001 PHE C 287 TYR 0.015 0.001 TYR A 67 ARG 0.004 0.000 ARG A 410 *********************** 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 94 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7413 (tptt) REVERT: C 103 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6799 (m-10) REVERT: C 411 HIS cc_start: 0.5379 (p90) cc_final: 0.5168 (p90) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 0.2723 time to fit residues: 36.5838 Evaluate side-chains 80 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 461 TYR 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 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 461 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 178 optimal weight: 0.0980 chunk 154 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17155 Z= 0.261 Angle : 0.629 9.900 23455 Z= 0.306 Chirality : 0.042 0.241 2750 Planarity : 0.004 0.041 2850 Dihedral : 13.045 156.384 2645 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.87 % Allowed : 14.69 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1955 helix: 1.70 (0.18), residues: 815 sheet: -0.91 (0.24), residues: 410 loop : -1.54 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 156 HIS 0.002 0.001 HIS E 411 PHE 0.023 0.002 PHE D 254 TYR 0.016 0.001 TYR D 64 ARG 0.007 0.000 ARG B 306 ********************** 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 85 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 116 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8470 (m-10) REVERT: C 103 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6977 (m-10) REVERT: C 442 LEU cc_start: 0.7455 (mt) cc_final: 0.7158 (pp) outliers start: 16 outliers final: 13 residues processed: 75 average time/residue: 0.2458 time to fit residues: 31.1456 Evaluate side-chains 78 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 461 TYR 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 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 461 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0670 chunk 47 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.096031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.063817 restraints weight = 55926.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.065189 restraints weight = 31928.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066069 restraints weight = 22841.972| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17155 Z= 0.177 Angle : 0.596 10.325 23455 Z= 0.290 Chirality : 0.042 0.231 2750 Planarity : 0.004 0.040 2850 Dihedral : 13.020 156.432 2645 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 14.80 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1955 helix: 1.77 (0.18), residues: 815 sheet: -0.80 (0.24), residues: 430 loop : -1.60 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.002 0.001 HIS C 411 PHE 0.021 0.001 PHE D 254 TYR 0.014 0.001 TYR A 67 ARG 0.006 0.000 ARG E 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2401.76 seconds wall clock time: 45 minutes 25.58 seconds (2725.58 seconds total)