Starting phenix.real_space_refine on Fri Mar 15 15:53:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/03_2024/7w3y_32296.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/03_2024/7w3y_32296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/03_2024/7w3y_32296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/03_2024/7w3y_32296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/03_2024/7w3y_32296.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/03_2024/7w3y_32296.pdb" } resolution = 3.0 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 80 5.16 5 C 7876 2.51 5 N 1996 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 138": "OD1" <-> "OD2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12088 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3022 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 1 Chain: "B" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3022 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 1 Chain: "C" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3022 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 1 Chain: "D" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3022 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 1 Time building chain proxies: 6.49, per 1000 atoms: 0.54 Number of scatterers: 12088 At special positions: 0 Unit cell: (116.61, 116.61, 125.736, 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 80 16.00 O 2136 8.00 N 1996 7.00 C 7876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 4.97 Conformation dependent library (CDL) restraints added in 2.2 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 74.0% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.598A pdb=" N GLU A 72 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.522A pdb=" N VAL A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 129 through 132 Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 165 through 175 removed outlier: 4.094A pdb=" N GLU A 174 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 203 removed outlier: 3.856A pdb=" N VAL A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.761A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.530A pdb=" N ILE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.551A pdb=" N ILE A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) Proline residue: A 269 - end of helix removed outlier: 3.711A pdb=" N GLY A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.340A pdb=" N LYS A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 removed outlier: 4.190A pdb=" N ARG A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 343 Processing helix chain 'A' and resid 353 through 366 removed outlier: 4.138A pdb=" N TRP A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 396 removed outlier: 3.543A pdb=" N LEU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 426 removed outlier: 4.615A pdb=" N VAL A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 69 through 75 removed outlier: 3.598A pdb=" N GLU B 72 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 removed outlier: 3.522A pdb=" N VAL B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'B' and resid 165 through 175 removed outlier: 4.094A pdb=" N GLU B 174 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 203 removed outlier: 3.856A pdb=" N VAL B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 247 removed outlier: 3.761A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.530A pdb=" N ILE B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.552A pdb=" N ILE B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) Proline residue: B 269 - end of helix removed outlier: 3.711A pdb=" N GLY B 273 " --> pdb=" O PRO B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.340A pdb=" N LYS B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 removed outlier: 4.189A pdb=" N ARG B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 343 Processing helix chain 'B' and resid 353 through 366 removed outlier: 4.137A pdb=" N TRP B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 396 removed outlier: 3.543A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 426 removed outlier: 4.615A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 69 through 75 removed outlier: 3.598A pdb=" N GLU C 72 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.522A pdb=" N VAL C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 121 Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 129 through 132 Processing helix chain 'C' and resid 133 through 147 Processing helix chain 'C' and resid 165 through 175 removed outlier: 4.094A pdb=" N GLU C 174 " --> pdb=" O TRP C 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 203 removed outlier: 3.856A pdb=" N VAL C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 192 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 222 through 247 removed outlier: 3.761A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 257 removed outlier: 3.530A pdb=" N ILE C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.551A pdb=" N ILE C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) Proline residue: C 269 - end of helix removed outlier: 3.711A pdb=" N GLY C 273 " --> pdb=" O PRO C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 Processing helix chain 'C' and resid 294 through 302 removed outlier: 4.340A pdb=" N LYS C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 removed outlier: 4.190A pdb=" N ARG C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 Processing helix chain 'C' and resid 353 through 366 removed outlier: 4.138A pdb=" N TRP C 359 " --> pdb=" O PRO C 355 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR C 360 " --> pdb=" O ALA C 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 366 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 396 removed outlier: 3.543A pdb=" N LEU C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 426 removed outlier: 4.615A pdb=" N VAL C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.598A pdb=" N GLU D 72 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.522A pdb=" N VAL D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 147 Processing helix chain 'D' and resid 165 through 175 removed outlier: 4.094A pdb=" N GLU D 174 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 203 removed outlier: 3.856A pdb=" N VAL D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 222 through 247 removed outlier: 3.761A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 removed outlier: 3.530A pdb=" N ILE D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.551A pdb=" N ILE D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) Proline residue: D 269 - end of helix removed outlier: 3.711A pdb=" N GLY D 273 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 Processing helix chain 'D' and resid 294 through 302 removed outlier: 4.340A pdb=" N LYS D 299 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 316 removed outlier: 4.190A pdb=" N ARG D 308 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 343 Processing helix chain 'D' and resid 353 through 366 removed outlier: 4.138A pdb=" N TRP D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR D 360 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 366 " --> pdb=" O ILE D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 396 removed outlier: 3.543A pdb=" N LEU D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 426 removed outlier: 4.615A pdb=" N VAL D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 Processing sheet with id=AA2, first strand: chain 'B' and resid 41 through 46 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 46 Processing sheet with id=AA4, first strand: chain 'D' and resid 41 through 46 732 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3744 1.34 - 1.46: 3128 1.46 - 1.58: 5396 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 12388 Sorted by residual: bond pdb=" C PHE A 292 " pdb=" N ARG A 293 " ideal model delta sigma weight residual 1.333 1.310 0.023 1.56e-02 4.11e+03 2.26e+00 bond pdb=" C PHE D 292 " pdb=" N ARG D 293 " ideal model delta sigma weight residual 1.333 1.310 0.023 1.56e-02 4.11e+03 2.26e+00 bond pdb=" C PHE C 292 " pdb=" N ARG C 293 " ideal model delta sigma weight residual 1.333 1.310 0.023 1.56e-02 4.11e+03 2.26e+00 bond pdb=" C PHE B 292 " pdb=" N ARG B 293 " ideal model delta sigma weight residual 1.333 1.310 0.023 1.56e-02 4.11e+03 2.23e+00 bond pdb=" CA VAL B 205 " pdb=" CB VAL B 205 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.29e-02 6.01e+03 1.53e+00 ... (remaining 12383 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.79: 280 106.79 - 113.61: 6731 113.61 - 120.43: 5379 120.43 - 127.25: 4294 127.25 - 134.07: 80 Bond angle restraints: 16764 Sorted by residual: angle pdb=" N TYR A 108 " pdb=" CA TYR A 108 " pdb=" C TYR A 108 " ideal model delta sigma weight residual 111.28 114.88 -3.60 1.09e+00 8.42e-01 1.09e+01 angle pdb=" N TYR C 108 " pdb=" CA TYR C 108 " pdb=" C TYR C 108 " ideal model delta sigma weight residual 111.28 114.88 -3.60 1.09e+00 8.42e-01 1.09e+01 angle pdb=" N TYR D 108 " pdb=" CA TYR D 108 " pdb=" C TYR D 108 " ideal model delta sigma weight residual 111.28 114.88 -3.60 1.09e+00 8.42e-01 1.09e+01 angle pdb=" C PRO A 398 " pdb=" N VAL A 399 " pdb=" CA VAL A 399 " ideal model delta sigma weight residual 120.43 123.59 -3.16 9.60e-01 1.09e+00 1.08e+01 angle pdb=" C PRO C 398 " pdb=" N VAL C 399 " pdb=" CA VAL C 399 " ideal model delta sigma weight residual 120.43 123.59 -3.16 9.60e-01 1.09e+00 1.08e+01 ... (remaining 16759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.49: 6391 14.49 - 28.98: 709 28.98 - 43.46: 172 43.46 - 57.95: 36 57.95 - 72.44: 8 Dihedral angle restraints: 7316 sinusoidal: 2924 harmonic: 4392 Sorted by residual: dihedral pdb=" CA ARG C 107 " pdb=" C ARG C 107 " pdb=" N TYR C 108 " pdb=" CA TYR C 108 " ideal model delta harmonic sigma weight residual 180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG D 107 " pdb=" C ARG D 107 " pdb=" N TYR D 108 " pdb=" CA TYR D 108 " ideal model delta harmonic sigma weight residual 180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG A 107 " pdb=" C ARG A 107 " pdb=" N TYR A 108 " pdb=" CA TYR A 108 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 879 0.027 - 0.055: 609 0.055 - 0.082: 252 0.082 - 0.109: 111 0.109 - 0.137: 21 Chirality restraints: 1872 Sorted by residual: chirality pdb=" CA PHE D 383 " pdb=" N PHE D 383 " pdb=" C PHE D 383 " pdb=" CB PHE D 383 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA PHE A 383 " pdb=" N PHE A 383 " pdb=" C PHE A 383 " pdb=" CB PHE A 383 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA PHE C 383 " pdb=" N PHE C 383 " pdb=" C PHE C 383 " pdb=" CB PHE C 383 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1869 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 354 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO B 355 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 355 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 354 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO C 355 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 355 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 355 " 0.024 5.00e-02 4.00e+02 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 203 2.67 - 3.23: 13004 3.23 - 3.79: 19104 3.79 - 4.34: 25124 4.34 - 4.90: 40817 Nonbonded interactions: 98252 Sorted by model distance: nonbonded pdb=" OG SER A 68 " pdb=" OE1 GLU A 70 " model vdw 2.117 2.440 nonbonded pdb=" OG SER C 68 " pdb=" OE1 GLU C 70 " model vdw 2.117 2.440 nonbonded pdb=" OG SER D 68 " pdb=" OE1 GLU D 70 " model vdw 2.117 2.440 nonbonded pdb=" OG SER B 68 " pdb=" OE1 GLU B 70 " model vdw 2.117 2.440 nonbonded pdb=" OG1 THR B 231 " pdb=" OH TYR B 270 " model vdw 2.170 2.440 ... (remaining 98247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 4.930 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.290 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 0.039 12388 Z= 0.389 Angle : 0.684 10.467 16764 Z= 0.405 Chirality : 0.044 0.137 1872 Planarity : 0.004 0.043 2096 Dihedral : 13.233 72.441 4492 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.91 % Allowed : 6.36 % Favored : 92.73 % 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: -3.33 (0.20), residues: 1476 helix: -1.61 (0.15), residues: 992 sheet: -5.29 (0.29), residues: 40 loop : -2.99 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 170 HIS 0.002 0.001 HIS B 303 PHE 0.013 0.001 PHE B 383 TYR 0.019 0.001 TYR C 186 ARG 0.003 0.000 ARG B 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 264 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6943 (t80) cc_final: 0.6537 (t80) REVERT: A 104 HIS cc_start: 0.8100 (m-70) cc_final: 0.7698 (m-70) REVERT: A 140 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8357 (ptmt) REVERT: A 259 MET cc_start: 0.8075 (mmm) cc_final: 0.7682 (mmm) REVERT: A 263 ASP cc_start: 0.8436 (m-30) cc_final: 0.8118 (m-30) REVERT: B 91 PHE cc_start: 0.6852 (t80) cc_final: 0.6512 (t80) REVERT: B 104 HIS cc_start: 0.8134 (m-70) cc_final: 0.7591 (m-70) REVERT: B 140 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8481 (ptmt) REVERT: B 259 MET cc_start: 0.8045 (mmm) cc_final: 0.7631 (mmm) REVERT: B 263 ASP cc_start: 0.8346 (m-30) cc_final: 0.8036 (m-30) REVERT: C 91 PHE cc_start: 0.6975 (t80) cc_final: 0.6566 (t80) REVERT: C 104 HIS cc_start: 0.8121 (m-70) cc_final: 0.7756 (m-70) REVERT: C 140 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8369 (ptmt) REVERT: C 259 MET cc_start: 0.8090 (mmm) cc_final: 0.7679 (mmm) REVERT: C 263 ASP cc_start: 0.8421 (m-30) cc_final: 0.8102 (m-30) REVERT: D 91 PHE cc_start: 0.6964 (t80) cc_final: 0.6561 (t80) REVERT: D 104 HIS cc_start: 0.8099 (m-70) cc_final: 0.7696 (m-70) REVERT: D 140 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8365 (ptmt) REVERT: D 259 MET cc_start: 0.8091 (mmm) cc_final: 0.7679 (mmm) REVERT: D 263 ASP cc_start: 0.8453 (m-30) cc_final: 0.8132 (m-30) outliers start: 12 outliers final: 6 residues processed: 268 average time/residue: 1.3494 time to fit residues: 389.0846 Evaluate side-chains 198 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN A 143 ASN B 76 ASN B 96 ASN B 143 ASN B 405 ASN B 413 ASN C 45 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 143 ASN C 413 ASN D 45 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN D 143 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12388 Z= 0.283 Angle : 0.609 9.472 16764 Z= 0.319 Chirality : 0.042 0.130 1872 Planarity : 0.005 0.052 2096 Dihedral : 4.753 35.711 1688 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.12 % Allowed : 17.58 % Favored : 80.30 % 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: -1.61 (0.22), residues: 1476 helix: -0.39 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -2.39 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 359 HIS 0.002 0.001 HIS B 303 PHE 0.022 0.001 PHE B 185 TYR 0.021 0.002 TYR C 186 ARG 0.010 0.001 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6961 (t80) cc_final: 0.6583 (t80) REVERT: A 104 HIS cc_start: 0.8003 (m-70) cc_final: 0.7559 (m-70) REVERT: A 133 TYR cc_start: 0.4886 (t80) cc_final: 0.4621 (t80) REVERT: A 235 MET cc_start: 0.7145 (ttm) cc_final: 0.6898 (ttp) REVERT: A 259 MET cc_start: 0.8067 (mmm) cc_final: 0.7748 (mmm) REVERT: A 263 ASP cc_start: 0.8432 (m-30) cc_final: 0.8151 (m-30) REVERT: B 91 PHE cc_start: 0.6865 (t80) cc_final: 0.6602 (t80) REVERT: B 104 HIS cc_start: 0.8094 (m-70) cc_final: 0.7521 (m-70) REVERT: B 133 TYR cc_start: 0.4882 (t80) cc_final: 0.4594 (t80) REVERT: B 136 TYR cc_start: 0.8334 (t80) cc_final: 0.8092 (t80) REVERT: B 259 MET cc_start: 0.8045 (mmm) cc_final: 0.7712 (mmm) REVERT: B 263 ASP cc_start: 0.8396 (m-30) cc_final: 0.8126 (m-30) REVERT: B 410 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7731 (t80) REVERT: B 412 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 91 PHE cc_start: 0.7049 (t80) cc_final: 0.6680 (t80) REVERT: C 104 HIS cc_start: 0.8091 (m-70) cc_final: 0.7719 (m-70) REVERT: C 133 TYR cc_start: 0.4890 (t80) cc_final: 0.4670 (t80) REVERT: C 259 MET cc_start: 0.8068 (mmm) cc_final: 0.7728 (mmm) REVERT: C 263 ASP cc_start: 0.8423 (m-30) cc_final: 0.8134 (m-30) REVERT: C 410 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7744 (t80) REVERT: D 91 PHE cc_start: 0.7041 (t80) cc_final: 0.6672 (t80) REVERT: D 104 HIS cc_start: 0.8072 (m-70) cc_final: 0.7653 (m-70) REVERT: D 133 TYR cc_start: 0.4888 (t80) cc_final: 0.4673 (t80) REVERT: D 259 MET cc_start: 0.8066 (mmm) cc_final: 0.7724 (mmm) REVERT: D 263 ASP cc_start: 0.8441 (m-30) cc_final: 0.8157 (m-30) outliers start: 28 outliers final: 12 residues processed: 224 average time/residue: 1.2777 time to fit residues: 309.1263 Evaluate side-chains 183 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 390 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 45 optimal weight: 0.0670 chunk 108 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 413 ASN C 76 ASN D 76 ASN D 413 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12388 Z= 0.189 Angle : 0.596 9.769 16764 Z= 0.305 Chirality : 0.041 0.144 1872 Planarity : 0.005 0.085 2096 Dihedral : 4.598 38.903 1684 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.03 % Allowed : 19.02 % Favored : 77.95 % 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: -0.83 (0.22), residues: 1476 helix: 0.24 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -2.11 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 359 HIS 0.001 0.000 HIS A 303 PHE 0.022 0.001 PHE B 185 TYR 0.020 0.001 TYR C 136 ARG 0.011 0.001 ARG D 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.5525 (OUTLIER) cc_final: 0.5111 (m-80) REVERT: A 91 PHE cc_start: 0.7046 (t80) cc_final: 0.6712 (t80) REVERT: A 104 HIS cc_start: 0.8011 (m-70) cc_final: 0.7612 (m-70) REVERT: A 169 MET cc_start: 0.7917 (ptp) cc_final: 0.7675 (ptt) REVERT: A 235 MET cc_start: 0.7121 (ttm) cc_final: 0.6894 (ttp) REVERT: A 259 MET cc_start: 0.8039 (mmm) cc_final: 0.7700 (mmm) REVERT: A 263 ASP cc_start: 0.8396 (m-30) cc_final: 0.8098 (m-30) REVERT: A 410 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7716 (t80) REVERT: A 413 ASN cc_start: 0.8845 (m110) cc_final: 0.8619 (t0) REVERT: B 91 PHE cc_start: 0.6956 (t80) cc_final: 0.6579 (t80) REVERT: B 104 HIS cc_start: 0.8054 (m-70) cc_final: 0.7540 (m-70) REVERT: B 133 TYR cc_start: 0.4670 (t80) cc_final: 0.4364 (t80) REVERT: B 169 MET cc_start: 0.7851 (ptp) cc_final: 0.7611 (ptt) REVERT: B 235 MET cc_start: 0.7123 (ttm) cc_final: 0.6888 (ttp) REVERT: B 259 MET cc_start: 0.8015 (mmm) cc_final: 0.7660 (mmm) REVERT: B 263 ASP cc_start: 0.8415 (m-30) cc_final: 0.8135 (m-30) REVERT: B 415 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7516 (mpp-170) REVERT: C 45 ASN cc_start: 0.6057 (OUTLIER) cc_final: 0.5580 (t0) REVERT: C 74 PHE cc_start: 0.5548 (OUTLIER) cc_final: 0.5113 (m-80) REVERT: C 91 PHE cc_start: 0.6944 (t80) cc_final: 0.6596 (t80) REVERT: C 104 HIS cc_start: 0.8098 (m-70) cc_final: 0.7743 (m-70) REVERT: C 169 MET cc_start: 0.7919 (ptp) cc_final: 0.7677 (ptt) REVERT: C 259 MET cc_start: 0.8058 (mmm) cc_final: 0.7747 (mmm) REVERT: C 263 ASP cc_start: 0.8394 (m-30) cc_final: 0.8119 (m-30) REVERT: C 410 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7760 (t80) REVERT: C 412 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D 74 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.5125 (m-80) REVERT: D 91 PHE cc_start: 0.7066 (t80) cc_final: 0.6814 (t80) REVERT: D 104 HIS cc_start: 0.8011 (m-70) cc_final: 0.7608 (m-70) REVERT: D 169 MET cc_start: 0.7906 (ptp) cc_final: 0.7681 (ptt) REVERT: D 259 MET cc_start: 0.8055 (mmm) cc_final: 0.7701 (mmm) REVERT: D 263 ASP cc_start: 0.8409 (m-30) cc_final: 0.8103 (m-30) REVERT: D 410 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7690 (t80) REVERT: D 413 ASN cc_start: 0.8846 (m110) cc_final: 0.8606 (t0) outliers start: 40 outliers final: 17 residues processed: 216 average time/residue: 1.1448 time to fit residues: 269.1146 Evaluate side-chains 202 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 410 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12388 Z= 0.198 Angle : 0.590 10.676 16764 Z= 0.299 Chirality : 0.040 0.138 1872 Planarity : 0.005 0.060 2096 Dihedral : 4.330 38.314 1682 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.71 % Allowed : 20.00 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.23), residues: 1476 helix: 0.57 (0.17), residues: 984 sheet: -3.91 (0.55), residues: 40 loop : -1.90 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 359 HIS 0.001 0.000 HIS D 303 PHE 0.011 0.001 PHE D 165 TYR 0.023 0.001 TYR B 136 ARG 0.011 0.001 ARG D 415 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 192 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7165 (t80) cc_final: 0.6922 (t80) REVERT: A 104 HIS cc_start: 0.8022 (m-70) cc_final: 0.7628 (m-70) REVERT: A 169 MET cc_start: 0.7933 (ptp) cc_final: 0.7703 (ptt) REVERT: A 235 MET cc_start: 0.7160 (ttm) cc_final: 0.6908 (ttp) REVERT: A 259 MET cc_start: 0.8026 (mmm) cc_final: 0.7734 (mmm) REVERT: A 263 ASP cc_start: 0.8461 (m-30) cc_final: 0.8223 (m-30) REVERT: A 410 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7753 (t80) REVERT: A 413 ASN cc_start: 0.8795 (m110) cc_final: 0.8530 (t0) REVERT: B 91 PHE cc_start: 0.7003 (t80) cc_final: 0.6711 (t80) REVERT: B 104 HIS cc_start: 0.8089 (m-70) cc_final: 0.7572 (m-70) REVERT: B 169 MET cc_start: 0.7902 (ptp) cc_final: 0.7671 (ptt) REVERT: B 174 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: B 235 MET cc_start: 0.7166 (ttm) cc_final: 0.6918 (ttp) REVERT: B 259 MET cc_start: 0.8014 (mmm) cc_final: 0.7709 (mmm) REVERT: B 263 ASP cc_start: 0.8443 (m-30) cc_final: 0.8227 (m-30) REVERT: C 45 ASN cc_start: 0.6185 (OUTLIER) cc_final: 0.5675 (t0) REVERT: C 91 PHE cc_start: 0.6986 (t80) cc_final: 0.6646 (t80) REVERT: C 104 HIS cc_start: 0.8098 (m-70) cc_final: 0.7709 (m-70) REVERT: C 169 MET cc_start: 0.7939 (ptp) cc_final: 0.7710 (ptt) REVERT: C 174 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: C 259 MET cc_start: 0.8043 (mmm) cc_final: 0.7674 (mmm) REVERT: C 263 ASP cc_start: 0.8453 (m-30) cc_final: 0.8196 (m-30) REVERT: D 45 ASN cc_start: 0.6130 (OUTLIER) cc_final: 0.5630 (t0) REVERT: D 91 PHE cc_start: 0.7133 (t80) cc_final: 0.6913 (t80) REVERT: D 104 HIS cc_start: 0.8024 (m-70) cc_final: 0.7626 (m-70) REVERT: D 169 MET cc_start: 0.7921 (ptp) cc_final: 0.7701 (ptt) REVERT: D 259 MET cc_start: 0.8029 (mmm) cc_final: 0.7647 (mmm) REVERT: D 263 ASP cc_start: 0.8465 (m-30) cc_final: 0.8206 (m-30) REVERT: D 410 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7753 (t80) outliers start: 49 outliers final: 24 residues processed: 233 average time/residue: 1.0806 time to fit residues: 275.3006 Evaluate side-chains 212 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 410 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 2 optimal weight: 20.0000 chunk 106 optimal weight: 0.0470 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12388 Z= 0.259 Angle : 0.607 10.639 16764 Z= 0.309 Chirality : 0.041 0.141 1872 Planarity : 0.005 0.050 2096 Dihedral : 4.285 36.822 1682 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.03 % Allowed : 21.67 % Favored : 75.30 % 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: -0.36 (0.23), residues: 1476 helix: 0.60 (0.17), residues: 980 sheet: -3.64 (0.58), residues: 40 loop : -1.64 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 359 HIS 0.001 0.000 HIS C 411 PHE 0.021 0.001 PHE B 185 TYR 0.027 0.002 TYR B 136 ARG 0.012 0.001 ARG D 415 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7164 (t80) cc_final: 0.6936 (t80) REVERT: A 104 HIS cc_start: 0.8059 (m-70) cc_final: 0.7657 (m-70) REVERT: A 169 MET cc_start: 0.8108 (ptp) cc_final: 0.7750 (ptt) REVERT: A 235 MET cc_start: 0.7167 (ttm) cc_final: 0.6915 (ttp) REVERT: A 259 MET cc_start: 0.8042 (mmm) cc_final: 0.7775 (mmm) REVERT: A 263 ASP cc_start: 0.8456 (m-30) cc_final: 0.8230 (m-30) REVERT: A 410 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7852 (t80) REVERT: A 413 ASN cc_start: 0.8923 (m110) cc_final: 0.8595 (t0) REVERT: B 91 PHE cc_start: 0.6998 (t80) cc_final: 0.6742 (t80) REVERT: B 104 HIS cc_start: 0.8067 (m-70) cc_final: 0.7512 (m-70) REVERT: B 169 MET cc_start: 0.7999 (ptp) cc_final: 0.7706 (ptt) REVERT: B 174 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: B 235 MET cc_start: 0.7189 (ttm) cc_final: 0.6935 (ttp) REVERT: B 259 MET cc_start: 0.8044 (mmm) cc_final: 0.7715 (mmm) REVERT: B 263 ASP cc_start: 0.8435 (m-30) cc_final: 0.8200 (m-30) REVERT: C 45 ASN cc_start: 0.6065 (OUTLIER) cc_final: 0.5598 (t0) REVERT: C 89 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8224 (mm-30) REVERT: C 91 PHE cc_start: 0.7105 (t80) cc_final: 0.6812 (t80) REVERT: C 104 HIS cc_start: 0.8118 (m-70) cc_final: 0.7732 (m-70) REVERT: C 169 MET cc_start: 0.8014 (ptp) cc_final: 0.7774 (ptt) REVERT: C 174 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: C 259 MET cc_start: 0.8048 (mmm) cc_final: 0.7690 (mmm) REVERT: C 263 ASP cc_start: 0.8445 (m-30) cc_final: 0.8204 (m-30) REVERT: D 45 ASN cc_start: 0.6112 (OUTLIER) cc_final: 0.5691 (t0) REVERT: D 91 PHE cc_start: 0.7073 (t80) cc_final: 0.6837 (t80) REVERT: D 104 HIS cc_start: 0.8050 (m-70) cc_final: 0.7644 (m-70) REVERT: D 169 MET cc_start: 0.8098 (ptp) cc_final: 0.7766 (ptt) REVERT: D 259 MET cc_start: 0.8008 (mmm) cc_final: 0.7651 (mmm) REVERT: D 263 ASP cc_start: 0.8455 (m-30) cc_final: 0.8216 (m-30) REVERT: D 413 ASN cc_start: 0.8902 (m110) cc_final: 0.8557 (t0) outliers start: 40 outliers final: 30 residues processed: 208 average time/residue: 1.0295 time to fit residues: 235.7571 Evaluate side-chains 205 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12388 Z= 0.262 Angle : 0.607 10.671 16764 Z= 0.309 Chirality : 0.041 0.140 1872 Planarity : 0.005 0.049 2096 Dihedral : 4.228 38.076 1682 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.11 % Allowed : 22.65 % Favored : 74.24 % 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: -0.22 (0.23), residues: 1476 helix: 0.62 (0.17), residues: 1000 sheet: -3.37 (0.61), residues: 40 loop : -1.47 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 359 HIS 0.001 0.000 HIS C 411 PHE 0.022 0.001 PHE B 185 TYR 0.030 0.002 TYR B 136 ARG 0.016 0.001 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 185 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7150 (t80) cc_final: 0.6912 (t80) REVERT: A 104 HIS cc_start: 0.8045 (m-70) cc_final: 0.7666 (m-70) REVERT: A 169 MET cc_start: 0.8182 (ptp) cc_final: 0.7811 (ptt) REVERT: A 235 MET cc_start: 0.7153 (ttm) cc_final: 0.6903 (ttp) REVERT: A 259 MET cc_start: 0.8040 (mmm) cc_final: 0.7755 (mmm) REVERT: A 263 ASP cc_start: 0.8459 (m-30) cc_final: 0.8218 (m-30) REVERT: A 413 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8514 (t0) REVERT: B 91 PHE cc_start: 0.6991 (t80) cc_final: 0.6739 (t80) REVERT: B 104 HIS cc_start: 0.8108 (m-70) cc_final: 0.7550 (m-70) REVERT: B 169 MET cc_start: 0.8089 (ptp) cc_final: 0.7850 (ptt) REVERT: B 174 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: B 235 MET cc_start: 0.7107 (ttm) cc_final: 0.6853 (ttp) REVERT: B 259 MET cc_start: 0.8053 (mmm) cc_final: 0.7743 (mmm) REVERT: B 263 ASP cc_start: 0.8464 (m-30) cc_final: 0.8254 (m-30) REVERT: C 45 ASN cc_start: 0.5976 (OUTLIER) cc_final: 0.5659 (t0) REVERT: C 91 PHE cc_start: 0.7079 (t80) cc_final: 0.6796 (t80) REVERT: C 104 HIS cc_start: 0.8134 (m-70) cc_final: 0.7752 (m-70) REVERT: C 169 MET cc_start: 0.8137 (ptp) cc_final: 0.7844 (ptt) REVERT: C 174 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: C 259 MET cc_start: 0.8054 (mmm) cc_final: 0.7723 (mmm) REVERT: C 263 ASP cc_start: 0.8496 (m-30) cc_final: 0.8267 (m-30) REVERT: C 410 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7787 (t80) REVERT: D 45 ASN cc_start: 0.5957 (OUTLIER) cc_final: 0.5679 (t0) REVERT: D 91 PHE cc_start: 0.7074 (t80) cc_final: 0.6851 (t80) REVERT: D 104 HIS cc_start: 0.8081 (m-70) cc_final: 0.7701 (m-70) REVERT: D 169 MET cc_start: 0.8170 (ptp) cc_final: 0.7827 (ptt) REVERT: D 259 MET cc_start: 0.8010 (mmm) cc_final: 0.7748 (mmm) REVERT: D 263 ASP cc_start: 0.8457 (m-30) cc_final: 0.8232 (m-30) REVERT: D 413 ASN cc_start: 0.8892 (m110) cc_final: 0.8597 (t0) outliers start: 41 outliers final: 28 residues processed: 214 average time/residue: 1.0635 time to fit residues: 249.4028 Evaluate side-chains 205 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12388 Z= 0.228 Angle : 0.619 10.837 16764 Z= 0.314 Chirality : 0.041 0.143 1872 Planarity : 0.004 0.048 2096 Dihedral : 4.150 36.423 1682 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.88 % Allowed : 23.48 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.23), residues: 1476 helix: 0.85 (0.17), residues: 980 sheet: -3.18 (0.64), residues: 40 loop : -1.44 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 359 HIS 0.001 0.000 HIS C 303 PHE 0.023 0.001 PHE B 185 TYR 0.036 0.001 TYR B 136 ARG 0.005 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7047 (t80) cc_final: 0.6772 (t80) REVERT: A 104 HIS cc_start: 0.8084 (m-70) cc_final: 0.7706 (m-70) REVERT: A 169 MET cc_start: 0.8165 (ptp) cc_final: 0.7841 (ptt) REVERT: A 235 MET cc_start: 0.7157 (ttm) cc_final: 0.6892 (ttp) REVERT: A 259 MET cc_start: 0.8032 (mmm) cc_final: 0.7767 (mmm) REVERT: A 413 ASN cc_start: 0.8820 (m110) cc_final: 0.8566 (t0) REVERT: B 91 PHE cc_start: 0.7064 (t80) cc_final: 0.6806 (t80) REVERT: B 104 HIS cc_start: 0.8127 (m-70) cc_final: 0.7597 (m-70) REVERT: B 169 MET cc_start: 0.8102 (ptp) cc_final: 0.7857 (ptt) REVERT: B 174 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8511 (mp0) REVERT: B 235 MET cc_start: 0.7112 (ttm) cc_final: 0.6858 (ttp) REVERT: B 240 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 259 MET cc_start: 0.8074 (mmm) cc_final: 0.7760 (mmm) REVERT: C 45 ASN cc_start: 0.6080 (OUTLIER) cc_final: 0.5776 (t0) REVERT: C 91 PHE cc_start: 0.7171 (t80) cc_final: 0.6915 (t80) REVERT: C 104 HIS cc_start: 0.8108 (m-70) cc_final: 0.7722 (m-70) REVERT: C 133 TYR cc_start: 0.4695 (t80) cc_final: 0.4302 (t80) REVERT: C 169 MET cc_start: 0.8115 (ptp) cc_final: 0.7836 (ptt) REVERT: C 259 MET cc_start: 0.8045 (mmm) cc_final: 0.7711 (mmm) REVERT: C 263 ASP cc_start: 0.8490 (m-30) cc_final: 0.8282 (m-30) REVERT: D 45 ASN cc_start: 0.5977 (OUTLIER) cc_final: 0.5737 (t0) REVERT: D 91 PHE cc_start: 0.7129 (t80) cc_final: 0.6920 (t80) REVERT: D 104 HIS cc_start: 0.8081 (m-70) cc_final: 0.7713 (m-70) REVERT: D 169 MET cc_start: 0.8160 (ptp) cc_final: 0.7821 (ptt) REVERT: D 259 MET cc_start: 0.8031 (mmm) cc_final: 0.7758 (mmm) REVERT: D 263 ASP cc_start: 0.8475 (m-30) cc_final: 0.8266 (m-30) REVERT: D 413 ASN cc_start: 0.8949 (m110) cc_final: 0.8601 (t0) outliers start: 38 outliers final: 29 residues processed: 214 average time/residue: 0.9969 time to fit residues: 234.7714 Evaluate side-chains 204 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 0.0470 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12388 Z= 0.204 Angle : 0.622 11.236 16764 Z= 0.315 Chirality : 0.041 0.206 1872 Planarity : 0.004 0.047 2096 Dihedral : 4.075 35.252 1682 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.80 % Allowed : 23.41 % Favored : 73.79 % 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: 0.15 (0.23), residues: 1476 helix: 0.96 (0.17), residues: 980 sheet: -3.14 (0.65), residues: 40 loop : -1.40 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 359 HIS 0.001 0.000 HIS A 411 PHE 0.024 0.001 PHE B 185 TYR 0.039 0.001 TYR C 136 ARG 0.012 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6996 (t80) cc_final: 0.6793 (t80) REVERT: A 104 HIS cc_start: 0.8079 (m-70) cc_final: 0.7716 (m-70) REVERT: A 169 MET cc_start: 0.8159 (ptp) cc_final: 0.7855 (ptt) REVERT: A 235 MET cc_start: 0.7102 (ttm) cc_final: 0.6826 (ttp) REVERT: A 240 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7325 (tm-30) REVERT: B 91 PHE cc_start: 0.7072 (t80) cc_final: 0.6835 (t80) REVERT: B 104 HIS cc_start: 0.8136 (m-70) cc_final: 0.7629 (m-70) REVERT: B 169 MET cc_start: 0.8102 (ptp) cc_final: 0.7859 (ptt) REVERT: B 174 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: B 235 MET cc_start: 0.7104 (ttm) cc_final: 0.6844 (ttp) REVERT: B 240 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7288 (tm-30) REVERT: C 45 ASN cc_start: 0.5989 (OUTLIER) cc_final: 0.5695 (t0) REVERT: C 91 PHE cc_start: 0.7190 (t80) cc_final: 0.6971 (t80) REVERT: C 104 HIS cc_start: 0.8163 (m-70) cc_final: 0.7808 (m-70) REVERT: C 169 MET cc_start: 0.8191 (ptp) cc_final: 0.7891 (ptt) REVERT: C 259 MET cc_start: 0.8029 (mmm) cc_final: 0.7720 (mmm) REVERT: D 91 PHE cc_start: 0.7144 (t80) cc_final: 0.6917 (t80) REVERT: D 104 HIS cc_start: 0.8096 (m-70) cc_final: 0.7754 (m-70) REVERT: D 169 MET cc_start: 0.8186 (ptp) cc_final: 0.7843 (ptt) REVERT: D 174 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: D 259 MET cc_start: 0.8025 (mmm) cc_final: 0.7741 (mmm) REVERT: D 413 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8554 (t0) outliers start: 37 outliers final: 26 residues processed: 216 average time/residue: 1.0647 time to fit residues: 254.4427 Evaluate side-chains 194 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 413 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12388 Z= 0.276 Angle : 0.657 11.142 16764 Z= 0.335 Chirality : 0.042 0.185 1872 Planarity : 0.005 0.050 2096 Dihedral : 4.023 20.869 1680 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.73 % Allowed : 23.56 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1476 helix: 0.91 (0.17), residues: 980 sheet: -2.99 (0.65), residues: 40 loop : -1.36 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.001 0.000 HIS A 303 PHE 0.023 0.001 PHE B 185 TYR 0.024 0.001 TYR A 136 ARG 0.014 0.001 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8094 (m-70) cc_final: 0.7719 (m-70) REVERT: A 169 MET cc_start: 0.8222 (ptp) cc_final: 0.7903 (ptt) REVERT: A 235 MET cc_start: 0.7092 (ttm) cc_final: 0.6824 (ttp) REVERT: A 240 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7379 (tm-30) REVERT: B 91 PHE cc_start: 0.7054 (t80) cc_final: 0.6803 (t80) REVERT: B 104 HIS cc_start: 0.8098 (m-70) cc_final: 0.7534 (m-70) REVERT: B 169 MET cc_start: 0.8151 (ptp) cc_final: 0.7906 (ptt) REVERT: B 174 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: B 235 MET cc_start: 0.7103 (ttm) cc_final: 0.6844 (ttp) REVERT: B 240 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 45 ASN cc_start: 0.6032 (OUTLIER) cc_final: 0.5706 (t0) REVERT: C 91 PHE cc_start: 0.7153 (t80) cc_final: 0.6924 (t80) REVERT: C 104 HIS cc_start: 0.8189 (m-70) cc_final: 0.7855 (m-70) REVERT: C 169 MET cc_start: 0.8213 (ptp) cc_final: 0.7901 (ptt) REVERT: C 410 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7818 (t80) REVERT: D 91 PHE cc_start: 0.7160 (t80) cc_final: 0.6900 (t80) REVERT: D 104 HIS cc_start: 0.8144 (m-70) cc_final: 0.7811 (m-70) REVERT: D 169 MET cc_start: 0.8214 (ptp) cc_final: 0.7863 (ptt) REVERT: D 413 ASN cc_start: 0.8943 (m110) cc_final: 0.8562 (t0) outliers start: 36 outliers final: 27 residues processed: 202 average time/residue: 1.0226 time to fit residues: 227.3713 Evaluate side-chains 190 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 97 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 135 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 90 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12388 Z= 0.189 Angle : 0.667 11.668 16764 Z= 0.335 Chirality : 0.041 0.178 1872 Planarity : 0.004 0.051 2096 Dihedral : 3.945 18.325 1680 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.20 % Allowed : 24.02 % Favored : 73.79 % 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: 0.32 (0.23), residues: 1476 helix: 1.04 (0.17), residues: 980 sheet: -2.75 (0.68), residues: 40 loop : -1.25 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.001 0.000 HIS C 303 PHE 0.024 0.001 PHE B 185 TYR 0.040 0.001 TYR B 136 ARG 0.013 0.000 ARG A 415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8056 (m-70) cc_final: 0.7577 (m-70) REVERT: A 169 MET cc_start: 0.8184 (ptp) cc_final: 0.7874 (ptt) REVERT: A 235 MET cc_start: 0.7108 (ttm) cc_final: 0.6841 (ttp) REVERT: A 240 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7398 (tm-30) REVERT: A 413 ASN cc_start: 0.8759 (m110) cc_final: 0.8524 (t0) REVERT: B 91 PHE cc_start: 0.7077 (t80) cc_final: 0.6854 (t80) REVERT: B 104 HIS cc_start: 0.8029 (m-70) cc_final: 0.7448 (m-70) REVERT: B 169 MET cc_start: 0.8116 (ptp) cc_final: 0.7885 (ptt) REVERT: B 174 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: B 235 MET cc_start: 0.7073 (ttm) cc_final: 0.6818 (ttp) REVERT: B 240 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 45 ASN cc_start: 0.5960 (OUTLIER) cc_final: 0.5650 (t0) REVERT: C 104 HIS cc_start: 0.8145 (m-70) cc_final: 0.7776 (m-70) REVERT: C 169 MET cc_start: 0.8171 (ptp) cc_final: 0.7895 (ptt) REVERT: C 413 ASN cc_start: 0.8855 (m110) cc_final: 0.8511 (t0) REVERT: D 49 ARG cc_start: 0.5905 (mmm160) cc_final: 0.5651 (mmm160) REVERT: D 104 HIS cc_start: 0.8146 (m-70) cc_final: 0.7782 (m-70) REVERT: D 169 MET cc_start: 0.8204 (ptp) cc_final: 0.7902 (ptt) REVERT: D 413 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8518 (t0) outliers start: 29 outliers final: 23 residues processed: 189 average time/residue: 0.9732 time to fit residues: 203.3100 Evaluate side-chains 190 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 413 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 117 optimal weight: 0.0970 chunk 49 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.157629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099850 restraints weight = 20157.050| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.56 r_work: 0.3217 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12388 Z= 0.184 Angle : 0.650 11.335 16764 Z= 0.326 Chirality : 0.040 0.172 1872 Planarity : 0.004 0.052 2096 Dihedral : 3.842 19.967 1680 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.89 % Allowed : 24.47 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.24), residues: 1476 helix: 1.16 (0.18), residues: 980 sheet: -2.57 (0.70), residues: 40 loop : -1.11 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 359 HIS 0.001 0.000 HIS A 303 PHE 0.024 0.001 PHE B 185 TYR 0.024 0.001 TYR A 136 ARG 0.012 0.000 ARG A 415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4787.47 seconds wall clock time: 85 minutes 21.68 seconds (5121.68 seconds total)