Starting phenix.real_space_refine (version: dev) on Mon Feb 20 12:53:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/02_2023/7w3y_32296.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/02_2023/7w3y_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_32296/02_2023/7w3y_32296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/02_2023/7w3y_32296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/02_2023/7w3y_32296.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3y_32296/02_2023/7w3y_32296.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 7.04, per 1000 atoms: 0.58 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: 4.99 Conformation dependent library (CDL) restraints added in 1.9 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: 0.48 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: 3.48 Time building geometry restraints manager: 5.38 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 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. 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: 0.820 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: 5.390 Check model and map are aligned: 0.200 Process input model: 33.910 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 % 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 *********************** 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 : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 268 average time/residue: 1.3775 time to fit residues: 397.5074 Evaluate side-chains 191 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.1075 time to fit residues: 2.7883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 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: 2.5988 ------------------------------------------------------------------------------- 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: 0.8468 moved from start: 0.2041 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= 0.371 Angle : 0.655 9.587 16764 Z= 0.344 Chirality : 0.044 0.133 1872 Planarity : 0.005 0.057 2096 Dihedral : 4.705 25.465 1680 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.22), residues: 1476 helix: -0.45 (0.16), residues: 992 sheet: None (None), residues: 0 loop : -2.35 (0.29), residues: 484 *********************** 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 219 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 1.451 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 212 average time/residue: 1.2749 time to fit residues: 293.3043 Evaluate side-chains 178 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 8 average time/residue: 0.1477 time to fit residues: 4.0604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 413 ASN B 414 GLN 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: 0.8433 moved from start: 0.2514 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= 0.217 Angle : 0.605 9.926 16764 Z= 0.310 Chirality : 0.041 0.143 1872 Planarity : 0.005 0.086 2096 Dihedral : 4.456 23.833 1680 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 3.18 % 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: -0.92 (0.22), residues: 1476 helix: 0.18 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -2.12 (0.28), residues: 504 *********************** 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 231 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 1.467 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: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 26 residues processed: 213 average time/residue: 1.1715 time to fit residues: 271.7851 Evaluate side-chains 195 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 16 residues processed: 14 average time/residue: 0.3959 time to fit residues: 8.7194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2772 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= 0.185 Angle : 0.596 11.161 16764 Z= 0.300 Chirality : 0.040 0.143 1872 Planarity : 0.005 0.062 2096 Dihedral : 4.255 22.528 1680 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 3.41 % 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: -0.54 (0.23), residues: 1476 helix: 0.46 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -1.98 (0.29), residues: 496 *********************** 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 222 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 177 time to evaluate : 1.448 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: symmetry clash outliers start: 45 outliers final: 29 residues processed: 221 average time/residue: 1.0717 time to fit residues: 260.1198 Evaluate side-chains 190 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 5 average time/residue: 0.1385 time to fit residues: 2.9725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.052 12388 Z= 0.501 Angle : 0.705 10.582 16764 Z= 0.363 Chirality : 0.046 0.142 1872 Planarity : 0.006 0.053 2096 Dihedral : 4.400 22.654 1680 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 3.48 % 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: -0.81 (0.23), residues: 1476 helix: 0.20 (0.17), residues: 1000 sheet: -3.78 (0.55), residues: 40 loop : -1.79 (0.33), residues: 436 *********************** 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 204 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 1.621 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: symmetry clash outliers start: 46 outliers final: 40 residues processed: 200 average time/residue: 1.1450 time to fit residues: 251.4048 Evaluate side-chains 194 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 37 residues processed: 3 average time/residue: 0.0953 time to fit residues: 2.3843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 118 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.3073 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= 0.188 Angle : 0.606 11.234 16764 Z= 0.304 Chirality : 0.041 0.145 1872 Planarity : 0.005 0.050 2096 Dihedral : 4.176 20.134 1680 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 3.56 % 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: -0.30 (0.23), residues: 1476 helix: 0.64 (0.17), residues: 980 sheet: -3.51 (0.60), residues: 40 loop : -1.64 (0.32), residues: 456 *********************** 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 224 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 177 time to evaluate : 1.604 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: symmetry clash outliers start: 47 outliers final: 37 residues processed: 212 average time/residue: 1.0747 time to fit residues: 249.7644 Evaluate side-chains 203 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 27 residues processed: 10 average time/residue: 0.4511 time to fit residues: 7.4414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 89 optimal weight: 0.0970 chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 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: 0.8420 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12388 Z= 0.198 Angle : 0.614 11.250 16764 Z= 0.307 Chirality : 0.040 0.142 1872 Planarity : 0.004 0.049 2096 Dihedral : 3.989 17.877 1680 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1476 helix: 0.84 (0.17), residues: 980 sheet: -3.18 (0.64), residues: 40 loop : -1.57 (0.31), residues: 456 *********************** 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 213 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 26 residues processed: 209 average time/residue: 1.0908 time to fit residues: 250.2306 Evaluate side-chains 191 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 3 average time/residue: 1.8309 time to fit residues: 7.8823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** D 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12388 Z= 0.184 Angle : 0.622 11.708 16764 Z= 0.309 Chirality : 0.040 0.144 1872 Planarity : 0.004 0.048 2096 Dihedral : 3.865 15.499 1680 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 2.73 % 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: 0.19 (0.23), residues: 1476 helix: 1.00 (0.17), residues: 980 sheet: -2.96 (0.67), residues: 40 loop : -1.44 (0.31), residues: 456 *********************** 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 222 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 28 residues processed: 215 average time/residue: 1.1518 time to fit residues: 271.6185 Evaluate side-chains 193 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 6 average time/residue: 0.3973 time to fit residues: 4.9151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 overall best weight: 1.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN D 305 GLN D 413 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 12388 Z= 0.221 Angle : 0.637 11.454 16764 Z= 0.322 Chirality : 0.041 0.151 1872 Planarity : 0.005 0.084 2096 Dihedral : 3.844 18.468 1680 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1476 helix: 1.05 (0.17), residues: 980 sheet: -2.87 (0.67), residues: 40 loop : -1.38 (0.31), residues: 456 *********************** 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 199 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 23 residues processed: 197 average time/residue: 1.0688 time to fit residues: 231.9379 Evaluate side-chains 182 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 2.1958 time to fit residues: 4.7435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN D 413 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 0.042 12388 Z= 0.190 Angle : 0.658 12.218 16764 Z= 0.325 Chirality : 0.040 0.144 1872 Planarity : 0.005 0.073 2096 Dihedral : 3.843 15.917 1680 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1476 helix: 1.13 (0.18), residues: 980 sheet: -2.69 (0.68), residues: 40 loop : -1.21 (0.31), residues: 456 ********************** 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 206 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 23 residues processed: 204 average time/residue: 1.0913 time to fit residues: 245.7154 Evaluate side-chains 183 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 2 average time/residue: 0.9755 time to fit residues: 4.1914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN D 305 GLN D 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.156537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098689 restraints weight = 20174.104| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.50 r_work: 0.3199 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12388 Z= 0.201 Angle : 0.656 11.321 16764 Z= 0.327 Chirality : 0.041 0.142 1872 Planarity : 0.005 0.076 2096 Dihedral : 3.848 18.536 1680 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.24), residues: 1476 helix: 1.24 (0.18), residues: 976 sheet: -2.54 (0.69), residues: 40 loop : -1.20 (0.32), residues: 460 =============================================================================== Job complete usr+sys time: 4643.86 seconds wall clock time: 84 minutes 3.34 seconds (5043.34 seconds total)