Starting phenix.real_space_refine on Fri Feb 16 05:35:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubt_20715/02_2024/6ubt_20715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubt_20715/02_2024/6ubt_20715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubt_20715/02_2024/6ubt_20715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubt_20715/02_2024/6ubt_20715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubt_20715/02_2024/6ubt_20715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ubt_20715/02_2024/6ubt_20715.pdb" } resolution = 3.55 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 100 5.16 5 C 9425 2.51 5 N 2355 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 36": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ARG 409": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14505 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2868 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 16, 'TRANS': 336} Chain breaks: 1 Chain: "B" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2868 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 16, 'TRANS': 336} Chain breaks: 1 Chain: "C" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2868 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 16, 'TRANS': 336} Chain breaks: 1 Chain: "D" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2868 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 16, 'TRANS': 336} Chain breaks: 1 Chain: "E" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2868 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 16, 'TRANS': 336} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 7.52, per 1000 atoms: 0.52 Number of scatterers: 14505 At special positions: 0 Unit cell: (97.2, 97.2, 135, 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 100 16.00 O 2625 8.00 N 2355 7.00 C 9425 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 62 " " NAG G 1 " - " ASN B 62 " " NAG H 1 " - " ASN C 62 " " NAG I 1 " - " ASN D 62 " " NAG J 1 " - " ASN E 62 " Time building additional restraints: 5.80 Conformation dependent library (CDL) restraints added in 2.6 seconds 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 37.6% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 295 removed outlier: 3.747A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 339 Processing helix chain 'A' and resid 398 through 440 Proline residue: A 419 - end of helix Processing helix chain 'B' and resid 33 through 41 Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 295 removed outlier: 3.747A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 339 Processing helix chain 'B' and resid 398 through 440 Proline residue: B 419 - end of helix Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 295 removed outlier: 3.748A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 339 Processing helix chain 'C' and resid 398 through 440 Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 33 through 41 Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 295 removed outlier: 3.748A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 339 Processing helix chain 'D' and resid 398 through 440 Proline residue: D 419 - end of helix Processing helix chain 'E' and resid 33 through 41 Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 removed outlier: 3.747A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 339 Processing helix chain 'E' and resid 398 through 440 Proline residue: E 419 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.721A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 8.604A pdb=" N GLN A 201 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE A 67 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 removed outlier: 4.987A pdb=" N SER A 74 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A 83 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET A 178 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 241 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET A 178 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS A 233 " --> pdb=" O CYS A 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 5.721A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 8.604A pdb=" N GLN B 201 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE B 67 " --> pdb=" O GLN B 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 76 removed outlier: 4.986A pdb=" N SER B 74 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 83 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET B 178 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 241 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET B 178 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS B 233 " --> pdb=" O CYS B 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 91 removed outlier: 5.722A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 89 through 91 removed outlier: 8.606A pdb=" N GLN C 201 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE C 67 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 73 through 76 removed outlier: 4.985A pdb=" N SER C 74 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C 83 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 106 through 108 Processing sheet with id=AB8, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET C 178 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 241 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET C 178 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N CYS C 233 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 89 through 91 removed outlier: 5.720A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 89 through 91 removed outlier: 8.605A pdb=" N GLN D 201 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 67 " --> pdb=" O GLN D 201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 73 through 76 removed outlier: 4.985A pdb=" N SER D 74 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG D 83 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AC5, first strand: chain 'D' and resid 123 through 124 removed outlier: 3.666A pdb=" N MET D 178 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 241 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 123 through 124 removed outlier: 3.666A pdb=" N MET D 178 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS D 233 " --> pdb=" O CYS D 222 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 89 through 91 removed outlier: 5.721A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 89 through 91 removed outlier: 8.605A pdb=" N GLN E 201 " --> pdb=" O CYS E 65 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE E 67 " --> pdb=" O GLN E 201 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 73 through 76 removed outlier: 4.986A pdb=" N SER E 74 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG E 83 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 106 through 108 Processing sheet with id=AD2, first strand: chain 'E' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET E 178 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU E 241 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET E 178 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS E 233 " --> pdb=" O CYS E 222 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2055 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: 5.22 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3782 1.34 - 1.46: 3065 1.46 - 1.58: 7833 1.58 - 1.70: 5 1.70 - 1.81: 170 Bond restraints: 14855 Sorted by residual: bond pdb=" C ALA D 273 " pdb=" N PRO D 274 " ideal model delta sigma weight residual 1.334 1.421 -0.087 2.34e-02 1.83e+03 1.37e+01 bond pdb=" CB ILE D 268 " pdb=" CG2 ILE D 268 " ideal model delta sigma weight residual 1.521 1.399 0.122 3.30e-02 9.18e+02 1.37e+01 bond pdb=" C ALA C 273 " pdb=" N PRO C 274 " ideal model delta sigma weight residual 1.334 1.420 -0.087 2.34e-02 1.83e+03 1.37e+01 bond pdb=" C ALA A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.334 1.420 -0.086 2.34e-02 1.83e+03 1.36e+01 bond pdb=" CB ILE A 268 " pdb=" CG2 ILE A 268 " ideal model delta sigma weight residual 1.521 1.399 0.122 3.30e-02 9.18e+02 1.36e+01 ... (remaining 14850 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.37: 399 105.37 - 112.69: 7257 112.69 - 120.01: 5698 120.01 - 127.32: 6569 127.32 - 134.64: 207 Bond angle restraints: 20130 Sorted by residual: angle pdb=" CG ARG B 276 " pdb=" CD ARG B 276 " pdb=" NE ARG B 276 " ideal model delta sigma weight residual 112.00 123.93 -11.93 2.20e+00 2.07e-01 2.94e+01 angle pdb=" CG ARG D 276 " pdb=" CD ARG D 276 " pdb=" NE ARG D 276 " ideal model delta sigma weight residual 112.00 123.93 -11.93 2.20e+00 2.07e-01 2.94e+01 angle pdb=" CG ARG E 276 " pdb=" CD ARG E 276 " pdb=" NE ARG E 276 " ideal model delta sigma weight residual 112.00 123.93 -11.93 2.20e+00 2.07e-01 2.94e+01 angle pdb=" CG ARG C 276 " pdb=" CD ARG C 276 " pdb=" NE ARG C 276 " ideal model delta sigma weight residual 112.00 123.89 -11.89 2.20e+00 2.07e-01 2.92e+01 angle pdb=" CG ARG A 276 " pdb=" CD ARG A 276 " pdb=" NE ARG A 276 " ideal model delta sigma weight residual 112.00 123.87 -11.87 2.20e+00 2.07e-01 2.91e+01 ... (remaining 20125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 8100 17.18 - 34.36: 803 34.36 - 51.54: 77 51.54 - 68.73: 20 68.73 - 85.91: 15 Dihedral angle restraints: 9015 sinusoidal: 3795 harmonic: 5220 Sorted by residual: dihedral pdb=" C ASN E 168 " pdb=" N ASN E 168 " pdb=" CA ASN E 168 " pdb=" CB ASN E 168 " ideal model delta harmonic sigma weight residual -122.60 -130.90 8.30 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C ASN D 168 " pdb=" N ASN D 168 " pdb=" CA ASN D 168 " pdb=" CB ASN D 168 " ideal model delta harmonic sigma weight residual -122.60 -130.88 8.28 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C ASN C 168 " pdb=" N ASN C 168 " pdb=" CA ASN C 168 " pdb=" CB ASN C 168 " ideal model delta harmonic sigma weight residual -122.60 -130.85 8.25 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 9012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1859 0.096 - 0.192: 356 0.192 - 0.288: 50 0.288 - 0.383: 5 0.383 - 0.479: 10 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 62 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 62 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 2277 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP E 118 " -0.026 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C TRP E 118 " 0.088 2.00e-02 2.50e+03 pdb=" O TRP E 118 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS E 119 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 118 " -0.026 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C TRP B 118 " 0.088 2.00e-02 2.50e+03 pdb=" O TRP B 118 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS B 119 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 118 " 0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C TRP D 118 " -0.088 2.00e-02 2.50e+03 pdb=" O TRP D 118 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS D 119 " 0.029 2.00e-02 2.50e+03 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3349 2.80 - 3.32: 13070 3.32 - 3.85: 24126 3.85 - 4.37: 25449 4.37 - 4.90: 45931 Nonbonded interactions: 111925 Sorted by model distance: nonbonded pdb=" O ILE B 268 " pdb=" NH2 ARG B 276 " model vdw 2.274 2.520 nonbonded pdb=" O ILE A 268 " pdb=" NH2 ARG A 276 " model vdw 2.274 2.520 nonbonded pdb=" O ILE E 268 " pdb=" NH2 ARG E 276 " model vdw 2.274 2.520 nonbonded pdb=" O ILE D 268 " pdb=" NH2 ARG D 276 " model vdw 2.274 2.520 nonbonded pdb=" O ILE C 268 " pdb=" NH2 ARG C 276 " model vdw 2.275 2.520 ... (remaining 111920 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' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.610 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 40.460 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.140 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.008 0.122 14855 Z= 0.487 Angle : 1.517 18.344 20130 Z= 0.833 Chirality : 0.083 0.479 2280 Planarity : 0.009 0.074 2510 Dihedral : 12.821 85.906 5625 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.31 % Allowed : 13.40 % Favored : 86.29 % 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: -1.97 (0.20), residues: 1745 helix: 0.86 (0.22), residues: 650 sheet: -2.38 (0.26), residues: 335 loop : -2.79 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 430 HIS 0.005 0.001 HIS C 335 PHE 0.032 0.003 PHE C 169 TYR 0.046 0.004 TYR E 325 ARG 0.006 0.001 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 263 TRP cc_start: 0.8287 (m-10) cc_final: 0.7961 (m-10) REVERT: E 263 TRP cc_start: 0.7949 (m-10) cc_final: 0.7578 (m-90) outliers start: 5 outliers final: 0 residues processed: 252 average time/residue: 0.2529 time to fit residues: 94.4651 Evaluate side-chains 153 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 168 ASN A 174 GLN B 55 ASN B 168 ASN C 55 ASN C 149 ASN C 168 ASN C 174 GLN D 55 ASN D 168 ASN E 55 ASN E 168 ASN E 174 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14855 Z= 0.308 Angle : 0.723 8.322 20130 Z= 0.376 Chirality : 0.046 0.250 2280 Planarity : 0.005 0.057 2510 Dihedral : 5.172 40.414 2135 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.83 % Allowed : 17.36 % Favored : 79.81 % 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: -1.30 (0.20), residues: 1745 helix: 1.42 (0.21), residues: 655 sheet: -1.68 (0.27), residues: 355 loop : -2.65 (0.18), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 263 HIS 0.003 0.001 HIS A 133 PHE 0.014 0.002 PHE B 169 TYR 0.011 0.002 TYR C 221 ARG 0.002 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8693 (m) REVERT: B 263 TRP cc_start: 0.8084 (m-10) cc_final: 0.7429 (m-10) REVERT: C 137 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8566 (m) REVERT: E 137 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8485 (m) outliers start: 45 outliers final: 14 residues processed: 180 average time/residue: 0.2034 time to fit residues: 58.7779 Evaluate side-chains 152 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 168 ASN B 139 ASN B 149 ASN C 168 ASN D 149 ASN D 168 ASN E 149 ASN E 168 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14855 Z= 0.195 Angle : 0.647 9.299 20130 Z= 0.327 Chirality : 0.044 0.239 2280 Planarity : 0.004 0.044 2510 Dihedral : 4.869 36.680 2135 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.01 % Allowed : 19.18 % Favored : 78.81 % 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: -0.71 (0.20), residues: 1745 helix: 2.33 (0.21), residues: 625 sheet: -1.40 (0.27), residues: 380 loop : -2.54 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 263 HIS 0.003 0.000 HIS E 335 PHE 0.018 0.001 PHE D 169 TYR 0.011 0.001 TYR E 246 ARG 0.002 0.000 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.784 Fit side-chains REVERT: A 187 MET cc_start: 0.8834 (tpp) cc_final: 0.8420 (mmp) REVERT: B 32 MET cc_start: 0.8516 (tmm) cc_final: 0.8260 (tmm) REVERT: B 287 MET cc_start: 0.8822 (tpp) cc_final: 0.8603 (tpt) REVERT: E 263 TRP cc_start: 0.8069 (m-10) cc_final: 0.7695 (m-10) REVERT: E 311 MET cc_start: 0.8824 (mmm) cc_final: 0.8600 (mmm) outliers start: 32 outliers final: 22 residues processed: 160 average time/residue: 0.2118 time to fit residues: 54.5958 Evaluate side-chains 162 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 168 ASN C 210 GLN D 168 ASN E 168 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14855 Z= 0.219 Angle : 0.630 9.482 20130 Z= 0.317 Chirality : 0.043 0.228 2280 Planarity : 0.004 0.040 2510 Dihedral : 4.795 35.727 2135 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.14 % Allowed : 18.93 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1745 helix: 2.57 (0.21), residues: 625 sheet: -1.09 (0.28), residues: 380 loop : -2.38 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 263 HIS 0.002 0.001 HIS E 335 PHE 0.024 0.001 PHE E 266 TYR 0.013 0.001 TYR C 325 ARG 0.002 0.000 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.748 Fit side-chains REVERT: A 137 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8655 (m) REVERT: A 187 MET cc_start: 0.8838 (tpp) cc_final: 0.8503 (mmp) REVERT: C 32 MET cc_start: 0.8272 (tmm) cc_final: 0.7957 (tmm) REVERT: C 137 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8454 (m) REVERT: D 32 MET cc_start: 0.8573 (tmm) cc_final: 0.8269 (tmm) REVERT: E 311 MET cc_start: 0.8875 (mmm) cc_final: 0.8663 (mmm) outliers start: 34 outliers final: 23 residues processed: 162 average time/residue: 0.2022 time to fit residues: 52.7996 Evaluate side-chains 165 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 139 ASN C 168 ASN D 168 ASN E 168 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14855 Z= 0.175 Angle : 0.622 9.638 20130 Z= 0.309 Chirality : 0.043 0.234 2280 Planarity : 0.004 0.037 2510 Dihedral : 4.646 33.368 2135 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.08 % Allowed : 20.00 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1745 helix: 2.63 (0.20), residues: 625 sheet: -0.94 (0.29), residues: 380 loop : -2.35 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 263 HIS 0.002 0.000 HIS C 335 PHE 0.018 0.001 PHE D 266 TYR 0.013 0.001 TYR E 325 ARG 0.002 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 1.809 Fit side-chains REVERT: A 32 MET cc_start: 0.8396 (tmm) cc_final: 0.8081 (tmm) REVERT: A 137 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8510 (m) REVERT: A 187 MET cc_start: 0.8748 (tpp) cc_final: 0.8531 (mmp) REVERT: B 32 MET cc_start: 0.8451 (tmm) cc_final: 0.8145 (tmm) REVERT: C 32 MET cc_start: 0.8243 (tmm) cc_final: 0.7966 (tmm) REVERT: C 137 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8446 (m) REVERT: E 32 MET cc_start: 0.8455 (tmm) cc_final: 0.8105 (tmm) outliers start: 33 outliers final: 26 residues processed: 166 average time/residue: 0.2115 time to fit residues: 56.8232 Evaluate side-chains 167 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 168 ASN D 168 ASN E 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14855 Z= 0.195 Angle : 0.616 10.250 20130 Z= 0.308 Chirality : 0.043 0.221 2280 Planarity : 0.003 0.036 2510 Dihedral : 4.590 32.397 2135 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.83 % Allowed : 20.44 % Favored : 76.73 % 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: -0.20 (0.21), residues: 1745 helix: 2.69 (0.20), residues: 625 sheet: -0.90 (0.29), residues: 380 loop : -2.33 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 263 HIS 0.002 0.000 HIS C 335 PHE 0.028 0.001 PHE D 266 TYR 0.014 0.001 TYR E 325 ARG 0.003 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 1.650 Fit side-chains REVERT: A 32 MET cc_start: 0.8420 (tmm) cc_final: 0.8123 (tmm) REVERT: A 137 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8567 (m) REVERT: C 137 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8463 (m) REVERT: E 32 MET cc_start: 0.8394 (tmm) cc_final: 0.8059 (tmm) outliers start: 45 outliers final: 27 residues processed: 170 average time/residue: 0.2057 time to fit residues: 56.6578 Evaluate side-chains 164 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN C 139 ASN D 139 ASN D 168 ASN E 168 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14855 Z= 0.188 Angle : 0.626 10.826 20130 Z= 0.312 Chirality : 0.043 0.220 2280 Planarity : 0.003 0.033 2510 Dihedral : 4.565 31.186 2135 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.77 % Allowed : 21.64 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1745 helix: 2.78 (0.20), residues: 620 sheet: -0.86 (0.29), residues: 380 loop : -2.36 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 263 HIS 0.001 0.000 HIS C 335 PHE 0.020 0.001 PHE B 266 TYR 0.014 0.001 TYR E 325 ARG 0.004 0.000 ARG E 415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.911 Fit side-chains REVERT: A 32 MET cc_start: 0.8370 (tmm) cc_final: 0.8076 (tmm) REVERT: A 137 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8502 (m) REVERT: C 137 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8481 (m) REVERT: D 168 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8851 (p0) REVERT: E 32 MET cc_start: 0.8386 (tmm) cc_final: 0.8091 (tmm) REVERT: E 168 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8907 (p0) outliers start: 44 outliers final: 28 residues processed: 173 average time/residue: 0.2184 time to fit residues: 59.7109 Evaluate side-chains 166 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 0.0470 chunk 83 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN D 168 ASN E 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14855 Z= 0.200 Angle : 0.631 11.625 20130 Z= 0.315 Chirality : 0.043 0.240 2280 Planarity : 0.003 0.031 2510 Dihedral : 4.564 32.415 2135 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.33 % Allowed : 22.08 % Favored : 75.60 % 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 (0.21), residues: 1745 helix: 2.77 (0.20), residues: 620 sheet: -0.84 (0.29), residues: 380 loop : -2.34 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 263 HIS 0.002 0.000 HIS C 239 PHE 0.014 0.001 PHE A 266 TYR 0.013 0.001 TYR E 325 ARG 0.002 0.000 ARG B 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.989 Fit side-chains REVERT: A 32 MET cc_start: 0.8352 (tmm) cc_final: 0.8129 (tmm) REVERT: A 187 MET cc_start: 0.8157 (mmp) cc_final: 0.7845 (mmp) REVERT: B 80 MET cc_start: 0.7574 (mmm) cc_final: 0.7277 (tpt) REVERT: C 137 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8498 (m) REVERT: D 168 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8844 (p0) REVERT: E 32 MET cc_start: 0.8457 (tmm) cc_final: 0.8177 (tmm) REVERT: E 168 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8892 (p0) outliers start: 37 outliers final: 28 residues processed: 163 average time/residue: 0.2202 time to fit residues: 57.2970 Evaluate side-chains 163 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN C 139 ASN D 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14855 Z= 0.247 Angle : 0.656 12.274 20130 Z= 0.325 Chirality : 0.044 0.230 2280 Planarity : 0.004 0.030 2510 Dihedral : 4.607 32.946 2135 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.45 % Allowed : 22.26 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1745 helix: 2.71 (0.20), residues: 625 sheet: -0.85 (0.29), residues: 380 loop : -2.31 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 263 HIS 0.001 0.001 HIS A 239 PHE 0.017 0.001 PHE A 266 TYR 0.015 0.001 TYR D 325 ARG 0.003 0.000 ARG C 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.836 Fit side-chains revert: symmetry clash REVERT: B 80 MET cc_start: 0.7663 (mmm) cc_final: 0.7397 (tpt) REVERT: C 137 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8507 (m) REVERT: E 32 MET cc_start: 0.8469 (tmm) cc_final: 0.8193 (tmm) outliers start: 39 outliers final: 32 residues processed: 164 average time/residue: 0.2285 time to fit residues: 58.7228 Evaluate side-chains 163 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 160 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.0020 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN E 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14855 Z= 0.182 Angle : 0.672 12.519 20130 Z= 0.327 Chirality : 0.044 0.277 2280 Planarity : 0.003 0.029 2510 Dihedral : 4.491 31.111 2135 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.51 % Allowed : 23.58 % Favored : 74.91 % 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: -0.13 (0.21), residues: 1745 helix: 2.63 (0.20), residues: 625 sheet: -0.77 (0.29), residues: 380 loop : -2.23 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 263 HIS 0.001 0.000 HIS C 335 PHE 0.029 0.001 PHE E 266 TYR 0.014 0.001 TYR D 325 ARG 0.003 0.000 ARG C 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.699 Fit side-chains revert: symmetry clash REVERT: B 32 MET cc_start: 0.8388 (tmm) cc_final: 0.8139 (tmm) REVERT: B 80 MET cc_start: 0.7541 (mmm) cc_final: 0.7321 (tpt) REVERT: C 137 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8475 (m) REVERT: E 32 MET cc_start: 0.8530 (tmm) cc_final: 0.8281 (tmm) REVERT: E 187 MET cc_start: 0.9107 (mmm) cc_final: 0.8872 (mmp) outliers start: 24 outliers final: 19 residues processed: 150 average time/residue: 0.2271 time to fit residues: 53.4557 Evaluate side-chains 151 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053389 restraints weight = 56872.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055244 restraints weight = 28232.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056428 restraints weight = 17962.287| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14855 Z= 0.193 Angle : 0.655 12.374 20130 Z= 0.321 Chirality : 0.044 0.326 2280 Planarity : 0.003 0.029 2510 Dihedral : 4.443 31.117 2135 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.82 % Allowed : 23.14 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1745 helix: 2.60 (0.20), residues: 625 sheet: -0.72 (0.29), residues: 380 loop : -2.21 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 263 HIS 0.001 0.000 HIS C 335 PHE 0.026 0.001 PHE E 266 TYR 0.015 0.001 TYR D 325 ARG 0.003 0.000 ARG C 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.07 seconds wall clock time: 45 minutes 49.73 seconds (2749.73 seconds total)