Starting phenix.real_space_refine on Fri Sep 27 03:28:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/09_2024/7m6o_23702.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/09_2024/7m6o_23702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/09_2024/7m6o_23702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/09_2024/7m6o_23702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/09_2024/7m6o_23702.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/09_2024/7m6o_23702.cif" } resolution = 2.84 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= 0.001 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 9555 2.51 5 N 2380 2.21 5 O 2635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14670 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 7.51, per 1000 atoms: 0.51 Number of scatterers: 14670 At special positions: 0 Unit cell: (93.16, 91.8, 137.36, 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 2635 8.00 N 2380 7.00 C 9555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 802 " - " ASN E 62 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 38.8% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.789A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.725A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.972A pdb=" N VAL A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 295 removed outlier: 4.127A pdb=" N VAL A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 340 removed outlier: 3.679A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 442 Proline residue: A 419 - end of helix removed outlier: 3.878A pdb=" N HIS A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.789A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.726A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.972A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 295 removed outlier: 4.127A pdb=" N VAL B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 340 removed outlier: 3.679A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 442 Proline residue: B 419 - end of helix removed outlier: 3.878A pdb=" N HIS B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 43 removed outlier: 3.788A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.726A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 264 removed outlier: 3.972A pdb=" N VAL C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 295 removed outlier: 4.127A pdb=" N VAL C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 340 removed outlier: 3.678A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 442 Proline residue: C 419 - end of helix removed outlier: 3.878A pdb=" N HIS C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.788A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.725A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 264 removed outlier: 3.971A pdb=" N VAL D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 295 removed outlier: 4.126A pdb=" N VAL D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 340 removed outlier: 3.679A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 442 Proline residue: D 419 - end of helix removed outlier: 3.879A pdb=" N HIS D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 43 removed outlier: 3.788A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.725A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 264 removed outlier: 3.973A pdb=" N VAL E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 removed outlier: 4.126A pdb=" N VAL E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 340 removed outlier: 3.679A pdb=" N LEU E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 442 Proline residue: E 419 - end of helix removed outlier: 3.879A pdb=" N HIS E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 108 removed outlier: 7.439A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.522A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 181 removed outlier: 3.522A pdb=" N ARG A 220 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 removed outlier: 7.439A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.523A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 181 Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 181 removed outlier: 3.522A pdb=" N ARG B 220 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'C' and resid 106 through 108 removed outlier: 7.439A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 132 removed outlier: 3.522A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 181 Processing sheet with id=AB5, first strand: chain 'C' and resid 173 through 181 removed outlier: 3.522A pdb=" N ARG C 220 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'D' and resid 106 through 108 removed outlier: 7.439A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.522A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 173 through 181 Processing sheet with id=AC1, first strand: chain 'D' and resid 173 through 181 removed outlier: 3.522A pdb=" N ARG D 220 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'E' and resid 106 through 108 removed outlier: 7.439A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 127 through 132 removed outlier: 3.523A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 173 through 181 Processing sheet with id=AC6, first strand: chain 'E' and resid 173 through 181 removed outlier: 3.522A pdb=" N ARG E 220 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 224 through 225 845 hydrogen bonds defined for protein. 2520 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: 4.62 Time building geometry restraints manager: 3.64 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: 4325 1.34 - 1.46: 3271 1.46 - 1.58: 7264 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 15030 Sorted by residual: bond pdb=" SD MET B 287 " pdb=" CE MET B 287 " ideal model delta sigma weight residual 1.791 1.729 0.062 2.50e-02 1.60e+03 6.07e+00 bond pdb=" SD MET E 287 " pdb=" CE MET E 287 " ideal model delta sigma weight residual 1.791 1.730 0.061 2.50e-02 1.60e+03 6.03e+00 bond pdb=" SD MET D 287 " pdb=" CE MET D 287 " ideal model delta sigma weight residual 1.791 1.730 0.061 2.50e-02 1.60e+03 5.96e+00 bond pdb=" SD MET A 287 " pdb=" CE MET A 287 " ideal model delta sigma weight residual 1.791 1.730 0.061 2.50e-02 1.60e+03 5.92e+00 bond pdb=" SD MET C 287 " pdb=" CE MET C 287 " ideal model delta sigma weight residual 1.791 1.731 0.060 2.50e-02 1.60e+03 5.84e+00 ... (remaining 15025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 18932 2.48 - 4.97: 1243 4.97 - 7.45: 169 7.45 - 9.93: 36 9.93 - 12.42: 10 Bond angle restraints: 20390 Sorted by residual: angle pdb=" CA TRP E 263 " pdb=" CB TRP E 263 " pdb=" CG TRP E 263 " ideal model delta sigma weight residual 113.60 124.11 -10.51 1.90e+00 2.77e-01 3.06e+01 angle pdb=" CA TRP A 263 " pdb=" CB TRP A 263 " pdb=" CG TRP A 263 " ideal model delta sigma weight residual 113.60 124.08 -10.48 1.90e+00 2.77e-01 3.04e+01 angle pdb=" CA TRP B 263 " pdb=" CB TRP B 263 " pdb=" CG TRP B 263 " ideal model delta sigma weight residual 113.60 124.07 -10.47 1.90e+00 2.77e-01 3.04e+01 angle pdb=" CA TRP C 263 " pdb=" CB TRP C 263 " pdb=" CG TRP C 263 " ideal model delta sigma weight residual 113.60 124.06 -10.46 1.90e+00 2.77e-01 3.03e+01 angle pdb=" CA TRP D 263 " pdb=" CB TRP D 263 " pdb=" CG TRP D 263 " ideal model delta sigma weight residual 113.60 124.06 -10.46 1.90e+00 2.77e-01 3.03e+01 ... (remaining 20385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 8381 16.73 - 33.46: 602 33.46 - 50.19: 90 50.19 - 66.92: 25 66.92 - 83.65: 10 Dihedral angle restraints: 9108 sinusoidal: 3828 harmonic: 5280 Sorted by residual: dihedral pdb=" N PHE E 418 " pdb=" C PHE E 418 " pdb=" CA PHE E 418 " pdb=" CB PHE E 418 " ideal model delta harmonic sigma weight residual 122.80 132.07 -9.27 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CA PHE A 418 " pdb=" CB PHE A 418 " ideal model delta harmonic sigma weight residual 122.80 132.06 -9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" N PHE D 418 " pdb=" C PHE D 418 " pdb=" CA PHE D 418 " pdb=" CB PHE D 418 " ideal model delta harmonic sigma weight residual 122.80 132.05 -9.25 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 9105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1813 0.096 - 0.191: 406 0.191 - 0.287: 41 0.287 - 0.383: 20 0.383 - 0.478: 10 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CB VAL D 264 " pdb=" CA VAL D 264 " pdb=" CG1 VAL D 264 " pdb=" CG2 VAL D 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB VAL C 264 " pdb=" CA VAL C 264 " pdb=" CG1 VAL C 264 " pdb=" CG2 VAL C 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CB VAL E 264 " pdb=" CA VAL E 264 " pdb=" CG1 VAL E 264 " pdb=" CG2 VAL E 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 2287 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 267 " 0.040 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP C 267 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP C 267 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 267 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 267 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 267 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 267 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 267 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 267 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 267 " 0.040 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP D 267 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP D 267 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP D 267 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 267 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 267 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 267 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 267 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 267 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 267 " 0.040 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP E 267 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP E 267 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP E 267 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 267 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 267 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 267 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 267 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 267 " 0.015 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 89 2.61 - 3.18: 11995 3.18 - 3.76: 21284 3.76 - 4.33: 28049 4.33 - 4.90: 47194 Nonbonded interactions: 108611 Sorted by model distance: nonbonded pdb=" SG CYS D 162 " pdb=" SG CYS D 176 " model vdw 2.041 3.760 nonbonded pdb=" SG CYS C 162 " pdb=" SG CYS C 176 " model vdw 2.041 3.760 nonbonded pdb=" SG CYS E 162 " pdb=" SG CYS E 176 " model vdw 2.041 3.760 nonbonded pdb=" SG CYS B 162 " pdb=" SG CYS B 176 " model vdw 2.042 3.760 nonbonded pdb=" OD2 ASP D 110 " pdb=" OG SER D 112 " model vdw 2.171 3.040 ... (remaining 108606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 442) selection = (chain 'B' and resid 32 through 442) selection = (chain 'C' and resid 32 through 442) selection = (chain 'D' and resid 32 through 442) selection = (chain 'E' and resid 32 through 442) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.320 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.009 0.117 15030 Z= 0.571 Angle : 1.376 12.416 20390 Z= 0.778 Chirality : 0.085 0.478 2290 Planarity : 0.009 0.076 2535 Dihedral : 12.009 83.653 5675 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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 (0.19), residues: 1765 helix: 1.57 (0.19), residues: 625 sheet: 0.35 (0.27), residues: 370 loop : -2.07 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP C 267 HIS 0.007 0.003 HIS B 133 PHE 0.035 0.005 PHE C 72 TYR 0.050 0.005 TYR B 325 ARG 0.010 0.001 ARG D 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.635 Fit side-chains REVERT: B 257 LEU cc_start: 0.9144 (tt) cc_final: 0.8923 (tp) REVERT: B 401 LYS cc_start: 0.8469 (mptt) cc_final: 0.7980 (mttp) REVERT: E 401 LYS cc_start: 0.8352 (mptt) cc_final: 0.8080 (tptt) outliers start: 0 outliers final: 1 residues processed: 266 average time/residue: 1.5013 time to fit residues: 432.4705 Evaluate side-chains 137 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN D 85 ASN E 85 ASN E 201 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15030 Z= 0.255 Angle : 0.730 7.394 20390 Z= 0.392 Chirality : 0.047 0.166 2290 Planarity : 0.005 0.056 2535 Dihedral : 6.543 71.591 2187 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.94 % Allowed : 13.48 % Favored : 84.58 % 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: 0.13 (0.19), residues: 1765 helix: 2.14 (0.19), residues: 645 sheet: 0.91 (0.26), residues: 375 loop : -2.39 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 267 HIS 0.003 0.001 HIS C 335 PHE 0.021 0.002 PHE D 319 TYR 0.019 0.002 TYR E 433 ARG 0.003 0.001 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 1.541 Fit side-chains REVERT: C 270 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7401 (mtp) outliers start: 31 outliers final: 16 residues processed: 171 average time/residue: 1.2237 time to fit residues: 230.9574 Evaluate side-chains 138 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 0.0470 chunk 171 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 290 GLN C 290 GLN D 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15030 Z= 0.197 Angle : 0.633 10.592 20390 Z= 0.336 Chirality : 0.045 0.153 2290 Planarity : 0.004 0.045 2535 Dihedral : 6.001 75.337 2185 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.45 % Allowed : 14.36 % Favored : 83.20 % 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: 0.28 (0.19), residues: 1765 helix: 2.21 (0.19), residues: 645 sheet: 1.13 (0.26), residues: 375 loop : -2.34 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 263 HIS 0.003 0.001 HIS C 335 PHE 0.016 0.001 PHE C 319 TYR 0.017 0.001 TYR E 433 ARG 0.003 0.000 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 1.617 Fit side-chains REVERT: B 285 LEU cc_start: 0.9238 (tt) cc_final: 0.8953 (tp) REVERT: C 410 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8993 (pt) outliers start: 39 outliers final: 15 residues processed: 155 average time/residue: 1.2460 time to fit residues: 213.0757 Evaluate side-chains 137 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 159 optimal weight: 0.0770 chunk 169 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 290 GLN C 290 GLN D 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15030 Z= 0.225 Angle : 0.608 10.164 20390 Z= 0.326 Chirality : 0.044 0.145 2290 Planarity : 0.004 0.036 2535 Dihedral : 6.290 82.892 2185 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.51 % Allowed : 14.42 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.19), residues: 1765 helix: 2.30 (0.19), residues: 645 sheet: 1.07 (0.26), residues: 375 loop : -2.21 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 310 HIS 0.003 0.001 HIS C 335 PHE 0.015 0.002 PHE E 192 TYR 0.016 0.002 TYR E 433 ARG 0.003 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 129 time to evaluate : 1.623 Fit side-chains REVERT: B 285 LEU cc_start: 0.9266 (tt) cc_final: 0.9025 (tp) REVERT: C 410 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8972 (pt) outliers start: 56 outliers final: 28 residues processed: 177 average time/residue: 1.2264 time to fit residues: 240.1665 Evaluate side-chains 148 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 290 GLN C 290 GLN C 329 ASN D 290 GLN E 290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15030 Z= 0.219 Angle : 0.604 12.150 20390 Z= 0.321 Chirality : 0.044 0.158 2290 Planarity : 0.004 0.029 2535 Dihedral : 6.377 85.617 2185 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.45 % Allowed : 16.18 % Favored : 80.38 % 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: 0.35 (0.19), residues: 1765 helix: 2.35 (0.19), residues: 645 sheet: 0.95 (0.26), residues: 375 loop : -2.25 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.003 0.001 HIS C 335 PHE 0.018 0.002 PHE E 428 TYR 0.014 0.002 TYR B 433 ARG 0.003 0.000 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 120 time to evaluate : 1.517 Fit side-chains REVERT: B 285 LEU cc_start: 0.9235 (tt) cc_final: 0.8996 (tp) REVERT: C 410 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8918 (pt) outliers start: 55 outliers final: 34 residues processed: 161 average time/residue: 1.2185 time to fit residues: 217.0461 Evaluate side-chains 153 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 201 GLN B 290 GLN C 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15030 Z= 0.336 Angle : 0.649 8.929 20390 Z= 0.349 Chirality : 0.046 0.166 2290 Planarity : 0.004 0.029 2535 Dihedral : 6.405 86.336 2185 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.82 % Allowed : 17.05 % Favored : 79.12 % 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: 0.17 (0.19), residues: 1765 helix: 1.93 (0.19), residues: 680 sheet: 0.82 (0.27), residues: 370 loop : -2.23 (0.19), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.003 0.001 HIS C 335 PHE 0.021 0.002 PHE A 319 TYR 0.018 0.002 TYR B 221 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 123 time to evaluate : 1.795 Fit side-chains REVERT: B 113 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7545 (pmm) REVERT: B 285 LEU cc_start: 0.9212 (tt) cc_final: 0.9005 (tp) REVERT: C 410 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8912 (pt) outliers start: 61 outliers final: 37 residues processed: 171 average time/residue: 1.2116 time to fit residues: 229.2233 Evaluate side-chains 159 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.0770 chunk 96 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15030 Z= 0.204 Angle : 0.598 8.469 20390 Z= 0.318 Chirality : 0.044 0.157 2290 Planarity : 0.003 0.031 2535 Dihedral : 6.186 87.986 2185 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.63 % Allowed : 17.99 % Favored : 79.37 % 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 (0.19), residues: 1765 helix: 2.07 (0.19), residues: 675 sheet: 0.85 (0.27), residues: 370 loop : -2.14 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS C 335 PHE 0.014 0.001 PHE A 319 TYR 0.015 0.002 TYR B 433 ARG 0.003 0.000 ARG E 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 118 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 MET cc_start: 0.9112 (mmm) cc_final: 0.8852 (tpp) REVERT: C 410 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8894 (pt) outliers start: 42 outliers final: 29 residues processed: 151 average time/residue: 1.2700 time to fit residues: 211.0269 Evaluate side-chains 147 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15030 Z= 0.296 Angle : 0.628 8.165 20390 Z= 0.336 Chirality : 0.045 0.156 2290 Planarity : 0.004 0.031 2535 Dihedral : 6.155 87.679 2185 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.01 % Allowed : 18.06 % 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: 0.21 (0.19), residues: 1765 helix: 1.97 (0.19), residues: 680 sheet: 0.79 (0.27), residues: 370 loop : -2.17 (0.19), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.003 0.001 HIS C 335 PHE 0.017 0.002 PHE A 319 TYR 0.016 0.002 TYR B 221 ARG 0.003 0.000 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 119 time to evaluate : 1.686 Fit side-chains REVERT: B 287 MET cc_start: 0.9157 (mmm) cc_final: 0.8899 (tpp) outliers start: 48 outliers final: 40 residues processed: 161 average time/residue: 1.2361 time to fit residues: 220.0804 Evaluate side-chains 159 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 148 optimal weight: 0.3980 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15030 Z= 0.201 Angle : 0.607 8.196 20390 Z= 0.321 Chirality : 0.044 0.165 2290 Planarity : 0.003 0.032 2535 Dihedral : 5.989 88.702 2185 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.51 % Allowed : 18.62 % Favored : 78.87 % 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: 0.35 (0.19), residues: 1765 helix: 2.07 (0.19), residues: 675 sheet: 0.84 (0.27), residues: 370 loop : -2.01 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS C 133 PHE 0.016 0.001 PHE A 319 TYR 0.015 0.002 TYR D 325 ARG 0.003 0.000 ARG E 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 1.705 Fit side-chains REVERT: A 113 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7595 (pmm) REVERT: B 171 MET cc_start: 0.8175 (ptp) cc_final: 0.7961 (mpp) REVERT: B 287 MET cc_start: 0.9141 (mmm) cc_final: 0.8926 (tpp) REVERT: E 287 MET cc_start: 0.9213 (mmm) cc_final: 0.8432 (tpp) outliers start: 40 outliers final: 30 residues processed: 152 average time/residue: 1.3086 time to fit residues: 219.0585 Evaluate side-chains 151 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15030 Z= 0.219 Angle : 0.616 8.375 20390 Z= 0.325 Chirality : 0.045 0.172 2290 Planarity : 0.004 0.032 2535 Dihedral : 5.922 89.322 2185 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.32 % Allowed : 18.81 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 1765 helix: 2.08 (0.19), residues: 675 sheet: 0.89 (0.27), residues: 370 loop : -2.00 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 PHE 0.023 0.002 PHE E 319 TYR 0.015 0.002 TYR A 325 ARG 0.006 0.000 ARG A 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 122 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7586 (pmm) REVERT: E 287 MET cc_start: 0.9213 (mmm) cc_final: 0.8988 (tpp) outliers start: 37 outliers final: 29 residues processed: 153 average time/residue: 1.3078 time to fit residues: 220.2112 Evaluate side-chains 152 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 0.0270 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 GLN E 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.094190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.064570 restraints weight = 35440.923| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.52 r_work: 0.2860 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15030 Z= 0.181 Angle : 0.600 8.412 20390 Z= 0.314 Chirality : 0.044 0.167 2290 Planarity : 0.003 0.033 2535 Dihedral : 5.784 89.092 2185 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.88 % Allowed : 19.37 % Favored : 78.75 % 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: 0.47 (0.20), residues: 1765 helix: 2.13 (0.19), residues: 675 sheet: 0.81 (0.27), residues: 380 loop : -1.88 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 310 HIS 0.002 0.001 HIS C 335 PHE 0.016 0.001 PHE A 319 TYR 0.015 0.001 TYR D 325 ARG 0.005 0.000 ARG A 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4770.64 seconds wall clock time: 87 minutes 38.21 seconds (5258.21 seconds total)