Starting phenix.real_space_refine on Tue Nov 18 14:35:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6o_23702/11_2025/7m6o_23702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6o_23702/11_2025/7m6o_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/cci-nas-00/data/ceres_data/7m6o_23702/11_2025/7m6o_23702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6o_23702/11_2025/7m6o_23702.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6o_23702/11_2025/7m6o_23702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6o_23702/11_2025/7m6o_23702.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 2.84, per 1000 atoms: 0.19 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=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 176 " distance=2.04 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 176 " distance=2.04 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 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: 1.06 Conformation dependent library (CDL) restraints added in 675.2 milliseconds 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: 0.50 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: 2.49 Time building geometry restraints manager: 1.48 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: 8385 16.73 - 33.46: 610 33.46 - 50.19: 90 50.19 - 66.92: 25 66.92 - 83.65: 10 Dihedral angle restraints: 9120 sinusoidal: 3840 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 9117 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: 2.17 - 2.72: 594 2.72 - 3.26: 13746 3.26 - 3.81: 21821 3.81 - 4.35: 26910 4.35 - 4.90: 45528 Nonbonded interactions: 108599 Sorted by model distance: nonbonded pdb=" OD2 ASP D 110 " pdb=" OG SER D 112 " model vdw 2.171 3.040 nonbonded pdb=" OD2 ASP E 110 " pdb=" OG SER E 112 " model vdw 2.171 3.040 nonbonded pdb=" OD2 ASP B 110 " pdb=" OG SER B 112 " model vdw 2.172 3.040 nonbonded pdb=" OD2 ASP C 110 " pdb=" OG SER C 112 " model vdw 2.172 3.040 nonbonded pdb=" OD2 ASP A 110 " pdb=" OG SER A 112 " model vdw 2.172 3.040 ... (remaining 108594 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: 0.01 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: 6.720 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.520 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.120 ------------------------------------------------------------------------------- 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 15040 Z= 0.396 Angle : 1.377 12.416 20415 Z= 0.778 Chirality : 0.085 0.478 2290 Planarity : 0.009 0.076 2535 Dihedral : 12.009 83.653 5675 Min Nonbonded Distance : 2.171 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG D 295 TYR 0.050 0.005 TYR B 325 PHE 0.035 0.005 PHE C 72 TRP 0.053 0.005 TRP C 267 HIS 0.007 0.003 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00882 (15030) covalent geometry : angle 1.37555 (20390) SS BOND : bond 0.01047 ( 5) SS BOND : angle 1.25325 ( 10) hydrogen bonds : bond 0.19438 ( 720) hydrogen bonds : angle 7.33821 ( 2520) link_NAG-ASN : bond 0.00418 ( 5) link_NAG-ASN : angle 2.76923 ( 15) *********************** 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 to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.495 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: 0.7518 time to fit residues: 215.0919 Evaluate side-chains 137 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.3792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.095473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.067172 restraints weight = 35995.417| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.51 r_work: 0.2921 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15040 Z= 0.171 Angle : 0.726 7.567 20415 Z= 0.389 Chirality : 0.047 0.170 2290 Planarity : 0.005 0.056 2535 Dihedral : 6.519 71.604 2187 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.01 % Allowed : 12.92 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 1765 helix: 2.15 (0.19), residues: 645 sheet: 0.90 (0.26), residues: 375 loop : -2.40 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 220 TYR 0.019 0.002 TYR E 433 PHE 0.021 0.002 PHE D 319 TRP 0.011 0.002 TRP C 267 HIS 0.004 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00370 (15030) covalent geometry : angle 0.72546 (20390) SS BOND : bond 0.00617 ( 5) SS BOND : angle 0.49849 ( 10) hydrogen bonds : bond 0.06856 ( 720) hydrogen bonds : angle 5.28031 ( 2520) link_NAG-ASN : bond 0.00093 ( 5) link_NAG-ASN : angle 1.47479 ( 15) *********************** 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 180 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.596 Fit side-chains REVERT: A 286 THR cc_start: 0.9139 (t) cc_final: 0.8915 (p) REVERT: B 113 MET cc_start: 0.8139 (pp-130) cc_final: 0.7853 (ppp) REVERT: B 190 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8643 (tm) REVERT: B 244 MET cc_start: 0.8201 (mmm) cc_final: 0.7918 (mmm) REVERT: C 270 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7677 (mtp) REVERT: D 113 MET cc_start: 0.8040 (pp-130) cc_final: 0.7706 (ppp) outliers start: 32 outliers final: 17 residues processed: 172 average time/residue: 0.6123 time to fit residues: 115.5220 Evaluate side-chains 142 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 190 LEU 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 210 GLN 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 111 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 164 optimal weight: 0.0010 chunk 116 optimal weight: 0.0370 chunk 83 optimal weight: 0.0980 chunk 166 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 140 optimal weight: 0.0870 chunk 149 optimal weight: 0.8980 overall best weight: 0.1642 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.097881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069745 restraints weight = 36083.566| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.54 r_work: 0.2970 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15040 Z= 0.133 Angle : 0.618 11.591 20415 Z= 0.326 Chirality : 0.044 0.154 2290 Planarity : 0.004 0.043 2535 Dihedral : 5.912 75.810 2185 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.13 % Allowed : 14.42 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1765 helix: 2.31 (0.20), residues: 645 sheet: 1.19 (0.26), residues: 375 loop : -2.25 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 220 TYR 0.018 0.001 TYR E 433 PHE 0.016 0.001 PHE D 319 TRP 0.024 0.002 TRP C 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00266 (15030) covalent geometry : angle 0.61847 (20390) SS BOND : bond 0.00389 ( 5) SS BOND : angle 0.19187 ( 10) hydrogen bonds : bond 0.05561 ( 720) hydrogen bonds : angle 4.66189 ( 2520) link_NAG-ASN : bond 0.00322 ( 5) link_NAG-ASN : angle 0.79529 ( 15) *********************** 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 to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: B 113 MET cc_start: 0.8239 (pp-130) cc_final: 0.7999 (ppp) REVERT: B 190 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8596 (tm) REVERT: B 420 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8754 (pt) REVERT: C 77 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8324 (mm-30) REVERT: C 113 MET cc_start: 0.8309 (ppp) cc_final: 0.8065 (ppp) REVERT: D 113 MET cc_start: 0.8159 (pp-130) cc_final: 0.7874 (ppp) REVERT: D 190 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8522 (tm) REVERT: E 287 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8179 (ttm) outliers start: 34 outliers final: 13 residues processed: 153 average time/residue: 0.6066 time to fit residues: 101.9424 Evaluate side-chains 140 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 77 GLU 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 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 416 VAL 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 45 VAL Chi-restraints excluded: chain E residue 287 MET 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 121 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.095531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066775 restraints weight = 35964.740| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.53 r_work: 0.2906 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15040 Z= 0.147 Angle : 0.605 10.310 20415 Z= 0.320 Chirality : 0.044 0.151 2290 Planarity : 0.004 0.038 2535 Dihedral : 6.110 81.712 2185 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.95 % Allowed : 14.80 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1765 helix: 2.31 (0.20), residues: 645 sheet: 1.31 (0.27), residues: 375 loop : -2.21 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 220 TYR 0.015 0.002 TYR E 433 PHE 0.013 0.001 PHE C 87 TRP 0.009 0.001 TRP A 310 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00336 (15030) covalent geometry : angle 0.60467 (20390) SS BOND : bond 0.00398 ( 5) SS BOND : angle 0.43482 ( 10) hydrogen bonds : bond 0.05380 ( 720) hydrogen bonds : angle 4.57253 ( 2520) link_NAG-ASN : bond 0.00052 ( 5) link_NAG-ASN : angle 1.13724 ( 15) *********************** 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 171 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.596 Fit side-chains REVERT: A 77 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: B 77 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: B 113 MET cc_start: 0.8286 (pp-130) cc_final: 0.8021 (ppp) REVERT: B 190 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8750 (tm) REVERT: C 77 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8464 (mm-30) REVERT: D 77 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8478 (mm-30) REVERT: D 113 MET cc_start: 0.8173 (pp-130) cc_final: 0.7953 (ppp) REVERT: D 270 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7686 (tpt) outliers start: 47 outliers final: 18 residues processed: 160 average time/residue: 0.6416 time to fit residues: 112.1986 Evaluate side-chains 140 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 190 LEU 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 77 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 77 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 270 MET 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 320 SER 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 152 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 0.0040 chunk 110 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.092905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.063496 restraints weight = 35983.476| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.51 r_work: 0.2827 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15040 Z= 0.191 Angle : 0.627 6.629 20415 Z= 0.338 Chirality : 0.045 0.154 2290 Planarity : 0.004 0.029 2535 Dihedral : 6.435 84.575 2185 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.57 % Allowed : 15.80 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1765 helix: 2.33 (0.19), residues: 645 sheet: 0.94 (0.26), residues: 375 loop : -2.22 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.015 0.002 TYR B 221 PHE 0.018 0.002 PHE E 428 TRP 0.009 0.001 TRP B 92 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00452 (15030) covalent geometry : angle 0.62650 (20390) SS BOND : bond 0.00484 ( 5) SS BOND : angle 0.78054 ( 10) hydrogen bonds : bond 0.05591 ( 720) hydrogen bonds : angle 4.59471 ( 2520) link_NAG-ASN : bond 0.00071 ( 5) link_NAG-ASN : angle 1.38451 ( 15) *********************** 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 178 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 0.582 Fit side-chains REVERT: A 77 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8419 (mm-30) REVERT: A 319 PHE cc_start: 0.8189 (t80) cc_final: 0.7985 (m-10) REVERT: B 113 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7990 (ppp) REVERT: B 187 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8925 (mmm) REVERT: B 190 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8807 (tm) REVERT: B 285 LEU cc_start: 0.9193 (tt) cc_final: 0.8976 (tp) REVERT: C 77 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8524 (mm-30) REVERT: D 113 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8033 (ppp) outliers start: 57 outliers final: 27 residues processed: 166 average time/residue: 0.6061 time to fit residues: 110.5800 Evaluate side-chains 152 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU 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 45 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 MET 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 77 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 110 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 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 290 GLN B 290 GLN C 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.065081 restraints weight = 35616.767| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.51 r_work: 0.2863 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15040 Z= 0.127 Angle : 0.575 7.388 20415 Z= 0.308 Chirality : 0.043 0.155 2290 Planarity : 0.003 0.028 2535 Dihedral : 6.284 86.788 2185 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.01 % Allowed : 17.81 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1765 helix: 2.40 (0.19), residues: 645 sheet: 0.96 (0.26), residues: 380 loop : -2.16 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 437 TYR 0.014 0.002 TYR A 433 PHE 0.019 0.001 PHE E 428 TRP 0.008 0.001 TRP A 310 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00280 (15030) covalent geometry : angle 0.57468 (20390) SS BOND : bond 0.00384 ( 5) SS BOND : angle 0.42421 ( 10) hydrogen bonds : bond 0.05002 ( 720) hydrogen bonds : angle 4.38912 ( 2520) link_NAG-ASN : bond 0.00218 ( 5) link_NAG-ASN : angle 0.90903 ( 15) *********************** 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 156 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: B 113 MET cc_start: 0.8295 (pp-130) cc_final: 0.7873 (ppp) REVERT: B 187 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8871 (mmm) REVERT: B 190 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8745 (tm) REVERT: B 285 LEU cc_start: 0.9189 (tt) cc_final: 0.8981 (tp) REVERT: C 77 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8525 (mm-30) REVERT: C 113 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8039 (pmm) REVERT: D 113 MET cc_start: 0.8216 (pp-130) cc_final: 0.7909 (ppp) REVERT: D 190 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8676 (tm) outliers start: 32 outliers final: 19 residues processed: 146 average time/residue: 0.6706 time to fit residues: 106.7570 Evaluate side-chains 143 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU 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 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER 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 285 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 289 THR 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 18 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 128 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.063694 restraints weight = 35509.667| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.49 r_work: 0.2834 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15040 Z= 0.159 Angle : 0.597 8.783 20415 Z= 0.321 Chirality : 0.044 0.167 2290 Planarity : 0.003 0.029 2535 Dihedral : 6.188 87.311 2185 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.13 % Allowed : 17.24 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1765 helix: 2.40 (0.19), residues: 645 sheet: 1.00 (0.27), residues: 370 loop : -2.13 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 437 TYR 0.014 0.002 TYR D 433 PHE 0.015 0.002 PHE A 87 TRP 0.006 0.001 TRP B 92 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00373 (15030) covalent geometry : angle 0.59638 (20390) SS BOND : bond 0.00411 ( 5) SS BOND : angle 0.59273 ( 10) hydrogen bonds : bond 0.05117 ( 720) hydrogen bonds : angle 4.42980 ( 2520) link_NAG-ASN : bond 0.00022 ( 5) link_NAG-ASN : angle 1.24130 ( 15) *********************** 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 167 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8470 (mm-30) REVERT: B 113 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7895 (ppp) REVERT: B 187 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8868 (mmm) REVERT: B 190 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8819 (tm) REVERT: B 285 LEU cc_start: 0.9180 (tt) cc_final: 0.8978 (tp) REVERT: C 77 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8507 (mm-30) REVERT: C 113 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7989 (pmm) REVERT: D 113 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7938 (ppp) REVERT: D 190 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8773 (tm) outliers start: 50 outliers final: 32 residues processed: 158 average time/residue: 0.6166 time to fit residues: 106.9382 Evaluate side-chains 157 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU 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 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 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 187 MET 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 45 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 150 VAL 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 416 VAL Chi-restraints excluded: chain D residue 113 MET 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 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 190 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 75 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064934 restraints weight = 35573.828| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.50 r_work: 0.2859 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15040 Z= 0.125 Angle : 0.572 8.409 20415 Z= 0.305 Chirality : 0.043 0.160 2290 Planarity : 0.003 0.029 2535 Dihedral : 5.997 88.449 2185 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.63 % Allowed : 17.62 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1765 helix: 2.46 (0.19), residues: 645 sheet: 1.02 (0.27), residues: 370 loop : -2.05 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.014 0.001 TYR A 325 PHE 0.011 0.001 PHE B 319 TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00281 (15030) covalent geometry : angle 0.57216 (20390) SS BOND : bond 0.00369 ( 5) SS BOND : angle 0.39850 ( 10) hydrogen bonds : bond 0.04682 ( 720) hydrogen bonds : angle 4.26890 ( 2520) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 0.91258 ( 15) *********************** 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 164 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8509 (mm-30) REVERT: B 113 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7998 (ppp) REVERT: B 187 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8817 (mmm) REVERT: B 190 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8780 (tm) REVERT: B 287 MET cc_start: 0.8896 (tpp) cc_final: 0.8528 (tpp) REVERT: C 77 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8539 (mm-30) REVERT: C 113 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7948 (pmm) REVERT: D 113 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7835 (ppp) REVERT: D 190 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8709 (tm) outliers start: 42 outliers final: 23 residues processed: 155 average time/residue: 0.6755 time to fit residues: 113.9451 Evaluate side-chains 150 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU 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 B residue 113 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 113 MET 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 416 VAL Chi-restraints excluded: chain D residue 113 MET 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 190 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER 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 5 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 0.0470 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064340 restraints weight = 35824.455| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.52 r_work: 0.2846 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15040 Z= 0.139 Angle : 0.593 8.371 20415 Z= 0.316 Chirality : 0.044 0.168 2290 Planarity : 0.003 0.030 2535 Dihedral : 5.916 88.153 2185 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.63 % Allowed : 18.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1765 helix: 2.44 (0.19), residues: 645 sheet: 1.01 (0.27), residues: 370 loop : -2.01 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 437 TYR 0.014 0.002 TYR E 325 PHE 0.018 0.001 PHE E 428 TRP 0.006 0.001 TRP B 92 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00322 (15030) covalent geometry : angle 0.59235 (20390) SS BOND : bond 0.00378 ( 5) SS BOND : angle 0.47480 ( 10) hydrogen bonds : bond 0.04710 ( 720) hydrogen bonds : angle 4.27773 ( 2520) link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 1.05475 ( 15) *********************** 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 163 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8533 (mm-30) REVERT: B 113 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7853 (ppp) REVERT: B 187 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8847 (mmm) REVERT: B 190 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8837 (tm) REVERT: B 287 MET cc_start: 0.8914 (tpp) cc_final: 0.8527 (tpp) REVERT: C 77 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8535 (mm-30) REVERT: C 113 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7880 (pmm) REVERT: D 113 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7955 (ppp) REVERT: D 190 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8748 (tm) REVERT: D 221 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7962 (p90) outliers start: 42 outliers final: 25 residues processed: 152 average time/residue: 0.6458 time to fit residues: 107.1896 Evaluate side-chains 153 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU 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 B residue 113 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 190 LEU 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 77 GLU Chi-restraints excluded: chain C residue 113 MET 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 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 221 TYR 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 190 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER 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 100 optimal weight: 9.9990 chunk 131 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.093972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064645 restraints weight = 35670.014| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.51 r_work: 0.2852 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15040 Z= 0.131 Angle : 0.590 8.437 20415 Z= 0.313 Chirality : 0.044 0.168 2290 Planarity : 0.003 0.029 2535 Dihedral : 5.844 88.512 2185 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.26 % Allowed : 18.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1765 helix: 2.06 (0.19), residues: 680 sheet: 1.03 (0.27), residues: 370 loop : -1.96 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.014 0.001 TYR E 325 PHE 0.013 0.001 PHE B 319 TRP 0.007 0.001 TRP A 310 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00302 (15030) covalent geometry : angle 0.58943 (20390) SS BOND : bond 0.00363 ( 5) SS BOND : angle 0.44657 ( 10) hydrogen bonds : bond 0.04578 ( 720) hydrogen bonds : angle 4.25269 ( 2520) link_NAG-ASN : bond 0.00135 ( 5) link_NAG-ASN : angle 0.92266 ( 15) ********************** 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 158 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: B 113 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8089 (ppp) REVERT: B 187 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8839 (mmm) REVERT: B 190 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8801 (tm) REVERT: B 287 MET cc_start: 0.8894 (tpp) cc_final: 0.8589 (tpp) REVERT: C 77 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8560 (mm-30) REVERT: D 113 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7869 (ppp) REVERT: D 190 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8735 (tm) REVERT: D 221 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7932 (p90) REVERT: E 113 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7801 (pmm) outliers start: 36 outliers final: 23 residues processed: 151 average time/residue: 0.6336 time to fit residues: 104.6314 Evaluate side-chains 152 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU 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 B residue 113 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 190 LEU 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 45 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 150 VAL 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 113 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 190 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 0.0270 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.093419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.064038 restraints weight = 35440.961| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.49 r_work: 0.2838 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 0.037 15040 Z= 0.147 Angle : 0.597 8.276 20415 Z= 0.318 Chirality : 0.044 0.174 2290 Planarity : 0.003 0.030 2535 Dihedral : 5.849 89.139 2185 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.63 % Allowed : 18.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 1765 helix: 2.05 (0.19), residues: 680 sheet: 1.00 (0.27), residues: 370 loop : -1.96 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.015 0.002 TYR E 325 PHE 0.015 0.002 PHE E 428 TRP 0.008 0.001 TRP A 263 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00343 (15030) covalent geometry : angle 0.59698 (20390) SS BOND : bond 0.00389 ( 5) SS BOND : angle 0.52346 ( 10) hydrogen bonds : bond 0.04699 ( 720) hydrogen bonds : angle 4.29883 ( 2520) link_NAG-ASN : bond 0.00051 ( 5) link_NAG-ASN : angle 1.07199 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4817.17 seconds wall clock time: 83 minutes 1.20 seconds (4981.20 seconds total)