Starting phenix.real_space_refine on Fri Jun 13 13:43:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6q_23704/06_2025/7m6q_23704.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6q_23704/06_2025/7m6q_23704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m6q_23704/06_2025/7m6q_23704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6q_23704/06_2025/7m6q_23704.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6q_23704/06_2025/7m6q_23704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6q_23704/06_2025/7m6q_23704.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9590 2.51 5 N 2390 2.21 5 O 2645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14725 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2903 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 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: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 7.13, per 1000 atoms: 0.48 Number of scatterers: 14725 At special positions: 0 Unit cell: (94.6, 92.4, 139.7, 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 2645 8.00 N 2390 7.00 C 9590 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 802 " - " ASN A 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 501 " - " ASN E 62 " Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 40.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.545A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 251 removed outlier: 3.893A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 removed outlier: 3.510A pdb=" N SER A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 341 Processing helix chain 'A' and resid 395 through 442 removed outlier: 3.962A pdb=" N MET A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.528A pdb=" N SER A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.544A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.893A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 269 removed outlier: 3.510A pdb=" N SER B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 341 Processing helix chain 'B' and resid 395 through 442 removed outlier: 3.962A pdb=" N MET B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.528A pdb=" N SER B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 43 removed outlier: 3.544A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 removed outlier: 3.894A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 269 removed outlier: 3.511A pdb=" N SER C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP C 267 " --> pdb=" O TRP C 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 341 Processing helix chain 'C' and resid 395 through 442 removed outlier: 3.962A pdb=" N MET C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.528A pdb=" N SER C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.545A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 removed outlier: 3.894A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 269 removed outlier: 3.511A pdb=" N SER D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP D 267 " --> pdb=" O TRP D 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 341 Processing helix chain 'D' and resid 395 through 442 removed outlier: 3.963A pdb=" N MET D 399 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.528A pdb=" N SER D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 43 removed outlier: 3.545A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 251 removed outlier: 3.894A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 269 removed outlier: 3.511A pdb=" N SER E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 341 Processing helix chain 'E' and resid 395 through 442 removed outlier: 3.962A pdb=" N MET E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 3.527A pdb=" N SER E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) removed outlier: 3.886A 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: 3.959A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.895A 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 131 removed outlier: 3.661A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.565A 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: 3.959A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.894A 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 131 removed outlier: 3.662A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.565A 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: 3.959A pdb=" N TRP C 92 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 5.895A 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 131 removed outlier: 3.663A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP C 92 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.565A 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: 3.958A pdb=" N TRP D 92 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.894A 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 131 removed outlier: 3.662A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP D 92 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 124 removed outlier: 3.565A 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: 3.959A pdb=" N TRP E 92 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.894A 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 131 removed outlier: 3.662A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP E 92 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AC6, first strand: chain 'E' and resid 123 through 124 removed outlier: 3.566A 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 225 860 hydrogen bonds defined for protein. 2505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 3.88 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: 4487 1.34 - 1.46: 3294 1.46 - 1.58: 7134 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 15085 Sorted by residual: bond pdb=" CB VAL C 259 " pdb=" CG2 VAL C 259 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.46e+00 bond pdb=" CB VAL B 259 " pdb=" CG2 VAL B 259 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.40e+00 bond pdb=" CB VAL E 259 " pdb=" CG2 VAL E 259 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.40e+00 bond pdb=" CB VAL D 259 " pdb=" CG2 VAL D 259 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.38e+00 bond pdb=" CB VAL A 259 " pdb=" CG2 VAL A 259 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.32e+00 ... (remaining 15080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 19277 2.28 - 4.56: 1000 4.56 - 6.83: 123 6.83 - 9.11: 55 9.11 - 11.39: 10 Bond angle restraints: 20465 Sorted by residual: angle pdb=" CA GLU B 215 " pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " ideal model delta sigma weight residual 114.10 122.90 -8.80 2.00e+00 2.50e-01 1.94e+01 angle pdb=" CA GLU A 215 " pdb=" CB GLU A 215 " pdb=" CG GLU A 215 " ideal model delta sigma weight residual 114.10 122.86 -8.76 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CA GLU C 215 " pdb=" CB GLU C 215 " pdb=" CG GLU C 215 " ideal model delta sigma weight residual 114.10 122.86 -8.76 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CA GLU D 215 " pdb=" CB GLU D 215 " pdb=" CG GLU D 215 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.91e+01 angle pdb=" CA GLU E 215 " pdb=" CB GLU E 215 " pdb=" CG GLU E 215 " ideal model delta sigma weight residual 114.10 122.84 -8.74 2.00e+00 2.50e-01 1.91e+01 ... (remaining 20460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 8960 35.91 - 71.82: 170 71.82 - 107.74: 15 107.74 - 143.65: 0 143.65 - 179.56: 10 Dihedral angle restraints: 9155 sinusoidal: 3845 harmonic: 5310 Sorted by residual: dihedral pdb=" C11 TCI D 803 " pdb=" C12 TCI D 803 " pdb=" C13 TCI D 803 " pdb=" C15 TCI D 803 " ideal model delta sinusoidal sigma weight residual 64.70 -114.86 179.56 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C11 TCI A 803 " pdb=" C12 TCI A 803 " pdb=" C13 TCI A 803 " pdb=" C15 TCI A 803 " ideal model delta sinusoidal sigma weight residual 64.70 -114.84 179.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C11 TCI E 502 " pdb=" C12 TCI E 502 " pdb=" C13 TCI E 502 " pdb=" C15 TCI E 502 " ideal model delta sinusoidal sigma weight residual 64.70 -114.84 179.54 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1868 0.088 - 0.177: 411 0.177 - 0.265: 11 0.265 - 0.354: 0 0.354 - 0.442: 10 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CA PHE E 418 " pdb=" N PHE E 418 " pdb=" C PHE E 418 " pdb=" CB PHE E 418 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA PHE A 418 " pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CB PHE A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CA PHE C 418 " pdb=" N PHE C 418 " pdb=" C PHE C 418 " pdb=" CB PHE C 418 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 2297 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 283 " 0.021 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR E 283 " -0.071 2.00e-02 2.50e+03 pdb=" O THR E 283 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL E 284 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 283 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C THR A 283 " -0.071 2.00e-02 2.50e+03 pdb=" O THR A 283 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL A 284 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 283 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C THR C 283 " 0.070 2.00e-02 2.50e+03 pdb=" O THR C 283 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL C 284 " -0.024 2.00e-02 2.50e+03 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3832 2.81 - 3.33: 13838 3.33 - 3.86: 23538 3.86 - 4.38: 25372 4.38 - 4.90: 44769 Nonbonded interactions: 111349 Sorted by model distance: nonbonded pdb=" OG1 THR C 186 " pdb=" OD1 ASN C 188 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR D 186 " pdb=" OD1 ASN D 188 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 186 " pdb=" OD1 ASN A 188 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR E 186 " pdb=" OD1 ASN E 188 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR B 186 " pdb=" OD1 ASN B 188 " model vdw 2.290 3.040 ... (remaining 111344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 442 or resid 802 through 803)) selection = (chain 'B' and (resid 32 through 442 or resid 802 through 803)) selection = (chain 'C' and (resid 32 through 442 or resid 802 through 803)) selection = (chain 'D' and (resid 32 through 442 or resid 802 through 803)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.990 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 0.071 15095 Z= 0.370 Angle : 1.161 11.390 20490 Z= 0.632 Chirality : 0.070 0.442 2300 Planarity : 0.008 0.065 2545 Dihedral : 15.900 179.560 5690 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1775 helix: 1.54 (0.19), residues: 665 sheet: 0.19 (0.27), residues: 380 loop : -2.33 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 430 HIS 0.004 0.001 HIS C 442 PHE 0.033 0.004 PHE E 169 TYR 0.027 0.003 TYR A 433 ARG 0.010 0.001 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 5) link_NAG-ASN : angle 2.56188 ( 15) hydrogen bonds : bond 0.19442 ( 720) hydrogen bonds : angle 6.80224 ( 2505) SS BOND : bond 0.01046 ( 5) SS BOND : angle 1.15600 ( 10) covalent geometry : bond 0.00853 (15085) covalent geometry : angle 1.15894 (20465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.578 Fit side-chains REVERT: A 267 TRP cc_start: 0.6770 (t-100) cc_final: 0.6330 (t-100) REVERT: A 428 PHE cc_start: 0.8463 (t80) cc_final: 0.8139 (m-80) REVERT: A 437 ARG cc_start: 0.7604 (mtp180) cc_final: 0.6383 (mtt180) REVERT: B 266 PHE cc_start: 0.6845 (m-10) cc_final: 0.6068 (m-80) REVERT: B 287 MET cc_start: 0.9094 (tpp) cc_final: 0.8809 (tpt) REVERT: B 428 PHE cc_start: 0.8589 (t80) cc_final: 0.8012 (t80) REVERT: B 437 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6465 (mtt180) REVERT: C 257 LEU cc_start: 0.8513 (tp) cc_final: 0.8140 (mt) REVERT: C 287 MET cc_start: 0.8974 (tpp) cc_final: 0.8633 (tpt) REVERT: C 428 PHE cc_start: 0.8587 (t80) cc_final: 0.7996 (t80) REVERT: C 437 ARG cc_start: 0.7408 (mtp180) cc_final: 0.6335 (mtm180) REVERT: D 190 LEU cc_start: 0.8641 (tt) cc_final: 0.8415 (tm) REVERT: D 287 MET cc_start: 0.9063 (tpp) cc_final: 0.8850 (tpt) REVERT: D 428 PHE cc_start: 0.8651 (t80) cc_final: 0.8095 (t80) REVERT: D 437 ARG cc_start: 0.7423 (mtp180) cc_final: 0.6463 (mtm180) REVERT: E 113 MET cc_start: 0.8532 (pmm) cc_final: 0.8165 (ppp) REVERT: E 308 ASP cc_start: 0.8690 (m-30) cc_final: 0.8356 (m-30) REVERT: E 428 PHE cc_start: 0.8630 (t80) cc_final: 0.8110 (t80) REVERT: E 437 ARG cc_start: 0.7489 (mtp180) cc_final: 0.6586 (mtm180) outliers start: 0 outliers final: 6 residues processed: 230 average time/residue: 1.2600 time to fit residues: 318.0960 Evaluate side-chains 132 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 115 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.093607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.069864 restraints weight = 32652.917| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.57 r_work: 0.2903 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15095 Z= 0.156 Angle : 0.697 9.452 20490 Z= 0.361 Chirality : 0.046 0.181 2300 Planarity : 0.004 0.046 2545 Dihedral : 16.549 179.082 2212 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.88 % Allowed : 10.22 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1775 helix: 2.32 (0.19), residues: 645 sheet: 0.77 (0.27), residues: 380 loop : -2.24 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 267 HIS 0.003 0.001 HIS A 335 PHE 0.012 0.001 PHE D 87 TYR 0.023 0.002 TYR E 325 ARG 0.003 0.000 ARG D 415 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 5) link_NAG-ASN : angle 0.92767 ( 15) hydrogen bonds : bond 0.06776 ( 720) hydrogen bonds : angle 4.90346 ( 2505) SS BOND : bond 0.00592 ( 5) SS BOND : angle 0.25657 ( 10) covalent geometry : bond 0.00339 (15085) covalent geometry : angle 0.69723 (20465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 1.732 Fit side-chains REVERT: A 171 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8380 (mpp) REVERT: A 267 TRP cc_start: 0.6614 (t-100) cc_final: 0.6166 (t-100) REVERT: A 426 ASN cc_start: 0.8636 (t0) cc_final: 0.8427 (t0) REVERT: A 428 PHE cc_start: 0.8732 (t80) cc_final: 0.8314 (m-80) REVERT: A 437 ARG cc_start: 0.7240 (mtp180) cc_final: 0.6269 (ptp-170) REVERT: B 79 THR cc_start: 0.8975 (m) cc_final: 0.8375 (p) REVERT: B 81 ASP cc_start: 0.8553 (p0) cc_final: 0.8183 (p0) REVERT: B 113 MET cc_start: 0.8551 (ppp) cc_final: 0.8096 (ppp) REVERT: B 266 PHE cc_start: 0.6265 (m-10) cc_final: 0.5827 (m-10) REVERT: B 428 PHE cc_start: 0.8779 (t80) cc_final: 0.8184 (t80) REVERT: B 437 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6114 (mtm180) REVERT: C 308 ASP cc_start: 0.8864 (m-30) cc_final: 0.8571 (m-30) REVERT: C 428 PHE cc_start: 0.8810 (t80) cc_final: 0.8113 (t80) REVERT: C 437 ARG cc_start: 0.6992 (mtp180) cc_final: 0.6159 (ptp-170) REVERT: D 79 THR cc_start: 0.8992 (m) cc_final: 0.8432 (p) REVERT: D 81 ASP cc_start: 0.8596 (p0) cc_final: 0.8337 (p0) REVERT: D 113 MET cc_start: 0.8361 (ppp) cc_final: 0.8034 (ppp) REVERT: D 243 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8801 (mt0) REVERT: D 244 MET cc_start: 0.9155 (mmm) cc_final: 0.8923 (tpp) REVERT: D 428 PHE cc_start: 0.8863 (t80) cc_final: 0.8300 (t80) REVERT: D 437 ARG cc_start: 0.7092 (mtp180) cc_final: 0.6149 (mtt180) REVERT: E 79 THR cc_start: 0.9081 (m) cc_final: 0.8645 (p) REVERT: E 81 ASP cc_start: 0.8495 (p0) cc_final: 0.8235 (p0) REVERT: E 113 MET cc_start: 0.8598 (pmm) cc_final: 0.7975 (ppp) REVERT: E 308 ASP cc_start: 0.9061 (m-30) cc_final: 0.8717 (m-30) REVERT: E 428 PHE cc_start: 0.8847 (t80) cc_final: 0.8273 (t80) REVERT: E 437 ARG cc_start: 0.7194 (mtp180) cc_final: 0.6186 (mtm180) outliers start: 46 outliers final: 17 residues processed: 184 average time/residue: 1.2086 time to fit residues: 246.5949 Evaluate side-chains 156 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 400 ARG Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.069483 restraints weight = 32700.057| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.57 r_work: 0.2895 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15095 Z= 0.140 Angle : 0.647 7.451 20490 Z= 0.329 Chirality : 0.044 0.160 2300 Planarity : 0.003 0.041 2545 Dihedral : 16.228 179.497 2210 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.63 % Allowed : 11.16 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1775 helix: 2.44 (0.19), residues: 645 sheet: 1.04 (0.26), residues: 370 loop : -2.08 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 267 HIS 0.003 0.001 HIS C 335 PHE 0.011 0.001 PHE D 87 TYR 0.019 0.002 TYR E 325 ARG 0.004 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 5) link_NAG-ASN : angle 0.93874 ( 15) hydrogen bonds : bond 0.05998 ( 720) hydrogen bonds : angle 4.40256 ( 2505) SS BOND : bond 0.00423 ( 5) SS BOND : angle 0.28052 ( 10) covalent geometry : bond 0.00304 (15085) covalent geometry : angle 0.64677 (20465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8769 (t80) cc_final: 0.8084 (t80) REVERT: A 437 ARG cc_start: 0.7237 (mtp180) cc_final: 0.6136 (mtm180) REVERT: B 79 THR cc_start: 0.8968 (m) cc_final: 0.8663 (p) REVERT: B 113 MET cc_start: 0.8610 (ppp) cc_final: 0.8163 (ppp) REVERT: B 196 GLU cc_start: 0.8568 (pm20) cc_final: 0.8316 (pm20) REVERT: B 266 PHE cc_start: 0.6427 (m-10) cc_final: 0.5892 (m-10) REVERT: B 428 PHE cc_start: 0.8771 (t80) cc_final: 0.8178 (t80) REVERT: C 428 PHE cc_start: 0.8808 (t80) cc_final: 0.8116 (t80) REVERT: C 437 ARG cc_start: 0.6904 (mtp180) cc_final: 0.5807 (mtm180) REVERT: D 113 MET cc_start: 0.8449 (ppp) cc_final: 0.8089 (ppp) REVERT: D 244 MET cc_start: 0.9145 (mmm) cc_final: 0.8933 (tpp) REVERT: D 428 PHE cc_start: 0.8839 (t80) cc_final: 0.8281 (t80) REVERT: D 437 ARG cc_start: 0.7044 (mtp180) cc_final: 0.6151 (mtm180) REVERT: E 79 THR cc_start: 0.9000 (m) cc_final: 0.8704 (p) REVERT: E 113 MET cc_start: 0.8563 (pmm) cc_final: 0.8087 (ppp) REVERT: E 308 ASP cc_start: 0.9054 (m-30) cc_final: 0.8798 (m-30) REVERT: E 428 PHE cc_start: 0.8832 (t80) cc_final: 0.8257 (t80) REVERT: E 437 ARG cc_start: 0.7029 (mtp180) cc_final: 0.6023 (mtm180) outliers start: 42 outliers final: 15 residues processed: 170 average time/residue: 1.1721 time to fit residues: 220.3712 Evaluate side-chains 145 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 155 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.068690 restraints weight = 32625.163| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.56 r_work: 0.2872 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15095 Z= 0.139 Angle : 0.616 7.950 20490 Z= 0.315 Chirality : 0.043 0.144 2300 Planarity : 0.003 0.038 2545 Dihedral : 15.853 179.092 2202 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.01 % Allowed : 12.48 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1775 helix: 2.54 (0.19), residues: 645 sheet: 0.96 (0.25), residues: 380 loop : -1.97 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 267 HIS 0.004 0.001 HIS A 335 PHE 0.014 0.001 PHE E 266 TYR 0.017 0.002 TYR D 325 ARG 0.004 0.000 ARG B 415 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 5) link_NAG-ASN : angle 0.90435 ( 15) hydrogen bonds : bond 0.05441 ( 720) hydrogen bonds : angle 4.14139 ( 2505) SS BOND : bond 0.00377 ( 5) SS BOND : angle 0.28099 ( 10) covalent geometry : bond 0.00314 (15085) covalent geometry : angle 0.61561 (20465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 ASN cc_start: 0.8757 (t0) cc_final: 0.8548 (t0) REVERT: A 428 PHE cc_start: 0.8763 (t80) cc_final: 0.8088 (t80) REVERT: A 437 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6036 (mtm180) REVERT: B 79 THR cc_start: 0.8888 (m) cc_final: 0.8541 (p) REVERT: B 113 MET cc_start: 0.8514 (ppp) cc_final: 0.8112 (ppp) REVERT: B 428 PHE cc_start: 0.8773 (t80) cc_final: 0.8175 (t80) REVERT: C 428 PHE cc_start: 0.8817 (t80) cc_final: 0.8131 (t80) REVERT: D 113 MET cc_start: 0.8413 (ppp) cc_final: 0.8118 (ppp) REVERT: D 428 PHE cc_start: 0.8804 (t80) cc_final: 0.8255 (t80) REVERT: D 437 ARG cc_start: 0.6952 (mtp180) cc_final: 0.6158 (mtm180) REVERT: E 79 THR cc_start: 0.8945 (m) cc_final: 0.8619 (p) REVERT: E 113 MET cc_start: 0.8548 (pmm) cc_final: 0.8048 (ppp) REVERT: E 187 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8549 (tpp) REVERT: E 308 ASP cc_start: 0.9045 (m-30) cc_final: 0.8792 (m-30) REVERT: E 428 PHE cc_start: 0.8835 (t80) cc_final: 0.8263 (t80) REVERT: E 437 ARG cc_start: 0.7081 (mtp180) cc_final: 0.6042 (mtm180) outliers start: 48 outliers final: 18 residues processed: 168 average time/residue: 1.2947 time to fit residues: 239.7222 Evaluate side-chains 150 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 35 optimal weight: 5.9990 chunk 100 optimal weight: 0.0070 chunk 138 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 159 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.093435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.069047 restraints weight = 33028.472| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.60 r_work: 0.2877 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15095 Z= 0.125 Angle : 0.606 9.064 20490 Z= 0.309 Chirality : 0.043 0.142 2300 Planarity : 0.003 0.036 2545 Dihedral : 15.763 179.520 2202 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.57 % Allowed : 14.04 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1775 helix: 2.85 (0.19), residues: 620 sheet: 1.05 (0.25), residues: 385 loop : -1.98 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 267 HIS 0.003 0.001 HIS A 335 PHE 0.014 0.001 PHE E 266 TYR 0.015 0.001 TYR A 325 ARG 0.002 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 5) link_NAG-ASN : angle 0.76484 ( 15) hydrogen bonds : bond 0.04960 ( 720) hydrogen bonds : angle 3.93582 ( 2505) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.20640 ( 10) covalent geometry : bond 0.00277 (15085) covalent geometry : angle 0.60630 (20465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8756 (t80) cc_final: 0.8083 (t80) REVERT: B 113 MET cc_start: 0.8437 (ppp) cc_final: 0.8088 (ppp) REVERT: B 196 GLU cc_start: 0.8550 (pm20) cc_final: 0.7687 (pm20) REVERT: B 197 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7749 (pmtt) REVERT: B 215 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8423 (tm-30) REVERT: B 266 PHE cc_start: 0.6627 (m-10) cc_final: 0.6371 (m-80) REVERT: B 428 PHE cc_start: 0.8753 (t80) cc_final: 0.8142 (t80) REVERT: C 196 GLU cc_start: 0.8402 (pm20) cc_final: 0.7538 (pm20) REVERT: C 197 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7969 (pmtt) REVERT: C 221 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8203 (p90) REVERT: C 428 PHE cc_start: 0.8864 (t80) cc_final: 0.8435 (t80) REVERT: D 113 MET cc_start: 0.8420 (ppp) cc_final: 0.8055 (ppp) REVERT: D 428 PHE cc_start: 0.8787 (t80) cc_final: 0.8233 (t80) REVERT: E 79 THR cc_start: 0.8912 (m) cc_final: 0.8552 (p) REVERT: E 113 MET cc_start: 0.8497 (pmm) cc_final: 0.8123 (ppp) REVERT: E 187 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8568 (tpp) REVERT: E 308 ASP cc_start: 0.9021 (m-30) cc_final: 0.8795 (m-30) REVERT: E 428 PHE cc_start: 0.8808 (t80) cc_final: 0.8260 (t80) outliers start: 41 outliers final: 20 residues processed: 167 average time/residue: 1.2418 time to fit residues: 229.8677 Evaluate side-chains 160 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 165 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 157 optimal weight: 0.0470 chunk 136 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN D 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.066982 restraints weight = 32960.781| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.61 r_work: 0.2832 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15095 Z= 0.151 Angle : 0.616 9.615 20490 Z= 0.316 Chirality : 0.043 0.146 2300 Planarity : 0.003 0.037 2545 Dihedral : 15.784 179.956 2202 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.45 % Allowed : 15.05 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1775 helix: 2.92 (0.19), residues: 615 sheet: 0.83 (0.24), residues: 410 loop : -1.96 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 267 HIS 0.003 0.001 HIS A 335 PHE 0.015 0.001 PHE E 266 TYR 0.017 0.002 TYR B 325 ARG 0.003 0.000 ARG E 415 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 5) link_NAG-ASN : angle 0.98943 ( 15) hydrogen bonds : bond 0.05092 ( 720) hydrogen bonds : angle 3.83219 ( 2505) SS BOND : bond 0.00365 ( 5) SS BOND : angle 0.40238 ( 10) covalent geometry : bond 0.00354 (15085) covalent geometry : angle 0.61593 (20465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8745 (t80) cc_final: 0.8078 (t80) REVERT: B 79 THR cc_start: 0.9035 (m) cc_final: 0.8598 (p) REVERT: B 113 MET cc_start: 0.8433 (ppp) cc_final: 0.8085 (ppp) REVERT: B 215 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8425 (tm-30) REVERT: B 221 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8269 (p90) REVERT: B 244 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8883 (tpp) REVERT: B 266 PHE cc_start: 0.6756 (m-10) cc_final: 0.6539 (m-80) REVERT: B 428 PHE cc_start: 0.8762 (t80) cc_final: 0.8150 (t80) REVERT: C 113 MET cc_start: 0.8450 (ppp) cc_final: 0.8193 (ppp) REVERT: C 221 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8115 (p90) REVERT: C 266 PHE cc_start: 0.7254 (m-10) cc_final: 0.6910 (m-80) REVERT: C 428 PHE cc_start: 0.8868 (t80) cc_final: 0.8419 (t80) REVERT: D 113 MET cc_start: 0.8434 (ppp) cc_final: 0.8040 (ppp) REVERT: D 221 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8360 (p90) REVERT: D 428 PHE cc_start: 0.8807 (t80) cc_final: 0.8256 (t80) REVERT: E 79 THR cc_start: 0.8933 (m) cc_final: 0.8694 (p) REVERT: E 113 MET cc_start: 0.8475 (pmm) cc_final: 0.8062 (ppp) REVERT: E 308 ASP cc_start: 0.9050 (m-30) cc_final: 0.8805 (m-30) REVERT: E 428 PHE cc_start: 0.8778 (t80) cc_final: 0.8199 (t80) outliers start: 39 outliers final: 24 residues processed: 156 average time/residue: 1.1401 time to fit residues: 197.4679 Evaluate side-chains 159 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.092091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.067308 restraints weight = 32959.322| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.61 r_work: 0.2837 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15095 Z= 0.135 Angle : 0.615 10.657 20490 Z= 0.312 Chirality : 0.043 0.143 2300 Planarity : 0.003 0.034 2545 Dihedral : 15.740 179.905 2202 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.63 % Allowed : 15.80 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.19), residues: 1775 helix: 3.01 (0.19), residues: 615 sheet: 0.84 (0.25), residues: 405 loop : -1.91 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 263 HIS 0.003 0.001 HIS A 335 PHE 0.014 0.001 PHE E 266 TYR 0.016 0.001 TYR A 433 ARG 0.003 0.000 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 5) link_NAG-ASN : angle 0.86383 ( 15) hydrogen bonds : bond 0.04830 ( 720) hydrogen bonds : angle 3.71926 ( 2505) SS BOND : bond 0.00329 ( 5) SS BOND : angle 0.30231 ( 10) covalent geometry : bond 0.00311 (15085) covalent geometry : angle 0.61477 (20465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: A 196 GLU cc_start: 0.8306 (pm20) cc_final: 0.7930 (pm20) REVERT: A 197 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8386 (pmtt) REVERT: A 428 PHE cc_start: 0.8768 (t80) cc_final: 0.8100 (t80) REVERT: B 113 MET cc_start: 0.8530 (ppp) cc_final: 0.8175 (ppp) REVERT: B 196 GLU cc_start: 0.8424 (pm20) cc_final: 0.8201 (pm20) REVERT: B 215 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8409 (tm-30) REVERT: B 221 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8201 (p90) REVERT: B 266 PHE cc_start: 0.6784 (m-10) cc_final: 0.6559 (m-80) REVERT: B 428 PHE cc_start: 0.8751 (t80) cc_final: 0.8134 (t80) REVERT: C 181 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8198 (pp20) REVERT: C 196 GLU cc_start: 0.8272 (pm20) cc_final: 0.7447 (pm20) REVERT: C 197 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8006 (pmtt) REVERT: C 221 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.8061 (p90) REVERT: C 266 PHE cc_start: 0.7223 (m-10) cc_final: 0.6889 (m-80) REVERT: C 428 PHE cc_start: 0.8859 (t80) cc_final: 0.8398 (t80) REVERT: D 113 MET cc_start: 0.8473 (ppp) cc_final: 0.8085 (ppp) REVERT: D 263 TRP cc_start: 0.7533 (m-10) cc_final: 0.7281 (m-10) REVERT: D 428 PHE cc_start: 0.8811 (t80) cc_final: 0.8265 (t80) REVERT: E 79 THR cc_start: 0.8918 (m) cc_final: 0.8643 (p) REVERT: E 113 MET cc_start: 0.8387 (pmm) cc_final: 0.8045 (ppp) REVERT: E 221 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8166 (p90) REVERT: E 263 TRP cc_start: 0.7956 (m-10) cc_final: 0.7545 (m-10) REVERT: E 308 ASP cc_start: 0.9030 (m-30) cc_final: 0.8784 (m-30) REVERT: E 428 PHE cc_start: 0.8778 (t80) cc_final: 0.8196 (t80) outliers start: 42 outliers final: 25 residues processed: 163 average time/residue: 1.2183 time to fit residues: 219.9766 Evaluate side-chains 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 119 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067425 restraints weight = 32702.074| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.60 r_work: 0.2841 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15095 Z= 0.129 Angle : 0.611 10.360 20490 Z= 0.309 Chirality : 0.043 0.143 2300 Planarity : 0.003 0.032 2545 Dihedral : 15.662 179.910 2202 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.63 % Allowed : 16.36 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 1775 helix: 2.97 (0.19), residues: 620 sheet: 0.82 (0.25), residues: 400 loop : -1.82 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 PHE 0.013 0.001 PHE E 266 TYR 0.016 0.001 TYR A 433 ARG 0.003 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 5) link_NAG-ASN : angle 0.82354 ( 15) hydrogen bonds : bond 0.04678 ( 720) hydrogen bonds : angle 3.66198 ( 2505) SS BOND : bond 0.00295 ( 5) SS BOND : angle 0.25005 ( 10) covalent geometry : bond 0.00294 (15085) covalent geometry : angle 0.61048 (20465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8272 (tm-30) REVERT: A 196 GLU cc_start: 0.8311 (pm20) cc_final: 0.7789 (pm20) REVERT: A 197 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8280 (pmtt) REVERT: A 428 PHE cc_start: 0.8780 (t80) cc_final: 0.8127 (t80) REVERT: B 79 THR cc_start: 0.8987 (m) cc_final: 0.8502 (p) REVERT: B 113 MET cc_start: 0.8521 (ppp) cc_final: 0.8169 (ppp) REVERT: B 196 GLU cc_start: 0.8283 (pm20) cc_final: 0.8055 (pm20) REVERT: B 215 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 221 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8223 (p90) REVERT: B 244 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8890 (tpp) REVERT: B 266 PHE cc_start: 0.6783 (m-10) cc_final: 0.6562 (m-80) REVERT: B 333 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7811 (ttp80) REVERT: B 428 PHE cc_start: 0.8767 (t80) cc_final: 0.8152 (t80) REVERT: C 181 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8281 (pp20) REVERT: C 221 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7989 (p90) REVERT: C 266 PHE cc_start: 0.7181 (m-10) cc_final: 0.6790 (m-80) REVERT: C 428 PHE cc_start: 0.8861 (t80) cc_final: 0.8445 (t80) REVERT: D 113 MET cc_start: 0.8476 (ppp) cc_final: 0.8062 (ppp) REVERT: D 263 TRP cc_start: 0.7526 (m-10) cc_final: 0.7235 (m-10) REVERT: D 270 MET cc_start: 0.3955 (pmm) cc_final: 0.3717 (mmm) REVERT: D 428 PHE cc_start: 0.8804 (t80) cc_final: 0.8257 (t80) REVERT: E 79 THR cc_start: 0.8830 (m) cc_final: 0.8553 (p) REVERT: E 113 MET cc_start: 0.8382 (pmm) cc_final: 0.8054 (ppp) REVERT: E 263 TRP cc_start: 0.7947 (m-10) cc_final: 0.7505 (m-10) REVERT: E 308 ASP cc_start: 0.9026 (m-30) cc_final: 0.8791 (m-30) REVERT: E 428 PHE cc_start: 0.8815 (t80) cc_final: 0.8244 (t80) outliers start: 42 outliers final: 24 residues processed: 158 average time/residue: 1.2279 time to fit residues: 214.3584 Evaluate side-chains 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 168 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 81 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.094504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069595 restraints weight = 31737.924| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.44 r_work: 0.2901 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15095 Z= 0.115 Angle : 0.608 12.176 20490 Z= 0.303 Chirality : 0.043 0.146 2300 Planarity : 0.003 0.031 2545 Dihedral : 15.394 178.381 2200 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.26 % Allowed : 17.05 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 1775 helix: 2.95 (0.19), residues: 625 sheet: 0.98 (0.26), residues: 370 loop : -1.73 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 263 HIS 0.002 0.000 HIS A 335 PHE 0.014 0.001 PHE E 266 TYR 0.016 0.001 TYR A 433 ARG 0.001 0.000 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 5) link_NAG-ASN : angle 0.69383 ( 15) hydrogen bonds : bond 0.04292 ( 720) hydrogen bonds : angle 3.56397 ( 2505) SS BOND : bond 0.00262 ( 5) SS BOND : angle 0.16923 ( 10) covalent geometry : bond 0.00256 (15085) covalent geometry : angle 0.60802 (20465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: A 196 GLU cc_start: 0.8312 (pm20) cc_final: 0.7757 (pm20) REVERT: A 197 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8127 (pmtt) REVERT: A 221 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7946 (p90) REVERT: A 428 PHE cc_start: 0.8795 (t80) cc_final: 0.8146 (t80) REVERT: B 79 THR cc_start: 0.8966 (m) cc_final: 0.8594 (p) REVERT: B 113 MET cc_start: 0.8565 (ppp) cc_final: 0.8222 (ppp) REVERT: B 215 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8335 (tm-30) REVERT: B 221 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.8232 (p90) REVERT: B 266 PHE cc_start: 0.6845 (m-10) cc_final: 0.6498 (m-80) REVERT: B 428 PHE cc_start: 0.8758 (t80) cc_final: 0.8141 (t80) REVERT: C 187 MET cc_start: 0.8411 (tpp) cc_final: 0.8190 (mmp) REVERT: C 196 GLU cc_start: 0.8399 (pm20) cc_final: 0.8186 (pm20) REVERT: C 221 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7939 (p90) REVERT: C 263 TRP cc_start: 0.7904 (m-10) cc_final: 0.7566 (m-10) REVERT: C 266 PHE cc_start: 0.7131 (m-10) cc_final: 0.6801 (m-80) REVERT: C 426 ASN cc_start: 0.8616 (t0) cc_final: 0.8364 (t0) REVERT: C 428 PHE cc_start: 0.8880 (t80) cc_final: 0.8458 (t80) REVERT: D 113 MET cc_start: 0.8481 (ppp) cc_final: 0.8060 (ppp) REVERT: D 221 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8202 (p90) REVERT: D 263 TRP cc_start: 0.7450 (m-10) cc_final: 0.7192 (m-10) REVERT: D 428 PHE cc_start: 0.8804 (t80) cc_final: 0.8255 (t80) REVERT: E 79 THR cc_start: 0.8922 (m) cc_final: 0.8689 (p) REVERT: E 113 MET cc_start: 0.8390 (pmm) cc_final: 0.8111 (ppp) REVERT: E 263 TRP cc_start: 0.7946 (m-10) cc_final: 0.7526 (m-10) REVERT: E 308 ASP cc_start: 0.8986 (m-30) cc_final: 0.8762 (m-30) REVERT: E 428 PHE cc_start: 0.8867 (t80) cc_final: 0.8288 (t80) outliers start: 36 outliers final: 18 residues processed: 156 average time/residue: 1.2375 time to fit residues: 213.7023 Evaluate side-chains 159 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 97 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 136 optimal weight: 0.0010 chunk 111 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN E 210 GLN E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.094464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.069489 restraints weight = 32335.170| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.48 r_work: 0.2897 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15095 Z= 0.118 Angle : 0.613 10.313 20490 Z= 0.307 Chirality : 0.043 0.159 2300 Planarity : 0.003 0.031 2545 Dihedral : 15.235 176.707 2200 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.01 % Allowed : 17.87 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1775 helix: 2.89 (0.19), residues: 630 sheet: 0.98 (0.26), residues: 370 loop : -1.68 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 263 HIS 0.002 0.001 HIS B 335 PHE 0.015 0.001 PHE E 266 TYR 0.016 0.001 TYR A 433 ARG 0.002 0.000 ARG C 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 5) link_NAG-ASN : angle 0.75319 ( 15) hydrogen bonds : bond 0.04222 ( 720) hydrogen bonds : angle 3.54094 ( 2505) SS BOND : bond 0.00269 ( 5) SS BOND : angle 0.23230 ( 10) covalent geometry : bond 0.00266 (15085) covalent geometry : angle 0.61252 (20465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: A 196 GLU cc_start: 0.8320 (pm20) cc_final: 0.7761 (pm20) REVERT: A 197 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8100 (pmtt) REVERT: A 428 PHE cc_start: 0.8755 (t80) cc_final: 0.8145 (t80) REVERT: B 79 THR cc_start: 0.8918 (m) cc_final: 0.8557 (p) REVERT: B 113 MET cc_start: 0.8545 (ppp) cc_final: 0.8114 (ppp) REVERT: B 215 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8366 (tm-30) REVERT: B 221 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.8236 (p90) REVERT: B 263 TRP cc_start: 0.7634 (m-10) cc_final: 0.6912 (m-10) REVERT: B 266 PHE cc_start: 0.6854 (m-10) cc_final: 0.6496 (m-80) REVERT: B 428 PHE cc_start: 0.8749 (t80) cc_final: 0.8130 (t80) REVERT: C 221 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7913 (p90) REVERT: C 263 TRP cc_start: 0.7849 (m-10) cc_final: 0.7530 (m-10) REVERT: C 266 PHE cc_start: 0.7123 (m-10) cc_final: 0.6835 (m-80) REVERT: C 426 ASN cc_start: 0.8595 (t0) cc_final: 0.8323 (t0) REVERT: C 428 PHE cc_start: 0.8871 (t80) cc_final: 0.8445 (t80) REVERT: D 113 MET cc_start: 0.8531 (ppp) cc_final: 0.8031 (ppp) REVERT: D 221 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8205 (p90) REVERT: D 428 PHE cc_start: 0.8789 (t80) cc_final: 0.8233 (t80) REVERT: E 79 THR cc_start: 0.8935 (m) cc_final: 0.8695 (p) REVERT: E 113 MET cc_start: 0.8400 (pmm) cc_final: 0.8153 (ppp) REVERT: E 196 GLU cc_start: 0.8298 (pm20) cc_final: 0.7974 (pm20) REVERT: E 197 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7955 (pmtt) REVERT: E 221 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.8065 (p90) REVERT: E 263 TRP cc_start: 0.7946 (m-10) cc_final: 0.7568 (m-10) REVERT: E 308 ASP cc_start: 0.8983 (m-30) cc_final: 0.8758 (m-30) REVERT: E 428 PHE cc_start: 0.8847 (t80) cc_final: 0.8282 (t80) outliers start: 32 outliers final: 20 residues processed: 158 average time/residue: 1.3670 time to fit residues: 239.4615 Evaluate side-chains 163 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 158 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.094296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.069284 restraints weight = 32447.128| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.49 r_work: 0.2893 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15095 Z= 0.124 Angle : 0.619 10.051 20490 Z= 0.309 Chirality : 0.043 0.158 2300 Planarity : 0.003 0.031 2545 Dihedral : 15.156 175.683 2200 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.07 % Allowed : 18.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1775 helix: 2.89 (0.19), residues: 630 sheet: 0.96 (0.26), residues: 370 loop : -1.67 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 PHE 0.017 0.001 PHE E 266 TYR 0.016 0.001 TYR A 433 ARG 0.002 0.000 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 5) link_NAG-ASN : angle 0.75386 ( 15) hydrogen bonds : bond 0.04253 ( 720) hydrogen bonds : angle 3.55415 ( 2505) SS BOND : bond 0.00273 ( 5) SS BOND : angle 0.23821 ( 10) covalent geometry : bond 0.00285 (15085) covalent geometry : angle 0.61866 (20465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8452.42 seconds wall clock time: 145 minutes 35.59 seconds (8735.59 seconds total)