Starting phenix.real_space_refine on Fri Sep 27 05:12:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6q_23704/09_2024/7m6q_23704.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6q_23704/09_2024/7m6q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6q_23704/09_2024/7m6q_23704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6q_23704/09_2024/7m6q_23704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6q_23704/09_2024/7m6q_23704.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6q_23704/09_2024/7m6q_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-5461/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: 7.48, per 1000 atoms: 0.51 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 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: 3.47 Conformation dependent library (CDL) restraints added in 1.8 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: 1.81 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: 4.79 Time building geometry restraints manager: 4.08 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: 8948 35.91 - 71.82: 170 71.82 - 107.74: 15 107.74 - 143.65: 0 143.65 - 179.56: 10 Dihedral angle restraints: 9143 sinusoidal: 3833 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 9140 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: 2.04 - 2.61: 125 2.61 - 3.18: 12499 3.18 - 3.76: 22017 3.76 - 4.33: 28754 4.33 - 4.90: 47966 Nonbonded interactions: 111361 Sorted by model distance: nonbonded pdb=" SG CYS C 162 " pdb=" SG CYS C 176 " model vdw 2.041 3.760 nonbonded pdb=" SG CYS B 162 " pdb=" SG CYS B 176 " model vdw 2.041 3.760 nonbonded pdb=" SG CYS E 162 " pdb=" SG CYS E 176 " model vdw 2.042 3.760 nonbonded pdb=" SG CYS D 162 " pdb=" SG CYS D 176 " model vdw 2.042 3.760 nonbonded pdb=" OG1 THR C 186 " pdb=" OD1 ASN C 188 " model vdw 2.289 3.040 ... (remaining 111356 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: 1.740 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 32.690 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.040 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.420 ------------------------------------------------------------------------------- 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 15085 Z= 0.560 Angle : 1.159 11.390 20465 Z= 0.632 Chirality : 0.070 0.442 2300 Planarity : 0.008 0.065 2545 Dihedral : 15.900 179.560 5690 Min Nonbonded Distance : 2.041 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.775 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: 1.1970 time to fit residues: 303.7371 Evaluate side-chains 132 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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: 0.2980 chunk 102 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15085 Z= 0.227 Angle : 0.708 9.401 20465 Z= 0.367 Chirality : 0.046 0.180 2300 Planarity : 0.004 0.046 2545 Dihedral : 16.576 179.046 2212 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.51 % Allowed : 10.53 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 1775 helix: 2.30 (0.19), residues: 645 sheet: 0.72 (0.27), residues: 380 loop : -2.27 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 267 HIS 0.004 0.001 HIS A 335 PHE 0.012 0.002 PHE D 87 TYR 0.022 0.002 TYR E 325 ARG 0.006 0.001 ARG D 415 *********************** 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 190 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 1.696 Fit side-chains REVERT: A 171 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8314 (mpp) REVERT: A 267 TRP cc_start: 0.6652 (t-100) cc_final: 0.6264 (t-100) REVERT: A 400 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5320 (mtm180) REVERT: A 426 ASN cc_start: 0.8733 (t0) cc_final: 0.8462 (t0) REVERT: A 428 PHE cc_start: 0.8489 (t80) cc_final: 0.8149 (m-80) REVERT: A 437 ARG cc_start: 0.7491 (mtp180) cc_final: 0.6316 (mtm180) REVERT: B 79 THR cc_start: 0.9103 (m) cc_final: 0.8510 (p) REVERT: B 81 ASP cc_start: 0.8378 (p0) cc_final: 0.8053 (p0) REVERT: B 266 PHE cc_start: 0.6163 (m-10) cc_final: 0.5844 (m-10) REVERT: B 287 MET cc_start: 0.9130 (tpp) cc_final: 0.8877 (tpt) REVERT: B 428 PHE cc_start: 0.8556 (t80) cc_final: 0.7975 (t80) REVERT: B 437 ARG cc_start: 0.7291 (mtp180) cc_final: 0.6461 (mtm180) REVERT: C 308 ASP cc_start: 0.8552 (m-30) cc_final: 0.8247 (m-30) REVERT: C 428 PHE cc_start: 0.8613 (t80) cc_final: 0.8021 (t80) REVERT: C 437 ARG cc_start: 0.7227 (mtp180) cc_final: 0.6244 (mtt180) REVERT: D 79 THR cc_start: 0.9100 (m) cc_final: 0.8582 (p) REVERT: D 113 MET cc_start: 0.8320 (ppp) cc_final: 0.8095 (ppp) REVERT: D 243 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8709 (mt0) REVERT: D 428 PHE cc_start: 0.8625 (t80) cc_final: 0.8110 (t80) REVERT: D 437 ARG cc_start: 0.7336 (mtp180) cc_final: 0.6448 (mtt180) REVERT: E 79 THR cc_start: 0.9218 (m) cc_final: 0.8815 (p) REVERT: E 81 ASP cc_start: 0.8345 (p0) cc_final: 0.8131 (p0) REVERT: E 113 MET cc_start: 0.8444 (pmm) cc_final: 0.8218 (ppp) REVERT: E 187 MET cc_start: 0.8750 (mmm) cc_final: 0.8533 (tpp) REVERT: E 308 ASP cc_start: 0.8647 (m-30) cc_final: 0.8321 (m-30) REVERT: E 428 PHE cc_start: 0.8637 (t80) cc_final: 0.8145 (t80) REVERT: E 437 ARG cc_start: 0.7424 (mtp180) cc_final: 0.6717 (ptp-170) outliers start: 40 outliers final: 15 residues processed: 176 average time/residue: 1.1977 time to fit residues: 233.1062 Evaluate side-chains 147 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET 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 A residue 400 ARG 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 154 ILE 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 138 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 54 optimal weight: 0.0670 chunk 127 optimal weight: 0.7980 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15085 Z= 0.253 Angle : 0.663 7.669 20465 Z= 0.341 Chirality : 0.045 0.147 2300 Planarity : 0.004 0.042 2545 Dihedral : 16.039 179.999 2206 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.95 % Allowed : 11.16 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1775 helix: 2.41 (0.19), residues: 645 sheet: 0.93 (0.25), residues: 380 loop : -2.16 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 267 HIS 0.003 0.001 HIS A 335 PHE 0.016 0.002 PHE D 87 TYR 0.020 0.002 TYR B 325 ARG 0.003 0.000 ARG A 242 *********************** 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 196 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 149 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8607 (t80) cc_final: 0.7900 (t80) REVERT: A 437 ARG cc_start: 0.7496 (mtp180) cc_final: 0.6397 (mtm180) REVERT: B 79 THR cc_start: 0.9170 (m) cc_final: 0.8831 (p) REVERT: B 287 MET cc_start: 0.9178 (tpp) cc_final: 0.8962 (tpt) REVERT: B 428 PHE cc_start: 0.8565 (t80) cc_final: 0.7980 (t80) REVERT: C 428 PHE cc_start: 0.8618 (t80) cc_final: 0.8021 (t80) REVERT: C 437 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6126 (mtm180) REVERT: D 79 THR cc_start: 0.9123 (m) cc_final: 0.8791 (p) REVERT: D 113 MET cc_start: 0.8362 (ppp) cc_final: 0.7935 (ppp) REVERT: D 428 PHE cc_start: 0.8600 (t80) cc_final: 0.8084 (t80) REVERT: D 437 ARG cc_start: 0.7304 (mtp180) cc_final: 0.6484 (mtm180) REVERT: E 308 ASP cc_start: 0.8648 (m-30) cc_final: 0.8427 (m-30) REVERT: E 428 PHE cc_start: 0.8667 (t80) cc_final: 0.8063 (t80) REVERT: E 437 ARG cc_start: 0.7441 (mtp180) cc_final: 0.6359 (mtm180) outliers start: 47 outliers final: 14 residues processed: 179 average time/residue: 1.1804 time to fit residues: 233.9858 Evaluate side-chains 148 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 A residue 416 VAL Chi-restraints excluded: chain B residue 244 MET 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 115 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 SER 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 157 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15085 Z= 0.194 Angle : 0.629 8.237 20465 Z= 0.321 Chirality : 0.044 0.146 2300 Planarity : 0.003 0.039 2545 Dihedral : 15.899 179.970 2202 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.20 % Allowed : 13.35 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.19), residues: 1775 helix: 2.80 (0.19), residues: 615 sheet: 0.93 (0.24), residues: 380 loop : -2.08 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 267 HIS 0.004 0.001 HIS C 335 PHE 0.015 0.001 PHE E 266 TYR 0.017 0.001 TYR A 325 ARG 0.007 0.000 ARG A 333 *********************** 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 193 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 142 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8528 (t80) cc_final: 0.7871 (t80) REVERT: A 437 ARG cc_start: 0.7412 (mtp180) cc_final: 0.6401 (mtm180) REVERT: B 79 THR cc_start: 0.9136 (m) cc_final: 0.8770 (p) REVERT: B 287 MET cc_start: 0.9099 (tpp) cc_final: 0.8898 (tpt) REVERT: B 428 PHE cc_start: 0.8543 (t80) cc_final: 0.7971 (t80) REVERT: C 428 PHE cc_start: 0.8605 (t80) cc_final: 0.8011 (t80) REVERT: D 113 MET cc_start: 0.8337 (ppp) cc_final: 0.8047 (ppp) REVERT: D 428 PHE cc_start: 0.8568 (t80) cc_final: 0.8077 (t80) REVERT: D 437 ARG cc_start: 0.7208 (mtp180) cc_final: 0.6498 (mtm180) REVERT: E 308 ASP cc_start: 0.8606 (m-30) cc_final: 0.8381 (m-30) REVERT: E 428 PHE cc_start: 0.8646 (t80) cc_final: 0.8086 (t80) REVERT: E 437 ARG cc_start: 0.7299 (mtp180) cc_final: 0.6335 (mtm180) outliers start: 51 outliers final: 23 residues processed: 174 average time/residue: 1.2792 time to fit residues: 244.7885 Evaluate side-chains 154 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 164 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 154 ILE Chi-restraints excluded: chain B residue 204 ASP 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 138 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 164 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 140 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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 179 GLN C 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15085 Z= 0.198 Angle : 0.617 8.772 20465 Z= 0.316 Chirality : 0.043 0.141 2300 Planarity : 0.003 0.032 2545 Dihedral : 15.838 179.616 2202 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.45 % Allowed : 15.11 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.19), residues: 1775 helix: 2.82 (0.19), residues: 620 sheet: 1.00 (0.25), residues: 385 loop : -2.02 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.003 0.001 HIS C 335 PHE 0.014 0.001 PHE E 266 TYR 0.016 0.002 TYR A 325 ARG 0.003 0.000 ARG B 333 *********************** 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 178 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8322 (mtm) REVERT: A 428 PHE cc_start: 0.8544 (t80) cc_final: 0.7895 (t80) REVERT: B 428 PHE cc_start: 0.8545 (t80) cc_final: 0.7960 (t80) REVERT: C 196 GLU cc_start: 0.7913 (pm20) cc_final: 0.7116 (pm20) REVERT: C 197 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8270 (pmtt) REVERT: C 428 PHE cc_start: 0.8651 (t80) cc_final: 0.8146 (t80) REVERT: D 113 MET cc_start: 0.8402 (ppp) cc_final: 0.8177 (ppp) REVERT: D 428 PHE cc_start: 0.8573 (t80) cc_final: 0.8075 (t80) REVERT: E 187 MET cc_start: 0.8803 (mmm) cc_final: 0.8539 (tpp) REVERT: E 308 ASP cc_start: 0.8567 (m-30) cc_final: 0.8362 (m-30) REVERT: E 428 PHE cc_start: 0.8620 (t80) cc_final: 0.8089 (t80) REVERT: E 437 ARG cc_start: 0.7266 (mtp180) cc_final: 0.6342 (mtm180) outliers start: 39 outliers final: 22 residues processed: 162 average time/residue: 1.2424 time to fit residues: 222.1633 Evaluate side-chains 158 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 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 154 ILE Chi-restraints excluded: chain B residue 204 ASP 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 154 ILE Chi-restraints excluded: chain C residue 197 LYS 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 171 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 264 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.0970 chunk 169 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15085 Z= 0.289 Angle : 0.649 9.281 20465 Z= 0.334 Chirality : 0.044 0.136 2300 Planarity : 0.004 0.032 2545 Dihedral : 15.908 179.917 2202 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.45 % Allowed : 16.30 % Favored : 81.25 % 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: 0.66 (0.19), residues: 1775 helix: 2.88 (0.19), residues: 615 sheet: 0.71 (0.24), residues: 410 loop : -1.98 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 92 HIS 0.004 0.001 HIS C 335 PHE 0.016 0.002 PHE D 87 TYR 0.018 0.002 TYR D 429 ARG 0.004 0.000 ARG E 242 *********************** 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 177 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8043 (pm20) cc_final: 0.7497 (pm20) REVERT: A 197 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8318 (pmtt) REVERT: A 428 PHE cc_start: 0.8597 (t80) cc_final: 0.7875 (t80) REVERT: B 428 PHE cc_start: 0.8565 (t80) cc_final: 0.7974 (t80) REVERT: C 221 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7937 (p90) REVERT: C 428 PHE cc_start: 0.8667 (t80) cc_final: 0.8172 (t80) REVERT: D 113 MET cc_start: 0.8423 (ppp) cc_final: 0.8196 (ppp) REVERT: D 221 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.8061 (p90) REVERT: D 428 PHE cc_start: 0.8593 (t80) cc_final: 0.8108 (t80) REVERT: E 308 ASP cc_start: 0.8655 (m-30) cc_final: 0.8441 (m-30) REVERT: E 428 PHE cc_start: 0.8616 (t80) cc_final: 0.8014 (t80) outliers start: 39 outliers final: 27 residues processed: 160 average time/residue: 1.1468 time to fit residues: 204.0958 Evaluate side-chains 163 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 204 ASP 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 150 VAL Chi-restraints excluded: chain C residue 154 ILE 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 277 VAL Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 244 MET 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 19 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 0.0670 chunk 94 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15085 Z= 0.185 Angle : 0.626 11.315 20465 Z= 0.318 Chirality : 0.043 0.144 2300 Planarity : 0.003 0.030 2545 Dihedral : 15.820 179.931 2202 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.63 % Allowed : 16.87 % Favored : 80.50 % 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: 0.74 (0.19), residues: 1775 helix: 2.99 (0.19), residues: 615 sheet: 0.77 (0.25), residues: 400 loop : -1.94 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 267 HIS 0.003 0.001 HIS C 335 PHE 0.017 0.001 PHE E 266 TYR 0.016 0.001 TYR B 325 ARG 0.003 0.000 ARG E 242 *********************** 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 178 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8427 (mtm) REVERT: A 181 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: A 263 TRP cc_start: 0.7979 (m-10) cc_final: 0.7740 (m-10) REVERT: A 428 PHE cc_start: 0.8513 (t80) cc_final: 0.7882 (t80) REVERT: B 428 PHE cc_start: 0.8543 (t80) cc_final: 0.7951 (t80) REVERT: C 196 GLU cc_start: 0.7713 (pm20) cc_final: 0.6989 (pm20) REVERT: C 197 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8284 (pmtt) REVERT: C 221 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7891 (p90) REVERT: C 428 PHE cc_start: 0.8651 (t80) cc_final: 0.8151 (t80) REVERT: D 113 MET cc_start: 0.8418 (ppp) cc_final: 0.8186 (ppp) REVERT: D 221 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.8005 (p90) REVERT: D 428 PHE cc_start: 0.8578 (t80) cc_final: 0.8091 (t80) REVERT: E 221 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7853 (p90) REVERT: E 308 ASP cc_start: 0.8564 (m-30) cc_final: 0.8364 (m-30) REVERT: E 428 PHE cc_start: 0.8594 (t80) cc_final: 0.7992 (t80) outliers start: 42 outliers final: 26 residues processed: 161 average time/residue: 1.2010 time to fit residues: 214.6428 Evaluate side-chains 165 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 154 ILE 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 B residue 323 LEU Chi-restraints excluded: chain C residue 154 ILE 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 277 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 164 MET 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 67 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 153 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15085 Z= 0.194 Angle : 0.618 10.946 20465 Z= 0.313 Chirality : 0.043 0.144 2300 Planarity : 0.003 0.047 2545 Dihedral : 15.715 179.577 2200 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 17.18 % Favored : 80.44 % 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: 0.78 (0.19), residues: 1775 helix: 2.96 (0.19), residues: 620 sheet: 0.74 (0.25), residues: 400 loop : -1.86 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 267 HIS 0.003 0.001 HIS C 335 PHE 0.016 0.001 PHE E 266 TYR 0.016 0.001 TYR B 325 ARG 0.010 0.000 ARG B 333 *********************** 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 174 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8380 (mtm) REVERT: A 181 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: A 263 TRP cc_start: 0.7947 (m-10) cc_final: 0.7661 (m-10) REVERT: A 428 PHE cc_start: 0.8523 (t80) cc_final: 0.7894 (t80) REVERT: B 79 THR cc_start: 0.9264 (m) cc_final: 0.8846 (p) REVERT: B 428 PHE cc_start: 0.8550 (t80) cc_final: 0.7956 (t80) REVERT: C 221 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7846 (p90) REVERT: C 428 PHE cc_start: 0.8655 (t80) cc_final: 0.8161 (t80) REVERT: D 113 MET cc_start: 0.8396 (ppp) cc_final: 0.8177 (ppp) REVERT: D 221 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7991 (p90) REVERT: D 263 TRP cc_start: 0.7884 (m-10) cc_final: 0.7610 (m-10) REVERT: D 428 PHE cc_start: 0.8579 (t80) cc_final: 0.8088 (t80) REVERT: E 263 TRP cc_start: 0.8174 (m-10) cc_final: 0.7761 (m-10) REVERT: E 428 PHE cc_start: 0.8589 (t80) cc_final: 0.8034 (t80) outliers start: 38 outliers final: 22 residues processed: 157 average time/residue: 1.2726 time to fit residues: 221.2762 Evaluate side-chains 161 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 154 ILE 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 154 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 138 ASP 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 138 ASP Chi-restraints excluded: chain E residue 150 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 0.0970 chunk 148 optimal weight: 0.9990 chunk 156 optimal weight: 0.0770 chunk 103 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15085 Z= 0.176 Angle : 0.619 10.477 20465 Z= 0.311 Chirality : 0.043 0.145 2300 Planarity : 0.003 0.032 2545 Dihedral : 15.612 179.968 2200 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.07 % Allowed : 17.93 % Favored : 80.00 % 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: 0.81 (0.19), residues: 1775 helix: 2.93 (0.19), residues: 625 sheet: 0.89 (0.26), residues: 370 loop : -1.80 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 267 HIS 0.003 0.001 HIS A 335 PHE 0.016 0.001 PHE E 266 TYR 0.015 0.001 TYR A 433 ARG 0.008 0.000 ARG B 333 *********************** 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 172 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8312 (mtm) REVERT: A 181 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: A 221 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7695 (p90) REVERT: A 263 TRP cc_start: 0.7896 (m-10) cc_final: 0.7529 (m-10) REVERT: A 428 PHE cc_start: 0.8531 (t80) cc_final: 0.7907 (t80) REVERT: B 79 THR cc_start: 0.9239 (m) cc_final: 0.8798 (p) REVERT: B 428 PHE cc_start: 0.8539 (t80) cc_final: 0.7963 (t80) REVERT: C 221 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7791 (p90) REVERT: C 263 TRP cc_start: 0.8132 (m-10) cc_final: 0.7692 (m-10) REVERT: C 428 PHE cc_start: 0.8651 (t80) cc_final: 0.8171 (t80) REVERT: D 113 MET cc_start: 0.8414 (ppp) cc_final: 0.8173 (ppp) REVERT: D 221 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7907 (p90) REVERT: D 263 TRP cc_start: 0.7771 (m-10) cc_final: 0.7448 (m-10) REVERT: D 428 PHE cc_start: 0.8574 (t80) cc_final: 0.8081 (t80) REVERT: E 263 TRP cc_start: 0.8175 (m-10) cc_final: 0.7723 (m-10) REVERT: E 428 PHE cc_start: 0.8608 (t80) cc_final: 0.8060 (t80) outliers start: 33 outliers final: 23 residues processed: 156 average time/residue: 1.1583 time to fit residues: 201.1558 Evaluate side-chains 164 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 154 ILE 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 B residue 323 LEU Chi-restraints excluded: chain C residue 154 ILE 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 277 VAL Chi-restraints excluded: chain D residue 138 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 138 ASP Chi-restraints excluded: chain E residue 150 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15085 Z= 0.260 Angle : 0.643 10.065 20465 Z= 0.327 Chirality : 0.044 0.140 2300 Planarity : 0.003 0.030 2545 Dihedral : 15.658 179.939 2200 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.01 % Allowed : 18.50 % Favored : 79.50 % 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: 0.79 (0.19), residues: 1775 helix: 3.09 (0.18), residues: 615 sheet: 0.74 (0.25), residues: 385 loop : -1.88 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 267 HIS 0.004 0.001 HIS C 335 PHE 0.016 0.001 PHE E 266 TYR 0.018 0.002 TYR D 429 ARG 0.005 0.000 ARG B 333 ********************** 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 169 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8379 (mtm) REVERT: A 221 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7655 (p90) REVERT: A 428 PHE cc_start: 0.8564 (t80) cc_final: 0.7928 (t80) REVERT: B 428 PHE cc_start: 0.8564 (t80) cc_final: 0.7954 (t80) REVERT: C 221 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7634 (p90) REVERT: C 428 PHE cc_start: 0.8668 (t80) cc_final: 0.8164 (t80) REVERT: D 113 MET cc_start: 0.8367 (ppp) cc_final: 0.8139 (ppp) REVERT: D 221 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7874 (p90) REVERT: D 263 TRP cc_start: 0.7938 (m-10) cc_final: 0.7600 (m-10) REVERT: D 428 PHE cc_start: 0.8555 (t80) cc_final: 0.8022 (t80) REVERT: E 221 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7837 (p90) REVERT: E 263 TRP cc_start: 0.8175 (m-10) cc_final: 0.7784 (m-10) REVERT: E 311 MET cc_start: 0.8746 (mmm) cc_final: 0.8475 (mmm) REVERT: E 428 PHE cc_start: 0.8661 (t80) cc_final: 0.8071 (t80) outliers start: 32 outliers final: 20 residues processed: 153 average time/residue: 1.1529 time to fit residues: 195.8529 Evaluate side-chains 161 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ILE 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 154 ILE 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 277 VAL 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 138 ASP Chi-restraints excluded: chain E residue 150 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 142 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.090045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.065112 restraints weight = 32866.146| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.57 r_work: 0.2793 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15085 Z= 0.237 Angle : 0.635 11.160 20465 Z= 0.323 Chirality : 0.044 0.147 2300 Planarity : 0.003 0.029 2545 Dihedral : 15.649 179.854 2200 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.19 % Allowed : 18.68 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1775 helix: 2.64 (0.19), residues: 650 sheet: 0.67 (0.25), residues: 385 loop : -1.89 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 263 HIS 0.004 0.001 HIS C 335 PHE 0.017 0.001 PHE D 266 TYR 0.017 0.002 TYR A 433 ARG 0.006 0.000 ARG B 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4504.29 seconds wall clock time: 79 minutes 59.62 seconds (4799.62 seconds total)