Starting phenix.real_space_refine on Tue Nov 18 15:09:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6q_23704/11_2025/7m6q_23704.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6q_23704/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/7m6q_23704/11_2025/7m6q_23704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6q_23704/11_2025/7m6q_23704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6q_23704/11_2025/7m6q_23704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6q_23704/11_2025/7m6q_23704.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'PHE: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: 3.13, per 1000 atoms: 0.21 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: 1.20 Conformation dependent library (CDL) restraints added in 662.7 milliseconds 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: 0.56 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: 2.60 Time building geometry restraints manager: 1.65 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.630 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.010 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (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 ARG 0.010 0.001 ARG C 220 TYR 0.027 0.003 TYR A 433 PHE 0.033 0.004 PHE E 169 TRP 0.011 0.002 TRP C 430 HIS 0.004 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00853 (15085) covalent geometry : angle 1.15894 (20465) SS BOND : bond 0.01046 ( 5) SS BOND : angle 1.15600 ( 10) hydrogen bonds : bond 0.19442 ( 720) hydrogen bonds : angle 6.80224 ( 2505) link_NAG-ASN : bond 0.00417 ( 5) link_NAG-ASN : angle 2.56188 ( 15) *********************** 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 : 0.632 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: 0.6322 time to fit residues: 159.4456 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 : 0.591 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN D 85 ASN E 85 ASN 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 = 0.094138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.070487 restraints weight = 32721.895| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.57 r_work: 0.2918 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15095 Z= 0.159 Angle : 0.705 9.803 20490 Z= 0.366 Chirality : 0.046 0.167 2300 Planarity : 0.004 0.047 2545 Dihedral : 16.648 179.120 2212 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.38 % Allowed : 10.97 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1775 helix: 2.28 (0.19), residues: 645 sheet: 0.77 (0.27), residues: 380 loop : -2.27 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 415 TYR 0.022 0.002 TYR E 325 PHE 0.011 0.001 PHE D 87 TRP 0.023 0.002 TRP E 267 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00332 (15085) covalent geometry : angle 0.70530 (20465) SS BOND : bond 0.00517 ( 5) SS BOND : angle 0.17128 ( 10) hydrogen bonds : bond 0.07191 ( 720) hydrogen bonds : angle 5.00327 ( 2505) link_NAG-ASN : bond 0.00283 ( 5) link_NAG-ASN : angle 1.04792 ( 15) *********************** 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 189 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.526 Fit side-chains REVERT: A 171 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8415 (mpp) REVERT: A 267 TRP cc_start: 0.6626 (t-100) cc_final: 0.6167 (t-100) REVERT: A 426 ASN cc_start: 0.8608 (t0) cc_final: 0.8394 (t0) REVERT: A 428 PHE cc_start: 0.8730 (t80) cc_final: 0.8306 (m-80) REVERT: A 437 ARG cc_start: 0.7240 (mtp180) cc_final: 0.6081 (mtm180) REVERT: B 79 THR cc_start: 0.8934 (m) cc_final: 0.8351 (p) REVERT: B 81 ASP cc_start: 0.8491 (p0) cc_final: 0.8108 (p0) REVERT: B 196 GLU cc_start: 0.8595 (pm20) cc_final: 0.8348 (pm20) REVERT: B 266 PHE cc_start: 0.6208 (m-10) cc_final: 0.5751 (m-10) REVERT: B 428 PHE cc_start: 0.8777 (t80) cc_final: 0.8195 (t80) REVERT: B 437 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6166 (mtt180) REVERT: C 308 ASP cc_start: 0.8868 (m-30) cc_final: 0.8582 (m-30) REVERT: C 428 PHE cc_start: 0.8810 (t80) cc_final: 0.8112 (t80) REVERT: C 437 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6057 (mtt180) REVERT: D 79 THR cc_start: 0.8961 (m) cc_final: 0.8402 (p) REVERT: D 81 ASP cc_start: 0.8560 (p0) cc_final: 0.8299 (p0) REVERT: D 113 MET cc_start: 0.8333 (ppp) cc_final: 0.7988 (ppp) REVERT: D 243 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8856 (mt0) REVERT: D 428 PHE cc_start: 0.8879 (t80) cc_final: 0.8307 (t80) REVERT: D 437 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6209 (mtt180) REVERT: E 79 THR cc_start: 0.9041 (m) cc_final: 0.8583 (p) REVERT: E 81 ASP cc_start: 0.8462 (p0) cc_final: 0.8205 (p0) REVERT: E 113 MET cc_start: 0.8622 (pmm) cc_final: 0.8080 (ppp) REVERT: E 187 MET cc_start: 0.8660 (mmm) cc_final: 0.8421 (tpp) REVERT: E 308 ASP cc_start: 0.9068 (m-30) cc_final: 0.8727 (m-30) REVERT: E 428 PHE cc_start: 0.8843 (t80) cc_final: 0.8264 (t80) REVERT: E 437 ARG cc_start: 0.7202 (mtp180) cc_final: 0.6201 (mtm180) outliers start: 38 outliers final: 14 residues processed: 175 average time/residue: 0.5988 time to fit residues: 115.5550 Evaluate side-chains 149 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 244 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 20 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.092029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.067812 restraints weight = 33244.576| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.59 r_work: 0.2857 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15095 Z= 0.160 Angle : 0.657 7.659 20490 Z= 0.337 Chirality : 0.045 0.185 2300 Planarity : 0.004 0.042 2545 Dihedral : 16.029 179.857 2206 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.95 % Allowed : 11.29 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1775 helix: 2.39 (0.19), residues: 645 sheet: 0.98 (0.25), residues: 380 loop : -2.12 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 333 TYR 0.019 0.002 TYR B 325 PHE 0.015 0.002 PHE D 87 TRP 0.016 0.001 TRP E 267 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00364 (15085) covalent geometry : angle 0.65648 (20465) SS BOND : bond 0.00456 ( 5) SS BOND : angle 0.43853 ( 10) hydrogen bonds : bond 0.06241 ( 720) hydrogen bonds : angle 4.44318 ( 2505) link_NAG-ASN : bond 0.00123 ( 5) link_NAG-ASN : angle 1.10192 ( 15) *********************** 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 193 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8803 (t80) cc_final: 0.8073 (t80) REVERT: A 437 ARG cc_start: 0.7248 (mtp180) cc_final: 0.6082 (mtm180) REVERT: B 79 THR cc_start: 0.8961 (m) cc_final: 0.8624 (p) REVERT: B 266 PHE cc_start: 0.6654 (m-10) cc_final: 0.6308 (m-10) REVERT: B 428 PHE cc_start: 0.8783 (t80) cc_final: 0.8172 (t80) REVERT: C 428 PHE cc_start: 0.8820 (t80) cc_final: 0.8128 (t80) REVERT: C 437 ARG cc_start: 0.6927 (mtp180) cc_final: 0.5828 (mtm180) REVERT: D 113 MET cc_start: 0.8443 (ppp) cc_final: 0.8070 (ppp) REVERT: D 244 MET cc_start: 0.9117 (mmm) cc_final: 0.8916 (tpp) REVERT: D 428 PHE cc_start: 0.8847 (t80) cc_final: 0.8285 (t80) REVERT: D 437 ARG cc_start: 0.7077 (mtp180) cc_final: 0.6146 (mtm180) REVERT: E 79 THR cc_start: 0.9015 (m) cc_final: 0.8684 (p) REVERT: E 113 MET cc_start: 0.8567 (pmm) cc_final: 0.8104 (ppp) REVERT: E 308 ASP cc_start: 0.9071 (m-30) cc_final: 0.8817 (m-30) REVERT: E 428 PHE cc_start: 0.8852 (t80) cc_final: 0.8237 (t80) REVERT: E 437 ARG cc_start: 0.7100 (mtp180) cc_final: 0.6056 (mtm180) outliers start: 47 outliers final: 15 residues processed: 177 average time/residue: 0.5745 time to fit residues: 112.4926 Evaluate side-chains 147 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 A residue 298 LEU 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 E residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 137 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 0.0170 chunk 87 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.092830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068519 restraints weight = 32899.902| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.58 r_work: 0.2869 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15095 Z= 0.134 Angle : 0.620 8.376 20490 Z= 0.317 Chirality : 0.044 0.146 2300 Planarity : 0.003 0.037 2545 Dihedral : 15.886 179.852 2202 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.01 % Allowed : 12.92 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1775 helix: 2.52 (0.19), residues: 645 sheet: 0.97 (0.25), residues: 380 loop : -1.99 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 333 TYR 0.017 0.001 TYR A 325 PHE 0.011 0.001 PHE C 87 TRP 0.013 0.001 TRP E 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00298 (15085) covalent geometry : angle 0.62012 (20465) SS BOND : bond 0.00390 ( 5) SS BOND : angle 0.24319 ( 10) hydrogen bonds : bond 0.05443 ( 720) hydrogen bonds : angle 4.13046 ( 2505) link_NAG-ASN : bond 0.00176 ( 5) link_NAG-ASN : angle 0.83934 ( 15) *********************** 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 190 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8753 (t80) cc_final: 0.8080 (t80) REVERT: A 437 ARG cc_start: 0.7135 (mtp180) cc_final: 0.5985 (mtm180) REVERT: B 196 GLU cc_start: 0.8623 (pm20) cc_final: 0.8309 (pm20) REVERT: B 215 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8426 (tm-30) REVERT: B 266 PHE cc_start: 0.6540 (m-10) cc_final: 0.6316 (m-10) REVERT: B 428 PHE cc_start: 0.8764 (t80) cc_final: 0.8164 (t80) REVERT: C 215 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 266 PHE cc_start: 0.7054 (m-10) cc_final: 0.6846 (m-80) REVERT: C 428 PHE cc_start: 0.8811 (t80) cc_final: 0.8124 (t80) REVERT: D 113 MET cc_start: 0.8385 (ppp) cc_final: 0.7990 (ppp) REVERT: D 181 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8022 (pp20) REVERT: D 244 MET cc_start: 0.9094 (mmm) cc_final: 0.8887 (tpp) REVERT: D 428 PHE cc_start: 0.8800 (t80) cc_final: 0.8251 (t80) REVERT: D 437 ARG cc_start: 0.6983 (mtp180) cc_final: 0.6186 (mtm180) REVERT: E 79 THR cc_start: 0.8917 (m) cc_final: 0.8554 (p) REVERT: E 113 MET cc_start: 0.8514 (pmm) cc_final: 0.8008 (ppp) REVERT: E 308 ASP cc_start: 0.9051 (m-30) cc_final: 0.8792 (m-30) REVERT: E 428 PHE cc_start: 0.8826 (t80) cc_final: 0.8250 (t80) REVERT: E 437 ARG cc_start: 0.7076 (mtp180) cc_final: 0.6033 (mtm180) outliers start: 48 outliers final: 19 residues processed: 172 average time/residue: 0.6275 time to fit residues: 118.3877 Evaluate side-chains 149 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 B residue 154 ILE Chi-restraints excluded: chain B residue 244 MET 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 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 181 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 48 optimal weight: 0.6980 chunk 164 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 22 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** B 85 ASN B 179 GLN D 85 ASN E 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.068073 restraints weight = 32984.323| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.60 r_work: 0.2856 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2740 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= 0.131 Angle : 0.607 8.769 20490 Z= 0.310 Chirality : 0.043 0.144 2300 Planarity : 0.003 0.035 2545 Dihedral : 15.814 179.171 2202 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.57 % Allowed : 14.29 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1775 helix: 2.89 (0.19), residues: 615 sheet: 1.02 (0.25), residues: 390 loop : -2.06 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.016 0.002 TYR B 325 PHE 0.012 0.001 PHE A 87 TRP 0.019 0.001 TRP B 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00298 (15085) covalent geometry : angle 0.60709 (20465) SS BOND : bond 0.00337 ( 5) SS BOND : angle 0.27165 ( 10) hydrogen bonds : bond 0.05085 ( 720) hydrogen bonds : angle 3.96452 ( 2505) link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 0.84402 ( 15) *********************** 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 to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8757 (t80) cc_final: 0.8088 (t80) REVERT: B 79 THR cc_start: 0.8981 (m) cc_final: 0.8605 (p) REVERT: B 196 GLU cc_start: 0.8584 (pm20) cc_final: 0.8338 (pm20) REVERT: B 215 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8425 (tm-30) REVERT: B 428 PHE cc_start: 0.8759 (t80) cc_final: 0.8143 (t80) REVERT: C 196 GLU cc_start: 0.8390 (pm20) cc_final: 0.7535 (pm20) REVERT: C 197 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8001 (pmtt) REVERT: C 221 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8177 (p90) REVERT: C 266 PHE cc_start: 0.7080 (m-10) cc_final: 0.6871 (m-10) REVERT: C 428 PHE cc_start: 0.8866 (t80) cc_final: 0.8411 (t80) REVERT: D 113 MET cc_start: 0.8479 (ppp) cc_final: 0.8108 (ppp) REVERT: D 244 MET cc_start: 0.9095 (mmm) cc_final: 0.8893 (tpp) REVERT: D 428 PHE cc_start: 0.8792 (t80) cc_final: 0.8237 (t80) REVERT: E 79 THR cc_start: 0.8959 (m) cc_final: 0.8587 (p) REVERT: E 113 MET cc_start: 0.8501 (pmm) cc_final: 0.8121 (ppp) REVERT: E 308 ASP cc_start: 0.9007 (m-30) cc_final: 0.8763 (m-30) REVERT: E 428 PHE cc_start: 0.8821 (t80) cc_final: 0.8271 (t80) outliers start: 41 outliers final: 20 residues processed: 161 average time/residue: 0.6001 time to fit residues: 106.9011 Evaluate side-chains 151 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 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 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 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 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 123 optimal weight: 0.0040 chunk 5 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 101 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7606 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.068043 restraints weight = 32688.730| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.60 r_work: 0.2855 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15095 Z= 0.131 Angle : 0.614 9.378 20490 Z= 0.313 Chirality : 0.043 0.151 2300 Planarity : 0.003 0.033 2545 Dihedral : 15.777 179.505 2202 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.57 % Allowed : 15.11 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1775 helix: 2.90 (0.19), residues: 615 sheet: 1.07 (0.26), residues: 375 loop : -1.99 (0.19), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 333 TYR 0.015 0.001 TYR E 325 PHE 0.011 0.001 PHE A 87 TRP 0.020 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00301 (15085) covalent geometry : angle 0.61435 (20465) SS BOND : bond 0.00303 ( 5) SS BOND : angle 0.27635 ( 10) hydrogen bonds : bond 0.04920 ( 720) hydrogen bonds : angle 3.78478 ( 2505) link_NAG-ASN : bond 0.00177 ( 5) link_NAG-ASN : angle 0.79443 ( 15) *********************** 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 172 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: A 428 PHE cc_start: 0.8722 (t80) cc_final: 0.8060 (t80) REVERT: B 196 GLU cc_start: 0.8602 (pm20) cc_final: 0.8366 (pm20) REVERT: B 215 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 428 PHE cc_start: 0.8762 (t80) cc_final: 0.8154 (t80) REVERT: C 221 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8126 (p90) REVERT: C 266 PHE cc_start: 0.7091 (m-10) cc_final: 0.6852 (m-10) REVERT: C 428 PHE cc_start: 0.8866 (t80) cc_final: 0.8437 (t80) REVERT: D 113 MET cc_start: 0.8492 (ppp) cc_final: 0.8129 (ppp) REVERT: D 428 PHE cc_start: 0.8789 (t80) cc_final: 0.8231 (t80) REVERT: E 79 THR cc_start: 0.8898 (m) cc_final: 0.8520 (p) REVERT: E 113 MET cc_start: 0.8481 (pmm) cc_final: 0.8126 (ppp) REVERT: E 221 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8267 (p90) REVERT: E 308 ASP cc_start: 0.9013 (m-30) cc_final: 0.8785 (m-30) REVERT: E 428 PHE cc_start: 0.8817 (t80) cc_final: 0.8266 (t80) outliers start: 41 outliers final: 26 residues processed: 155 average time/residue: 0.5987 time to fit residues: 102.7276 Evaluate side-chains 159 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 298 LEU 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 244 MET 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 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 171 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 115 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 145 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.090816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.066054 restraints weight = 32741.267| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.59 r_work: 0.2812 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15095 Z= 0.160 Angle : 0.631 10.340 20490 Z= 0.322 Chirality : 0.043 0.139 2300 Planarity : 0.003 0.034 2545 Dihedral : 15.816 179.780 2202 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.70 % Allowed : 16.24 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1775 helix: 2.71 (0.19), residues: 645 sheet: 0.75 (0.24), residues: 410 loop : -1.95 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 333 TYR 0.017 0.002 TYR E 325 PHE 0.014 0.001 PHE D 87 TRP 0.031 0.001 TRP A 263 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00373 (15085) covalent geometry : angle 0.63053 (20465) SS BOND : bond 0.00361 ( 5) SS BOND : angle 0.41432 ( 10) hydrogen bonds : bond 0.05122 ( 720) hydrogen bonds : angle 3.78930 ( 2505) link_NAG-ASN : bond 0.00052 ( 5) link_NAG-ASN : angle 1.04871 ( 15) *********************** 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 176 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: A 428 PHE cc_start: 0.8781 (t80) cc_final: 0.8125 (t80) REVERT: B 215 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8435 (tm-30) REVERT: B 244 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8783 (tpp) REVERT: B 428 PHE cc_start: 0.8764 (t80) cc_final: 0.8138 (t80) REVERT: C 196 GLU cc_start: 0.8344 (pm20) cc_final: 0.7611 (pm20) REVERT: C 197 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8092 (pmtt) REVERT: C 221 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7957 (p90) REVERT: C 266 PHE cc_start: 0.7084 (m-10) cc_final: 0.6763 (m-10) REVERT: C 428 PHE cc_start: 0.8875 (t80) cc_final: 0.8422 (t80) REVERT: D 113 MET cc_start: 0.8458 (ppp) cc_final: 0.8075 (ppp) REVERT: D 428 PHE cc_start: 0.8819 (t80) cc_final: 0.8269 (t80) REVERT: E 79 THR cc_start: 0.8896 (m) cc_final: 0.8641 (p) REVERT: E 113 MET cc_start: 0.8454 (pmm) cc_final: 0.8083 (ppp) REVERT: E 221 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.8148 (p90) REVERT: E 308 ASP cc_start: 0.9049 (m-30) cc_final: 0.8807 (m-30) REVERT: E 428 PHE cc_start: 0.8795 (t80) cc_final: 0.8166 (t80) outliers start: 43 outliers final: 23 residues processed: 157 average time/residue: 0.5895 time to fit residues: 102.3365 Evaluate side-chains 161 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 181 GLU 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 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 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 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 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 42 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.091306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.066477 restraints weight = 32823.525| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.60 r_work: 0.2820 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15095 Z= 0.138 Angle : 0.625 10.451 20490 Z= 0.316 Chirality : 0.043 0.151 2300 Planarity : 0.003 0.035 2545 Dihedral : 15.719 179.743 2200 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.26 % Allowed : 16.93 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 1775 helix: 3.01 (0.19), residues: 615 sheet: 0.77 (0.25), residues: 400 loop : -1.93 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 333 TYR 0.017 0.002 TYR A 433 PHE 0.015 0.001 PHE D 266 TRP 0.041 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00319 (15085) covalent geometry : angle 0.62495 (20465) SS BOND : bond 0.00333 ( 5) SS BOND : angle 0.33231 ( 10) hydrogen bonds : bond 0.04879 ( 720) hydrogen bonds : angle 3.71731 ( 2505) link_NAG-ASN : bond 0.00153 ( 5) link_NAG-ASN : angle 0.85004 ( 15) *********************** 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 171 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: A 428 PHE cc_start: 0.8779 (t80) cc_final: 0.8134 (t80) REVERT: B 215 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8420 (tm-30) REVERT: B 333 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7811 (ttp80) REVERT: B 428 PHE cc_start: 0.8768 (t80) cc_final: 0.8146 (t80) REVERT: C 221 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7972 (p90) REVERT: C 266 PHE cc_start: 0.7016 (m-10) cc_final: 0.6789 (m-80) REVERT: C 270 MET cc_start: 0.2758 (mmm) cc_final: 0.2147 (mmm) REVERT: C 428 PHE cc_start: 0.8860 (t80) cc_final: 0.8429 (t80) REVERT: D 113 MET cc_start: 0.8462 (ppp) cc_final: 0.8104 (ppp) REVERT: D 221 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8229 (p90) REVERT: D 263 TRP cc_start: 0.7528 (m-10) cc_final: 0.7268 (m-10) REVERT: D 270 MET cc_start: 0.4094 (pmm) cc_final: 0.3655 (mmm) REVERT: D 428 PHE cc_start: 0.8807 (t80) cc_final: 0.8256 (t80) REVERT: E 79 THR cc_start: 0.8901 (m) cc_final: 0.8637 (p) REVERT: E 113 MET cc_start: 0.8385 (pmm) cc_final: 0.8059 (ppp) REVERT: E 221 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8220 (p90) REVERT: E 308 ASP cc_start: 0.9044 (m-30) cc_final: 0.8798 (m-30) REVERT: E 428 PHE cc_start: 0.8813 (t80) cc_final: 0.8235 (t80) outliers start: 36 outliers final: 22 residues processed: 155 average time/residue: 0.5797 time to fit residues: 99.6783 Evaluate side-chains 160 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 204 ASP 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 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 171 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 285 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 41 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.093361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068467 restraints weight = 32337.437| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.48 r_work: 0.2876 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15095 Z= 0.120 Angle : 0.617 10.971 20490 Z= 0.309 Chirality : 0.043 0.146 2300 Planarity : 0.003 0.032 2545 Dihedral : 15.551 179.870 2200 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.82 % Allowed : 17.55 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1775 helix: 2.91 (0.19), residues: 625 sheet: 0.90 (0.25), residues: 380 loop : -1.82 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 333 TYR 0.016 0.001 TYR A 433 PHE 0.015 0.001 PHE D 266 TRP 0.038 0.001 TRP A 263 HIS 0.002 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00270 (15085) covalent geometry : angle 0.61746 (20465) SS BOND : bond 0.00287 ( 5) SS BOND : angle 0.21894 ( 10) hydrogen bonds : bond 0.04493 ( 720) hydrogen bonds : angle 3.59241 ( 2505) link_NAG-ASN : bond 0.00214 ( 5) link_NAG-ASN : angle 0.72731 ( 15) *********************** 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 168 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: A 221 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7976 (p90) REVERT: A 428 PHE cc_start: 0.8781 (t80) cc_final: 0.8122 (t80) REVERT: B 215 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 428 PHE cc_start: 0.8752 (t80) cc_final: 0.8119 (t80) REVERT: C 196 GLU cc_start: 0.8278 (pm20) cc_final: 0.7590 (pm20) REVERT: C 197 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8001 (pmtt) REVERT: C 221 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7920 (p90) REVERT: C 263 TRP cc_start: 0.7878 (m-10) cc_final: 0.7478 (m-10) REVERT: C 426 ASN cc_start: 0.8600 (t0) cc_final: 0.8354 (t0) REVERT: C 428 PHE cc_start: 0.8872 (t80) cc_final: 0.8449 (t80) REVERT: D 113 MET cc_start: 0.8493 (ppp) cc_final: 0.8129 (ppp) REVERT: D 221 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.8169 (p90) REVERT: D 263 TRP cc_start: 0.7487 (m-10) cc_final: 0.7198 (m-10) REVERT: D 428 PHE cc_start: 0.8802 (t80) cc_final: 0.8248 (t80) REVERT: E 79 THR cc_start: 0.8952 (m) cc_final: 0.8708 (p) REVERT: E 113 MET cc_start: 0.8423 (pmm) cc_final: 0.8119 (ppp) REVERT: E 187 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8657 (tpp) REVERT: E 263 TRP cc_start: 0.7991 (m-10) cc_final: 0.7530 (m-10) REVERT: E 308 ASP cc_start: 0.8990 (m-30) cc_final: 0.8772 (m-30) REVERT: E 428 PHE cc_start: 0.8857 (t80) cc_final: 0.8302 (t80) outliers start: 29 outliers final: 18 residues processed: 154 average time/residue: 0.5801 time to fit residues: 98.8157 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 154 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 264 VAL 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 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 204 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 264 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 187 MET 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 63 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 151 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068610 restraints weight = 32238.856| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.48 r_work: 0.2881 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15095 Z= 0.122 Angle : 0.611 10.271 20490 Z= 0.308 Chirality : 0.043 0.145 2300 Planarity : 0.003 0.032 2545 Dihedral : 15.397 178.360 2200 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.82 % Allowed : 17.93 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1775 helix: 2.93 (0.19), residues: 625 sheet: 0.90 (0.26), residues: 370 loop : -1.77 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.017 0.001 TYR A 433 PHE 0.014 0.001 PHE D 266 TRP 0.031 0.001 TRP A 263 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00276 (15085) covalent geometry : angle 0.61109 (20465) SS BOND : bond 0.00283 ( 5) SS BOND : angle 0.25280 ( 10) hydrogen bonds : bond 0.04379 ( 720) hydrogen bonds : angle 3.55051 ( 2505) link_NAG-ASN : bond 0.00181 ( 5) link_NAG-ASN : angle 0.75565 ( 15) ********************** 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 to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: A 221 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7936 (p90) REVERT: A 428 PHE cc_start: 0.8784 (t80) cc_final: 0.8154 (t80) REVERT: B 215 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8384 (tm-30) REVERT: B 428 PHE cc_start: 0.8754 (t80) cc_final: 0.8119 (t80) REVERT: C 221 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7895 (p90) REVERT: C 263 TRP cc_start: 0.7896 (m-10) cc_final: 0.7481 (m-10) REVERT: C 426 ASN cc_start: 0.8605 (t0) cc_final: 0.8337 (t0) REVERT: C 428 PHE cc_start: 0.8879 (t80) cc_final: 0.8465 (t80) REVERT: D 113 MET cc_start: 0.8505 (ppp) cc_final: 0.8060 (ppp) REVERT: D 221 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.8107 (p90) REVERT: D 263 TRP cc_start: 0.7458 (m-10) cc_final: 0.7205 (m-10) REVERT: D 428 PHE cc_start: 0.8803 (t80) cc_final: 0.8248 (t80) REVERT: E 79 THR cc_start: 0.8942 (m) cc_final: 0.8696 (p) REVERT: E 113 MET cc_start: 0.8420 (pmm) cc_final: 0.8162 (ppp) REVERT: E 187 MET cc_start: 0.8848 (mmm) cc_final: 0.8631 (tpp) REVERT: E 221 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.8129 (p90) REVERT: E 263 TRP cc_start: 0.7953 (m-10) cc_final: 0.7525 (m-10) REVERT: E 308 ASP cc_start: 0.8994 (m-30) cc_final: 0.8777 (m-30) REVERT: E 428 PHE cc_start: 0.8854 (t80) cc_final: 0.8295 (t80) outliers start: 29 outliers final: 19 residues processed: 154 average time/residue: 0.5941 time to fit residues: 101.1487 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 : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 264 VAL 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 221 TYR Chi-restraints excluded: chain C residue 265 SER 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 285 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 129 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.091951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.067005 restraints weight = 32374.673| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.46 r_work: 0.2849 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15095 Z= 0.151 Angle : 0.646 10.078 20490 Z= 0.322 Chirality : 0.043 0.162 2300 Planarity : 0.003 0.033 2545 Dihedral : 15.381 177.851 2200 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.88 % Allowed : 18.31 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1775 helix: 2.94 (0.19), residues: 625 sheet: 0.70 (0.25), residues: 400 loop : -1.73 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.017 0.002 TYR A 433 PHE 0.015 0.001 PHE D 266 TRP 0.032 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00355 (15085) covalent geometry : angle 0.64610 (20465) SS BOND : bond 0.00338 ( 5) SS BOND : angle 0.41480 ( 10) hydrogen bonds : bond 0.04662 ( 720) hydrogen bonds : angle 3.64800 ( 2505) link_NAG-ASN : bond 0.00079 ( 5) link_NAG-ASN : angle 0.96283 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4365.57 seconds wall clock time: 75 minutes 19.02 seconds (4519.02 seconds total)