Starting phenix.real_space_refine on Sun Jul 28 10:35:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xot_38540/07_2024/8xot_38540.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xot_38540/07_2024/8xot_38540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xot_38540/07_2024/8xot_38540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xot_38540/07_2024/8xot_38540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xot_38540/07_2024/8xot_38540.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xot_38540/07_2024/8xot_38540.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.081 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 276 5.16 5 C 27828 2.51 5 N 8064 2.21 5 O 8364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 43": "OE1" <-> "OE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "b TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 79": "OD1" <-> "OD2" Residue "b PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 256": "OE1" <-> "OE2" Residue "b TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 460": "OE1" <-> "OE2" Residue "b GLU 478": "OE1" <-> "OE2" Residue "B1 GLU 43": "OE1" <-> "OE2" Residue "B1 ASP 46": "OD1" <-> "OD2" Residue "B1 ASP 197": "OD1" <-> "OD2" Residue "B1 ASP 209": "OD1" <-> "OD2" Residue "B1 GLU 241": "OE1" <-> "OE2" Residue "B1 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 GLU 256": "OE1" <-> "OE2" Residue "B1 TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 ASP 446": "OD1" <-> "OD2" Residue "B1 GLU 463": "OE1" <-> "OE2" Residue "B1 GLU 476": "OE1" <-> "OE2" Residue "b1 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b1 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b1 GLU 285": "OE1" <-> "OE2" Residue "b1 ASP 456": "OD1" <-> "OD2" Residue "b1 GLU 463": "OE1" <-> "OE2" Residue "b1 GLU 478": "OE1" <-> "OE2" Residue "B2 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 241": "OE1" <-> "OE2" Residue "B2 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 256": "OE1" <-> "OE2" Residue "B2 ASP 262": "OD1" <-> "OD2" Residue "B2 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 463": "OE1" <-> "OE2" Residue "b2 GLU 43": "OE1" <-> "OE2" Residue "b2 ASP 46": "OD1" <-> "OD2" Residue "b2 ASP 197": "OD1" <-> "OD2" Residue "b2 ASP 262": "OD1" <-> "OD2" Residue "b2 GLU 285": "OE1" <-> "OE2" Residue "b2 ASP 446": "OD1" <-> "OD2" Residue "b2 ASP 456": "OD1" <-> "OD2" Residue "b2 GLU 463": "OE1" <-> "OE2" Residue "b2 ASP 484": "OD1" <-> "OD2" Residue "b2 ASP 485": "OD1" <-> "OD2" Residue "B3 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 ASP 79": "OD1" <-> "OD2" Residue "B3 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 241": "OE1" <-> "OE2" Residue "B3 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 256": "OE1" <-> "OE2" Residue "B3 ASP 262": "OD1" <-> "OD2" Residue "B3 PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 ASP 456": "OD1" <-> "OD2" Residue "B3 GLU 463": "OE1" <-> "OE2" Residue "b3 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b3 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b3 GLU 460": "OE1" <-> "OE2" Residue "b3 GLU 478": "OE1" <-> "OE2" Residue "b3 GLU 488": "OE1" <-> "OE2" Residue "B4 ASP 61": "OD1" <-> "OD2" Residue "B4 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 GLU 120": "OE1" <-> "OE2" Residue "B4 GLU 241": "OE1" <-> "OE2" Residue "B4 GLU 285": "OE1" <-> "OE2" Residue "B4 TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 ASP 485": "OD1" <-> "OD2" Residue "b4 GLU 43": "OE1" <-> "OE2" Residue "b4 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b4 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b4 GLU 256": "OE1" <-> "OE2" Residue "b4 GLU 283": "OE1" <-> "OE2" Residue "b4 GLU 285": "OE1" <-> "OE2" Residue "b4 ASP 346": "OD1" <-> "OD2" Residue "b4 GLU 463": "OE1" <-> "OE2" Residue "b4 GLU 478": "OE1" <-> "OE2" Residue "b4 ASP 484": "OD1" <-> "OD2" Residue "b4 ASP 485": "OD1" <-> "OD2" Residue "B5 GLU 140": "OE1" <-> "OE2" Residue "B5 GLU 241": "OE1" <-> "OE2" Residue "B5 GLU 256": "OE1" <-> "OE2" Residue "B5 GLU 285": "OE1" <-> "OE2" Residue "B5 GLU 355": "OE1" <-> "OE2" Residue "B5 GLU 391": "OE1" <-> "OE2" Residue "B5 TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b5 GLU 43": "OE1" <-> "OE2" Residue "b5 ASP 46": "OD1" <-> "OD2" Residue "b5 GLU 120": "OE1" <-> "OE2" Residue "b5 ASP 209": "OD1" <-> "OD2" Residue "b5 GLU 241": "OE1" <-> "OE2" Residue "b5 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b5 ASP 346": "OD1" <-> "OD2" Residue "b5 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b5 ASP 446": "OD1" <-> "OD2" Residue "b5 ASP 484": "OD1" <-> "OD2" Residue "b5 ASP 485": "OD1" <-> "OD2" Time to flip residues: 0.54s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 44532 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "b" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B1" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "b1" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B2" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "b2" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B3" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "b3" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B4" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "b4" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B5" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "b5" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 22.38, per 1000 atoms: 0.50 Number of scatterers: 44532 At special positions: 0 Unit cell: (160.704, 160.704, 134.574, 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 276 16.00 O 8364 8.00 N 8064 7.00 C 27828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS b 123 " - pdb=" SG CYS b 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB1 123 " - pdb=" SG CYSB1 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb1 123 " - pdb=" SG CYSb1 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB2 123 " - pdb=" SG CYSB2 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb2 123 " - pdb=" SG CYSb2 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB3 123 " - pdb=" SG CYSB3 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb3 123 " - pdb=" SG CYSb3 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB4 123 " - pdb=" SG CYSB4 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb4 123 " - pdb=" SG CYSb4 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB5 123 " - pdb=" SG CYSB5 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb5 123 " - pdb=" SG CYSb5 125 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 18.28 Conformation dependent library (CDL) restraints added in 9.2 seconds 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10560 Finding SS restraints... Secondary structure from input PDB file: 249 helices and 48 sheets defined 57.6% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 100 through 120 removed outlier: 3.823A pdb=" N GLU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 149 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 254 through 276 removed outlier: 3.561A pdb=" N ALA B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 302 Processing helix chain 'B' and resid 304 through 321 Processing helix chain 'B' and resid 350 through 367 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.609A pdb=" N LEU B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 403 Processing helix chain 'B' and resid 403 through 422 Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 474 through 482 removed outlier: 3.919A pdb=" N GLU B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 503 Processing helix chain 'b' and resid 34 through 38 Processing helix chain 'b' and resid 49 through 67 removed outlier: 4.574A pdb=" N THR b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG b 55 " --> pdb=" O PRO b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 82 removed outlier: 3.625A pdb=" N VAL b 82 " --> pdb=" O GLN b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 98 Processing helix chain 'b' and resid 100 through 120 removed outlier: 3.584A pdb=" N GLU b 117 " --> pdb=" O ALA b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 149 Processing helix chain 'b' and resid 173 through 177 Processing helix chain 'b' and resid 179 through 183 Processing helix chain 'b' and resid 249 through 253 removed outlier: 3.504A pdb=" N TYR b 252 " --> pdb=" O ASN b 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER b 253 " --> pdb=" O VAL b 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 249 through 253' Processing helix chain 'b' and resid 254 through 276 removed outlier: 3.734A pdb=" N ALA b 276 " --> pdb=" O ALA b 272 " (cutoff:3.500A) Processing helix chain 'b' and resid 289 through 302 Processing helix chain 'b' and resid 304 through 321 removed outlier: 3.665A pdb=" N THR b 308 " --> pdb=" O ARG b 304 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 367 removed outlier: 3.505A pdb=" N PHE b 354 " --> pdb=" O GLY b 350 " (cutoff:3.500A) Processing helix chain 'b' and resid 369 through 374 Processing helix chain 'b' and resid 381 through 403 Processing helix chain 'b' and resid 403 through 422 Processing helix chain 'b' and resid 438 through 443 Processing helix chain 'b' and resid 457 through 470 Processing helix chain 'b' and resid 474 through 482 removed outlier: 3.745A pdb=" N GLU b 478 " --> pdb=" O THR b 474 " (cutoff:3.500A) Processing helix chain 'b' and resid 485 through 503 Processing helix chain 'B1' and resid 34 through 38 Processing helix chain 'B1' and resid 44 through 50 Processing helix chain 'B1' and resid 52 through 67 Processing helix chain 'B1' and resid 67 through 82 removed outlier: 3.526A pdb=" N ALAB1 71 " --> pdb=" O ASNB1 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VALB1 82 " --> pdb=" O GLNB1 78 " (cutoff:3.500A) Processing helix chain 'B1' and resid 93 through 98 Processing helix chain 'B1' and resid 100 through 120 removed outlier: 3.631A pdb=" N GLUB1 120 " --> pdb=" O LYSB1 116 " (cutoff:3.500A) Processing helix chain 'B1' and resid 133 through 149 Processing helix chain 'B1' and resid 173 through 177 Processing helix chain 'B1' and resid 179 through 183 Processing helix chain 'B1' and resid 249 through 253 Processing helix chain 'B1' and resid 254 through 276 Processing helix chain 'B1' and resid 289 through 302 Processing helix chain 'B1' and resid 303 through 321 removed outlier: 4.414A pdb=" N LEUB1 307 " --> pdb=" O GLNB1 303 " (cutoff:3.500A) Processing helix chain 'B1' and resid 350 through 367 Processing helix chain 'B1' and resid 369 through 374 Processing helix chain 'B1' and resid 381 through 403 removed outlier: 3.529A pdb=" N ALAB1 385 " --> pdb=" O SERB1 381 " (cutoff:3.500A) Processing helix chain 'B1' and resid 403 through 422 Processing helix chain 'B1' and resid 438 through 444 Processing helix chain 'B1' and resid 457 through 470 Processing helix chain 'B1' and resid 474 through 481 removed outlier: 3.837A pdb=" N GLUB1 478 " --> pdb=" O THRB1 474 " (cutoff:3.500A) Processing helix chain 'B1' and resid 485 through 503 Processing helix chain 'b1' and resid 34 through 38 Processing helix chain 'b1' and resid 49 through 51 No H-bonds generated for 'chain 'b1' and resid 49 through 51' Processing helix chain 'b1' and resid 52 through 67 Processing helix chain 'b1' and resid 67 through 82 Processing helix chain 'b1' and resid 93 through 98 Processing helix chain 'b1' and resid 100 through 120 removed outlier: 3.626A pdb=" N GLUb1 117 " --> pdb=" O ALAb1 113 " (cutoff:3.500A) Processing helix chain 'b1' and resid 133 through 149 Processing helix chain 'b1' and resid 173 through 177 Processing helix chain 'b1' and resid 179 through 183 Processing helix chain 'b1' and resid 249 through 253 Processing helix chain 'b1' and resid 254 through 276 removed outlier: 3.602A pdb=" N ALAb1 276 " --> pdb=" O ALAb1 272 " (cutoff:3.500A) Processing helix chain 'b1' and resid 288 through 302 Processing helix chain 'b1' and resid 303 through 321 removed outlier: 4.489A pdb=" N LEUb1 307 " --> pdb=" O GLNb1 303 " (cutoff:3.500A) Processing helix chain 'b1' and resid 350 through 367 Processing helix chain 'b1' and resid 369 through 374 Processing helix chain 'b1' and resid 381 through 403 Processing helix chain 'b1' and resid 403 through 422 Processing helix chain 'b1' and resid 438 through 444 Processing helix chain 'b1' and resid 457 through 470 Processing helix chain 'b1' and resid 474 through 481 removed outlier: 3.642A pdb=" N GLUb1 478 " --> pdb=" O THRb1 474 " (cutoff:3.500A) Processing helix chain 'b1' and resid 485 through 503 Processing helix chain 'B2' and resid 34 through 38 Processing helix chain 'B2' and resid 52 through 67 Processing helix chain 'B2' and resid 67 through 82 removed outlier: 3.905A pdb=" N VALB2 82 " --> pdb=" O GLNB2 78 " (cutoff:3.500A) Processing helix chain 'B2' and resid 93 through 98 Processing helix chain 'B2' and resid 100 through 120 removed outlier: 3.664A pdb=" N GLUB2 117 " --> pdb=" O ALAB2 113 " (cutoff:3.500A) Processing helix chain 'B2' and resid 133 through 149 Processing helix chain 'B2' and resid 173 through 177 Processing helix chain 'B2' and resid 179 through 183 Processing helix chain 'B2' and resid 249 through 253 Processing helix chain 'B2' and resid 254 through 276 removed outlier: 3.513A pdb=" N ALAB2 276 " --> pdb=" O ALAB2 272 " (cutoff:3.500A) Processing helix chain 'B2' and resid 289 through 302 Processing helix chain 'B2' and resid 304 through 321 removed outlier: 3.640A pdb=" N TRPB2 310 " --> pdb=" O ARGB2 306 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALAB2 319 " --> pdb=" O ALAB2 315 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALAB2 320 " --> pdb=" O ALAB2 316 " (cutoff:3.500A) Processing helix chain 'B2' and resid 350 through 367 removed outlier: 3.613A pdb=" N GLNB2 356 " --> pdb=" O SERB2 352 " (cutoff:3.500A) Processing helix chain 'B2' and resid 369 through 375 Processing helix chain 'B2' and resid 381 through 403 Processing helix chain 'B2' and resid 403 through 422 Processing helix chain 'B2' and resid 438 through 443 Processing helix chain 'B2' and resid 457 through 470 Processing helix chain 'B2' and resid 474 through 482 removed outlier: 3.849A pdb=" N GLUB2 478 " --> pdb=" O THRB2 474 " (cutoff:3.500A) Processing helix chain 'B2' and resid 485 through 503 Processing helix chain 'b2' and resid 34 through 38 Processing helix chain 'b2' and resid 44 through 50 Processing helix chain 'b2' and resid 52 through 67 Processing helix chain 'b2' and resid 67 through 82 removed outlier: 3.690A pdb=" N VALb2 82 " --> pdb=" O GLNb2 78 " (cutoff:3.500A) Processing helix chain 'b2' and resid 93 through 98 Processing helix chain 'b2' and resid 100 through 120 removed outlier: 3.876A pdb=" N GLUb2 117 " --> pdb=" O ALAb2 113 " (cutoff:3.500A) Processing helix chain 'b2' and resid 133 through 149 Processing helix chain 'b2' and resid 173 through 177 Processing helix chain 'b2' and resid 179 through 183 Processing helix chain 'b2' and resid 249 through 253 Processing helix chain 'b2' and resid 254 through 275 Processing helix chain 'b2' and resid 288 through 302 Processing helix chain 'b2' and resid 303 through 321 removed outlier: 4.281A pdb=" N LEUb2 307 " --> pdb=" O GLNb2 303 " (cutoff:3.500A) Processing helix chain 'b2' and resid 350 through 367 Processing helix chain 'b2' and resid 369 through 375 Processing helix chain 'b2' and resid 381 through 403 Processing helix chain 'b2' and resid 403 through 422 Processing helix chain 'b2' and resid 438 through 444 Processing helix chain 'b2' and resid 457 through 470 Processing helix chain 'b2' and resid 474 through 482 removed outlier: 3.596A pdb=" N GLUb2 478 " --> pdb=" O THRb2 474 " (cutoff:3.500A) Processing helix chain 'b2' and resid 485 through 503 Processing helix chain 'B3' and resid 34 through 38 Processing helix chain 'B3' and resid 44 through 50 Processing helix chain 'B3' and resid 52 through 67 Processing helix chain 'B3' and resid 67 through 82 Processing helix chain 'B3' and resid 93 through 98 Processing helix chain 'B3' and resid 100 through 120 removed outlier: 3.601A pdb=" N GLUB3 117 " --> pdb=" O ALAB3 113 " (cutoff:3.500A) Processing helix chain 'B3' and resid 133 through 149 Processing helix chain 'B3' and resid 173 through 177 Processing helix chain 'B3' and resid 179 through 183 Processing helix chain 'B3' and resid 249 through 253 Processing helix chain 'B3' and resid 254 through 275 Processing helix chain 'B3' and resid 289 through 302 Processing helix chain 'B3' and resid 303 through 321 removed outlier: 4.301A pdb=" N LEUB3 307 " --> pdb=" O GLNB3 303 " (cutoff:3.500A) Processing helix chain 'B3' and resid 350 through 367 Processing helix chain 'B3' and resid 369 through 374 Processing helix chain 'B3' and resid 381 through 403 Processing helix chain 'B3' and resid 403 through 422 Processing helix chain 'B3' and resid 438 through 444 Processing helix chain 'B3' and resid 457 through 470 removed outlier: 3.561A pdb=" N VALB3 461 " --> pdb=" O GLYB3 457 " (cutoff:3.500A) Processing helix chain 'B3' and resid 474 through 482 removed outlier: 3.627A pdb=" N GLUB3 478 " --> pdb=" O THRB3 474 " (cutoff:3.500A) Processing helix chain 'B3' and resid 485 through 503 Processing helix chain 'b3' and resid 34 through 38 Processing helix chain 'b3' and resid 44 through 50 Processing helix chain 'b3' and resid 52 through 67 Processing helix chain 'b3' and resid 67 through 82 removed outlier: 3.873A pdb=" N VALb3 82 " --> pdb=" O GLNb3 78 " (cutoff:3.500A) Processing helix chain 'b3' and resid 93 through 98 Processing helix chain 'b3' and resid 100 through 120 removed outlier: 3.634A pdb=" N GLUb3 117 " --> pdb=" O ALAb3 113 " (cutoff:3.500A) Processing helix chain 'b3' and resid 133 through 149 Processing helix chain 'b3' and resid 173 through 177 Processing helix chain 'b3' and resid 179 through 183 Processing helix chain 'b3' and resid 249 through 253 removed outlier: 3.906A pdb=" N SERb3 253 " --> pdb=" O VALb3 250 " (cutoff:3.500A) Processing helix chain 'b3' and resid 254 through 275 Processing helix chain 'b3' and resid 289 through 302 Processing helix chain 'b3' and resid 304 through 321 removed outlier: 3.943A pdb=" N TRPb3 310 " --> pdb=" O ARGb3 306 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALAb3 320 " --> pdb=" O ALAb3 316 " (cutoff:3.500A) Processing helix chain 'b3' and resid 350 through 367 Processing helix chain 'b3' and resid 369 through 374 Processing helix chain 'b3' and resid 381 through 403 Processing helix chain 'b3' and resid 403 through 422 Processing helix chain 'b3' and resid 438 through 443 Processing helix chain 'b3' and resid 457 through 470 Processing helix chain 'b3' and resid 474 through 481 removed outlier: 3.992A pdb=" N GLUb3 478 " --> pdb=" O THRb3 474 " (cutoff:3.500A) Processing helix chain 'b3' and resid 485 through 503 Processing helix chain 'B4' and resid 34 through 38 Processing helix chain 'B4' and resid 44 through 50 Processing helix chain 'B4' and resid 52 through 67 Processing helix chain 'B4' and resid 67 through 82 Processing helix chain 'B4' and resid 93 through 98 Processing helix chain 'B4' and resid 100 through 120 removed outlier: 3.879A pdb=" N GLUB4 117 " --> pdb=" O ALAB4 113 " (cutoff:3.500A) Processing helix chain 'B4' and resid 133 through 149 Processing helix chain 'B4' and resid 173 through 177 Processing helix chain 'B4' and resid 179 through 183 Processing helix chain 'B4' and resid 249 through 253 removed outlier: 3.628A pdb=" N SERB4 253 " --> pdb=" O VALB4 250 " (cutoff:3.500A) Processing helix chain 'B4' and resid 254 through 276 removed outlier: 3.732A pdb=" N THRB4 263 " --> pdb=" O LYSB4 259 " (cutoff:3.500A) Processing helix chain 'B4' and resid 288 through 302 Processing helix chain 'B4' and resid 303 through 321 removed outlier: 4.318A pdb=" N LEUB4 307 " --> pdb=" O GLNB4 303 " (cutoff:3.500A) Processing helix chain 'B4' and resid 350 through 367 Processing helix chain 'B4' and resid 369 through 374 Processing helix chain 'B4' and resid 381 through 403 Processing helix chain 'B4' and resid 403 through 422 Processing helix chain 'B4' and resid 438 through 444 Processing helix chain 'B4' and resid 457 through 471 Processing helix chain 'B4' and resid 474 through 482 removed outlier: 3.563A pdb=" N GLUB4 478 " --> pdb=" O THRB4 474 " (cutoff:3.500A) Processing helix chain 'B4' and resid 485 through 503 Processing helix chain 'b4' and resid 34 through 38 removed outlier: 3.502A pdb=" N TRPb4 38 " --> pdb=" O LEUb4 35 " (cutoff:3.500A) Processing helix chain 'b4' and resid 44 through 50 Processing helix chain 'b4' and resid 52 through 67 Processing helix chain 'b4' and resid 67 through 82 removed outlier: 3.506A pdb=" N ALAb4 71 " --> pdb=" O ASNb4 67 " (cutoff:3.500A) Processing helix chain 'b4' and resid 93 through 98 Processing helix chain 'b4' and resid 100 through 120 removed outlier: 3.816A pdb=" N GLUb4 120 " --> pdb=" O LYSb4 116 " (cutoff:3.500A) Processing helix chain 'b4' and resid 133 through 149 Processing helix chain 'b4' and resid 173 through 177 Processing helix chain 'b4' and resid 179 through 183 Processing helix chain 'b4' and resid 249 through 253 Processing helix chain 'b4' and resid 254 through 275 Processing helix chain 'b4' and resid 289 through 302 Processing helix chain 'b4' and resid 303 through 321 removed outlier: 4.494A pdb=" N LEUb4 307 " --> pdb=" O GLNb4 303 " (cutoff:3.500A) Processing helix chain 'b4' and resid 350 through 367 Processing helix chain 'b4' and resid 369 through 374 Processing helix chain 'b4' and resid 381 through 403 Processing helix chain 'b4' and resid 403 through 422 Processing helix chain 'b4' and resid 438 through 444 Processing helix chain 'b4' and resid 457 through 470 Processing helix chain 'b4' and resid 474 through 481 Processing helix chain 'b4' and resid 485 through 503 Processing helix chain 'B5' and resid 34 through 38 Processing helix chain 'B5' and resid 44 through 67 Proline residue: B5 51 - end of helix removed outlier: 4.553A pdb=" N THRB5 54 " --> pdb=" O LEUB5 50 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARGB5 55 " --> pdb=" O PROB5 51 " (cutoff:3.500A) Processing helix chain 'B5' and resid 67 through 82 removed outlier: 3.732A pdb=" N VALB5 82 " --> pdb=" O GLNB5 78 " (cutoff:3.500A) Processing helix chain 'B5' and resid 93 through 98 Processing helix chain 'B5' and resid 100 through 120 removed outlier: 3.675A pdb=" N GLUB5 117 " --> pdb=" O ALAB5 113 " (cutoff:3.500A) Processing helix chain 'B5' and resid 133 through 149 Processing helix chain 'B5' and resid 173 through 177 Processing helix chain 'B5' and resid 179 through 183 Processing helix chain 'B5' and resid 249 through 253 Processing helix chain 'B5' and resid 254 through 275 removed outlier: 3.637A pdb=" N METB5 258 " --> pdb=" O VALB5 254 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYSB5 259 " --> pdb=" O METB5 255 " (cutoff:3.500A) Processing helix chain 'B5' and resid 289 through 302 Processing helix chain 'B5' and resid 303 through 321 removed outlier: 4.408A pdb=" N LEUB5 307 " --> pdb=" O GLNB5 303 " (cutoff:3.500A) Processing helix chain 'B5' and resid 350 through 367 Processing helix chain 'B5' and resid 369 through 375 Processing helix chain 'B5' and resid 381 through 403 Processing helix chain 'B5' and resid 403 through 422 Processing helix chain 'B5' and resid 438 through 443 Processing helix chain 'B5' and resid 457 through 470 Processing helix chain 'B5' and resid 474 through 482 removed outlier: 3.971A pdb=" N GLUB5 478 " --> pdb=" O THRB5 474 " (cutoff:3.500A) Processing helix chain 'B5' and resid 485 through 503 Processing helix chain 'b5' and resid 34 through 38 Processing helix chain 'b5' and resid 44 through 50 Processing helix chain 'b5' and resid 52 through 67 Processing helix chain 'b5' and resid 67 through 82 removed outlier: 3.718A pdb=" N VALb5 82 " --> pdb=" O GLNb5 78 " (cutoff:3.500A) Processing helix chain 'b5' and resid 93 through 98 Processing helix chain 'b5' and resid 100 through 120 removed outlier: 3.974A pdb=" N GLUb5 120 " --> pdb=" O LYSb5 116 " (cutoff:3.500A) Processing helix chain 'b5' and resid 133 through 149 Processing helix chain 'b5' and resid 173 through 177 Processing helix chain 'b5' and resid 179 through 183 Processing helix chain 'b5' and resid 249 through 253 removed outlier: 3.856A pdb=" N SERb5 253 " --> pdb=" O VALb5 250 " (cutoff:3.500A) Processing helix chain 'b5' and resid 254 through 276 Processing helix chain 'b5' and resid 288 through 302 Processing helix chain 'b5' and resid 303 through 321 removed outlier: 4.415A pdb=" N LEUb5 307 " --> pdb=" O GLNb5 303 " (cutoff:3.500A) Processing helix chain 'b5' and resid 350 through 367 Processing helix chain 'b5' and resid 369 through 375 Processing helix chain 'b5' and resid 381 through 403 removed outlier: 4.198A pdb=" N GLUb5 391 " --> pdb=" O ALAb5 387 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SERb5 392 " --> pdb=" O SERb5 388 " (cutoff:3.500A) Processing helix chain 'b5' and resid 403 through 422 Processing helix chain 'b5' and resid 438 through 443 Processing helix chain 'b5' and resid 457 through 470 Processing helix chain 'b5' and resid 474 through 481 removed outlier: 3.647A pdb=" N GLUb5 478 " --> pdb=" O THRb5 474 " (cutoff:3.500A) Processing helix chain 'b5' and resid 485 through 503 Processing sheet with id=AA1, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 172 removed outlier: 4.025A pdb=" N PHE B 152 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 189 through 190 removed outlier: 3.666A pdb=" N GLY B 203 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.727A pdb=" N THR B 281 " --> pdb=" O ASN b 340 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN b 340 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 283 " --> pdb=" O SER b 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 340 removed outlier: 3.559A pdb=" N SER B 338 " --> pdb=" O GLUb5 283 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLUb5 283 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 340 " --> pdb=" O THRb5 281 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THRb5 281 " --> pdb=" O ASN B 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'b' and resid 87 through 90 Processing sheet with id=AA7, first strand: chain 'b' and resid 167 through 172 removed outlier: 3.872A pdb=" N PHE b 152 " --> pdb=" O VAL b 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 189 through 190 removed outlier: 3.609A pdb=" N GLY b 203 " --> pdb=" O GLN b 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 278 through 284 Processing sheet with id=AB1, first strand: chain 'B1' and resid 87 through 90 Processing sheet with id=AB2, first strand: chain 'B1' and resid 167 through 172 removed outlier: 4.086A pdb=" N PHEB1 152 " --> pdb=" O VALB1 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B1' and resid 189 through 190 removed outlier: 6.758A pdb=" N GLNB1 194 " --> pdb=" O LEUB1 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B1' and resid 279 through 284 removed outlier: 3.533A pdb=" N ALAB1 279 " --> pdb=" O GLNb1 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b1' and resid 87 through 90 Processing sheet with id=AB6, first strand: chain 'b1' and resid 167 through 172 removed outlier: 4.062A pdb=" N PHEb1 152 " --> pdb=" O VALb1 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b1' and resid 189 through 190 removed outlier: 3.636A pdb=" N GLYb1 203 " --> pdb=" O GLNb1 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b1' and resid 281 through 284 removed outlier: 3.750A pdb=" N THRb1 281 " --> pdb=" O ASNB2 340 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLUb1 283 " --> pdb=" O SERB2 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B2' and resid 87 through 90 Processing sheet with id=AC1, first strand: chain 'B2' and resid 167 through 172 removed outlier: 3.943A pdb=" N PHEB2 152 " --> pdb=" O VALB2 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B2' and resid 189 through 190 removed outlier: 3.644A pdb=" N GLYB2 203 " --> pdb=" O GLNB2 194 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B2' and resid 281 through 284 removed outlier: 3.611A pdb=" N GLUB2 283 " --> pdb=" O SERb2 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b2' and resid 87 through 90 Processing sheet with id=AC5, first strand: chain 'b2' and resid 167 through 172 removed outlier: 4.061A pdb=" N PHEb2 152 " --> pdb=" O VALb2 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b2' and resid 189 through 190 removed outlier: 6.710A pdb=" N GLNb2 194 " --> pdb=" O LEUb2 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b2' and resid 332 through 335 removed outlier: 8.382A pdb=" N LEUb2 333 " --> pdb=" O ALAb2 280 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILEb2 282 " --> pdb=" O LEUb2 333 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SERb2 284 " --> pdb=" O PROb2 335 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLUb2 283 " --> pdb=" O SERB3 338 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B3' and resid 87 through 90 Processing sheet with id=AC9, first strand: chain 'B3' and resid 167 through 172 removed outlier: 4.074A pdb=" N PHEB3 152 " --> pdb=" O VALB3 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 189 through 190 removed outlier: 3.632A pdb=" N GLYB3 203 " --> pdb=" O GLNB3 194 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B3' and resid 281 through 284 removed outlier: 3.645A pdb=" N THRB3 281 " --> pdb=" O ASNb3 340 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLUB3 283 " --> pdb=" O SERb3 338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b3' and resid 87 through 90 Processing sheet with id=AD4, first strand: chain 'b3' and resid 167 through 172 removed outlier: 3.950A pdb=" N PHEb3 152 " --> pdb=" O VALb3 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b3' and resid 189 through 190 removed outlier: 6.702A pdb=" N GLNb3 194 " --> pdb=" O LEUb3 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'b3' and resid 278 through 284 Processing sheet with id=AD7, first strand: chain 'B4' and resid 87 through 90 Processing sheet with id=AD8, first strand: chain 'B4' and resid 167 through 172 removed outlier: 4.043A pdb=" N PHEB4 152 " --> pdb=" O VALB4 172 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B4' and resid 189 through 190 removed outlier: 6.717A pdb=" N GLNB4 194 " --> pdb=" O LEUB4 202 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B4' and resid 281 through 284 removed outlier: 3.555A pdb=" N THRB4 281 " --> pdb=" O ASNb4 340 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLUB4 283 " --> pdb=" O SERb4 338 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b4' and resid 87 through 90 Processing sheet with id=AE3, first strand: chain 'b4' and resid 167 through 172 removed outlier: 3.915A pdb=" N PHEb4 152 " --> pdb=" O VALb4 172 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b4' and resid 189 through 190 removed outlier: 3.666A pdb=" N GLYb4 203 " --> pdb=" O GLNb4 194 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b4' and resid 281 through 284 removed outlier: 3.865A pdb=" N THRb4 281 " --> pdb=" O ASNB5 340 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASNB5 340 " --> pdb=" O THRb4 281 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLUb4 283 " --> pdb=" O SERB5 338 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B5' and resid 87 through 90 Processing sheet with id=AE7, first strand: chain 'B5' and resid 167 through 172 removed outlier: 3.896A pdb=" N PHEB5 152 " --> pdb=" O VALB5 172 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B5' and resid 189 through 190 removed outlier: 6.753A pdb=" N GLNB5 194 " --> pdb=" O LEUB5 202 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B5' and resid 332 through 335 removed outlier: 7.207A pdb=" N ILEB5 282 " --> pdb=" O LEUB5 333 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SERB5 284 " --> pdb=" O PROB5 335 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THRB5 281 " --> pdb=" O ASNb5 340 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASNb5 340 " --> pdb=" O THRB5 281 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLUB5 283 " --> pdb=" O SERb5 338 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'b5' and resid 87 through 90 Processing sheet with id=AF2, first strand: chain 'b5' and resid 167 through 172 removed outlier: 4.090A pdb=" N PHEb5 152 " --> pdb=" O VALb5 172 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b5' and resid 189 through 190 removed outlier: 6.704A pdb=" N GLNb5 194 " --> pdb=" O LEUb5 202 " (cutoff:3.500A) 2529 hydrogen bonds defined for protein. 7236 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: 16.97 Time building geometry restraints manager: 19.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13563 1.33 - 1.46: 9721 1.46 - 1.58: 21764 1.58 - 1.70: 0 1.70 - 1.83: 468 Bond restraints: 45516 Sorted by residual: bond pdb=" CA PRO B 40 " pdb=" C PRO B 40 " ideal model delta sigma weight residual 1.517 1.499 0.018 6.70e-03 2.23e+04 6.94e+00 bond pdb=" SD METb2 260 " pdb=" CE METb2 260 " ideal model delta sigma weight residual 1.791 1.738 0.053 2.50e-02 1.60e+03 4.46e+00 bond pdb=" CA PROB3 40 " pdb=" C PROB3 40 " ideal model delta sigma weight residual 1.517 1.503 0.014 6.70e-03 2.23e+04 4.25e+00 bond pdb=" CB PROb3 216 " pdb=" CG PROb3 216 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.56e+00 bond pdb=" CB LYSB2 459 " pdb=" CG LYSB2 459 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 ... (remaining 45511 not shown) Histogram of bond angle deviations from ideal: 96.77 - 104.22: 601 104.22 - 111.66: 19868 111.66 - 119.11: 15774 119.11 - 126.56: 24545 126.56 - 134.01: 784 Bond angle restraints: 61572 Sorted by residual: angle pdb=" CA METb2 260 " pdb=" CB METb2 260 " pdb=" CG METb2 260 " ideal model delta sigma weight residual 114.10 123.84 -9.74 2.00e+00 2.50e-01 2.37e+01 angle pdb=" CA LEU b 341 " pdb=" CB LEU b 341 " pdb=" CG LEU b 341 " ideal model delta sigma weight residual 116.30 132.51 -16.21 3.50e+00 8.16e-02 2.15e+01 angle pdb=" C LYSB4 259 " pdb=" N METB4 260 " pdb=" CA METB4 260 " ideal model delta sigma weight residual 121.14 113.35 7.79 1.75e+00 3.27e-01 1.98e+01 angle pdb=" CA METb4 260 " pdb=" CB METb4 260 " pdb=" CG METb4 260 " ideal model delta sigma weight residual 114.10 122.93 -8.83 2.00e+00 2.50e-01 1.95e+01 angle pdb=" CB METb2 260 " pdb=" CG METb2 260 " pdb=" SD METb2 260 " ideal model delta sigma weight residual 112.70 125.56 -12.86 3.00e+00 1.11e-01 1.84e+01 ... (remaining 61567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 23254 17.99 - 35.98: 3160 35.98 - 53.97: 631 53.97 - 71.97: 122 71.97 - 89.96: 25 Dihedral angle restraints: 27192 sinusoidal: 10752 harmonic: 16440 Sorted by residual: dihedral pdb=" CA ALAB2 321 " pdb=" C ALAB2 321 " pdb=" N PROB2 322 " pdb=" CA PROB2 322 " ideal model delta harmonic sigma weight residual 180.00 -145.19 -34.81 0 5.00e+00 4.00e-02 4.85e+01 dihedral pdb=" CB CYSb3 123 " pdb=" SG CYSb3 123 " pdb=" SG CYSb3 125 " pdb=" CB CYSb3 125 " ideal model delta sinusoidal sigma weight residual -86.00 -141.71 55.71 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYSb5 123 " pdb=" SG CYSb5 123 " pdb=" SG CYSb5 125 " pdb=" CB CYSb5 125 " ideal model delta sinusoidal sigma weight residual -86.00 -141.64 55.64 1 1.00e+01 1.00e-02 4.18e+01 ... (remaining 27189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5424 0.061 - 0.122: 912 0.122 - 0.183: 59 0.183 - 0.244: 12 0.244 - 0.306: 1 Chirality restraints: 6408 Sorted by residual: chirality pdb=" CG LEUb2 76 " pdb=" CB LEUb2 76 " pdb=" CD1 LEUb2 76 " pdb=" CD2 LEUb2 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CG LEUB1 76 " pdb=" CB LEUB1 76 " pdb=" CD1 LEUB1 76 " pdb=" CD2 LEUB1 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA METb1 260 " pdb=" N METb1 260 " pdb=" C METb1 260 " pdb=" CB METb1 260 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 6405 not shown) Planarity restraints: 8172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALAB2 321 " -0.086 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PROB2 322 " 0.233 5.00e-02 4.00e+02 pdb=" CA PROB2 322 " -0.077 5.00e-02 4.00e+02 pdb=" CD PROB2 322 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALAb5 321 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PROb5 322 " -0.204 5.00e-02 4.00e+02 pdb=" CA PROb5 322 " 0.063 5.00e-02 4.00e+02 pdb=" CD PROb5 322 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALAb1 321 " -0.078 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PROb1 322 " 0.204 5.00e-02 4.00e+02 pdb=" CA PROb1 322 " -0.063 5.00e-02 4.00e+02 pdb=" CD PROb1 322 " -0.063 5.00e-02 4.00e+02 ... (remaining 8169 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1414 2.67 - 3.23: 47794 3.23 - 3.78: 79023 3.78 - 4.34: 97514 4.34 - 4.90: 156129 Nonbonded interactions: 381874 Sorted by model distance: nonbonded pdb=" OG SERb5 369 " pdb=" OE1 GLNb5 372 " model vdw 2.109 2.440 nonbonded pdb=" OG SERB4 369 " pdb=" OE1 GLUB4 371 " model vdw 2.139 2.440 nonbonded pdb=" OD1 ASNb4 390 " pdb=" NH2 ARGb4 452 " model vdw 2.159 2.520 nonbonded pdb=" OG SER B 369 " pdb=" OE1 GLN B 372 " model vdw 2.162 2.440 nonbonded pdb=" OE1 GLNB1 356 " pdb=" OH TYRB1 370 " model vdw 2.162 2.440 ... (remaining 381869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'B1' selection = chain 'B2' selection = chain 'B3' selection = chain 'B4' selection = chain 'B5' selection = chain 'b' selection = chain 'b1' selection = chain 'b2' selection = chain 'b3' selection = chain 'b4' selection = chain 'b5' } 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 group one per residue 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.640 Check model and map are aligned: 0.300 Set scattering table: 0.450 Process input model: 116.380 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.005 0.080 45516 Z= 0.302 Angle : 0.809 16.212 61572 Z= 0.414 Chirality : 0.044 0.306 6408 Planarity : 0.006 0.135 8172 Dihedral : 16.394 89.957 16596 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.17 % Favored : 94.47 % Rotamer: Outliers : 0.67 % Allowed : 28.04 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 5664 helix: 1.25 (0.10), residues: 2772 sheet: -0.22 (0.22), residues: 552 loop : 0.01 (0.14), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPB3 393 HIS 0.005 0.001 HISB2 145 PHE 0.040 0.002 PHE B 396 TYR 0.028 0.001 TYRB5 395 ARG 0.012 0.001 ARGB1 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 837 time to evaluate : 6.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.9612 (ptp) cc_final: 0.9368 (pmm) REVERT: B 270 GLN cc_start: 0.9632 (mm-40) cc_final: 0.9398 (mm-40) REVERT: b 116 LYS cc_start: 0.9610 (ptpp) cc_final: 0.9402 (ptpp) REVERT: b 399 ARG cc_start: 0.9247 (tpp80) cc_final: 0.8745 (tpp80) REVERT: b 466 MET cc_start: 0.9574 (mmm) cc_final: 0.9373 (mtp) REVERT: B1 75 GLN cc_start: 0.8740 (tp40) cc_final: 0.8465 (tp-100) REVERT: B1 137 MET cc_start: 0.9475 (mmp) cc_final: 0.9263 (mmp) REVERT: B1 238 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8182 (tm-30) REVERT: B1 411 MET cc_start: 0.9608 (mtm) cc_final: 0.9188 (mtm) REVERT: b1 77 HIS cc_start: 0.9517 (m-70) cc_final: 0.9248 (m90) REVERT: b1 79 ASP cc_start: 0.8333 (m-30) cc_final: 0.8066 (m-30) REVERT: b2 411 MET cc_start: 0.9453 (mtm) cc_final: 0.9117 (mtm) REVERT: B3 87 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7850 (ptm160) REVERT: b3 144 MET cc_start: 0.9606 (ttp) cc_final: 0.9327 (ttm) REVERT: b3 277 MET cc_start: 0.9225 (mmm) cc_final: 0.8943 (mmm) REVERT: b4 270 GLN cc_start: 0.9655 (mm-40) cc_final: 0.9340 (mm-40) REVERT: B5 136 MET cc_start: 0.9379 (ptp) cc_final: 0.9135 (pmm) REVERT: B5 255 MET cc_start: 0.9265 (mtp) cc_final: 0.8757 (tpp) REVERT: B5 399 ARG cc_start: 0.9408 (tpp80) cc_final: 0.9084 (tpp80) REVERT: b5 277 MET cc_start: 0.9203 (tpt) cc_final: 0.8900 (tpp) REVERT: b5 397 MET cc_start: 0.9003 (mmm) cc_final: 0.8798 (mmp) REVERT: b5 411 MET cc_start: 0.9631 (mtm) cc_final: 0.9192 (mtm) outliers start: 30 outliers final: 15 residues processed: 853 average time/residue: 0.5860 time to fit residues: 808.2769 Evaluate side-chains 818 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 803 time to evaluate : 5.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 46 ASP Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain B3 residue 133 THR Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 84 SER Chi-restraints excluded: chain b3 residue 133 THR Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 137 MET Chi-restraints excluded: chain B5 residue 133 THR Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 256 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 476 optimal weight: 0.9980 chunk 427 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 442 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 268 optimal weight: 0.5980 chunk 329 optimal weight: 50.0000 chunk 512 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 194 GLN ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 372 GLN B1 194 GLN ** B1 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 75 GLN b1 356 GLN b1 372 GLN b1 376 ASN ** B2 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 194 GLN b2 372 GLN ** B3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 372 GLN b3 194 GLN B4 266 ASN B4 372 GLN b4 194 GLN ** B5 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 372 GLN b5 356 GLN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 45516 Z= 0.218 Angle : 0.623 13.566 61572 Z= 0.323 Chirality : 0.041 0.246 6408 Planarity : 0.006 0.117 8172 Dihedral : 4.649 51.900 6376 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.89 % Favored : 94.79 % Rotamer: Outliers : 2.59 % Allowed : 24.84 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.12), residues: 5664 helix: 1.34 (0.10), residues: 2928 sheet: -0.22 (0.22), residues: 552 loop : 0.08 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPB3 393 HIS 0.003 0.001 HIS B 332 PHE 0.037 0.001 PHEb4 396 TYR 0.019 0.001 TYRb4 395 ARG 0.007 0.000 ARGB2 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 860 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 GLN cc_start: 0.9607 (mm-40) cc_final: 0.9312 (mm-40) REVERT: B 399 ARG cc_start: 0.9056 (tpp80) cc_final: 0.8759 (tpp80) REVERT: B 458 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9339 (mm) REVERT: B 482 ARG cc_start: 0.9471 (mmm-85) cc_final: 0.9248 (mtp85) REVERT: b 78 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8840 (mm-40) REVERT: b 266 ASN cc_start: 0.9522 (m-40) cc_final: 0.9283 (m110) REVERT: b 380 MET cc_start: 0.8349 (tpt) cc_final: 0.8098 (tpt) REVERT: b 399 ARG cc_start: 0.9227 (tpp80) cc_final: 0.8512 (tpp80) REVERT: b 466 MET cc_start: 0.9570 (mmm) cc_final: 0.9351 (mtp) REVERT: b 477 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8681 (mtmt) REVERT: B1 75 GLN cc_start: 0.8941 (tp40) cc_final: 0.8047 (tp-100) REVERT: B1 116 LYS cc_start: 0.9640 (ttpp) cc_final: 0.9420 (pttm) REVERT: B1 238 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B1 360 ARG cc_start: 0.9588 (OUTLIER) cc_final: 0.8968 (ttm110) REVERT: B1 397 MET cc_start: 0.8879 (mmm) cc_final: 0.8625 (mmm) REVERT: b1 43 GLU cc_start: 0.8751 (pm20) cc_final: 0.8542 (pm20) REVERT: b1 75 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8060 (tp-100) REVERT: b1 255 MET cc_start: 0.9175 (mtp) cc_final: 0.8848 (mpp) REVERT: b1 399 ARG cc_start: 0.9165 (tpp80) cc_final: 0.8802 (tpp80) REVERT: B2 43 GLU cc_start: 0.8795 (pm20) cc_final: 0.8588 (pm20) REVERT: B2 137 MET cc_start: 0.9542 (mmt) cc_final: 0.9125 (mpp) REVERT: B2 277 MET cc_start: 0.9217 (tpt) cc_final: 0.8915 (tpp) REVERT: b2 137 MET cc_start: 0.9577 (tpp) cc_final: 0.9206 (mmp) REVERT: b2 360 ARG cc_start: 0.9602 (OUTLIER) cc_final: 0.8886 (ttm110) REVERT: B3 69 TYR cc_start: 0.9455 (m-80) cc_final: 0.9042 (m-80) REVERT: B3 87 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7726 (ptm-80) REVERT: B3 460 GLU cc_start: 0.8529 (mp0) cc_final: 0.8320 (mp0) REVERT: b3 144 MET cc_start: 0.9604 (ttp) cc_final: 0.9277 (ttm) REVERT: b3 266 ASN cc_start: 0.9333 (m-40) cc_final: 0.9087 (m110) REVERT: b3 277 MET cc_start: 0.9089 (mmm) cc_final: 0.8791 (mmm) REVERT: b3 346 ASP cc_start: 0.8837 (t0) cc_final: 0.8398 (t0) REVERT: B4 75 GLN cc_start: 0.8772 (tp40) cc_final: 0.8373 (tp-100) REVERT: B4 137 MET cc_start: 0.9386 (mmp) cc_final: 0.9186 (mmt) REVERT: B4 252 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8733 (t80) REVERT: B4 277 MET cc_start: 0.9225 (mmm) cc_final: 0.8898 (tpt) REVERT: B4 278 TYR cc_start: 0.8037 (t80) cc_final: 0.7642 (t80) REVERT: B4 360 ARG cc_start: 0.9521 (OUTLIER) cc_final: 0.9012 (ttm110) REVERT: b4 69 TYR cc_start: 0.9457 (m-80) cc_final: 0.9125 (m-80) REVERT: b4 75 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8202 (tp-100) REVERT: b4 116 LYS cc_start: 0.9475 (pptt) cc_final: 0.9263 (pptt) REVERT: b4 277 MET cc_start: 0.9284 (mmm) cc_final: 0.8829 (tpt) REVERT: b4 346 ASP cc_start: 0.8824 (t0) cc_final: 0.8373 (t0) REVERT: b4 459 LYS cc_start: 0.9379 (mmmm) cc_final: 0.9168 (mmmm) REVERT: B5 78 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8688 (mm-40) REVERT: B5 255 MET cc_start: 0.9204 (mtp) cc_final: 0.8660 (tpp) REVERT: B5 277 MET cc_start: 0.9210 (tpt) cc_final: 0.8994 (mmm) REVERT: B5 360 ARG cc_start: 0.9510 (OUTLIER) cc_final: 0.8753 (ttm110) REVERT: B5 399 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8749 (tpp80) REVERT: b5 75 GLN cc_start: 0.8673 (tp40) cc_final: 0.8274 (tp-100) outliers start: 116 outliers final: 65 residues processed: 942 average time/residue: 0.5929 time to fit residues: 910.5699 Evaluate side-chains 888 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 815 time to evaluate : 5.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 78 GLN Chi-restraints excluded: chain b residue 182 ASN Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 282 ILE Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 254 VAL Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 484 ASP Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 356 GLN Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain b1 residue 484 ASP Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 181 ASN Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 252 TYR Chi-restraints excluded: chain B4 residue 256 GLU Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain b4 residue 323 VAL Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 391 GLU Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 455 ILE Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 256 GLU Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 353 VAL Chi-restraints excluded: chain b5 residue 384 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 284 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 426 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 513 optimal weight: 10.0000 chunk 554 optimal weight: 9.9990 chunk 456 optimal weight: 2.9990 chunk 508 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 411 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN b 194 GLN ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 372 GLN B1 34 GLN B1 372 GLN B1 493 GLN b1 75 GLN b1 194 GLN b1 372 GLN b1 376 ASN b2 372 GLN B3 340 ASN B3 372 GLN b3 194 GLN B4 372 GLN B5 194 GLN ** B5 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 194 GLN ** b5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 356 GLN b5 493 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 45516 Z= 0.340 Angle : 0.646 11.157 61572 Z= 0.342 Chirality : 0.041 0.246 6408 Planarity : 0.006 0.118 8172 Dihedral : 4.497 48.313 6354 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.31 % Favored : 94.39 % Rotamer: Outliers : 4.31 % Allowed : 24.58 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.11), residues: 5664 helix: 1.52 (0.10), residues: 2856 sheet: -0.31 (0.22), residues: 552 loop : -0.00 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPB3 393 HIS 0.005 0.001 HISB4 80 PHE 0.031 0.001 PHEb4 396 TYR 0.022 0.001 TYR b 486 ARG 0.008 0.000 ARGB2 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 817 time to evaluate : 5.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8643 (tp40) cc_final: 0.8143 (tp40) REVERT: B 270 GLN cc_start: 0.9647 (mm-40) cc_final: 0.9305 (mm-40) REVERT: B 399 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8902 (tpp80) REVERT: B 458 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9367 (mm) REVERT: B 482 ARG cc_start: 0.9544 (mmm-85) cc_final: 0.9278 (mtp85) REVERT: b 136 MET cc_start: 0.9095 (pmm) cc_final: 0.8737 (pmm) REVERT: b 144 MET cc_start: 0.9622 (ttp) cc_final: 0.9266 (ttm) REVERT: b 266 ASN cc_start: 0.9565 (m-40) cc_final: 0.9297 (m110) REVERT: b 277 MET cc_start: 0.9355 (tpt) cc_final: 0.9146 (tpt) REVERT: b 399 ARG cc_start: 0.9221 (tpp80) cc_final: 0.8710 (tpp80) REVERT: b 477 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8590 (mtmt) REVERT: B1 69 TYR cc_start: 0.9562 (m-80) cc_final: 0.9201 (m-80) REVERT: B1 75 GLN cc_start: 0.9077 (tp40) cc_final: 0.8305 (tp-100) REVERT: B1 238 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B1 268 GLN cc_start: 0.9492 (tp40) cc_final: 0.9192 (tp40) REVERT: B1 355 GLU cc_start: 0.8899 (pp20) cc_final: 0.8534 (pp20) REVERT: B1 356 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8508 (mm-40) REVERT: B1 360 ARG cc_start: 0.9584 (OUTLIER) cc_final: 0.8999 (ttm110) REVERT: B1 397 MET cc_start: 0.8950 (mmm) cc_final: 0.8688 (mmm) REVERT: b1 75 GLN cc_start: 0.8801 (tp40) cc_final: 0.8309 (tp40) REVERT: b1 79 ASP cc_start: 0.8566 (m-30) cc_final: 0.8148 (m-30) REVERT: b1 147 PHE cc_start: 0.9383 (p90) cc_final: 0.9104 (p90) REVERT: b1 255 MET cc_start: 0.9137 (mtp) cc_final: 0.8730 (mpp) REVERT: b1 265 GLN cc_start: 0.9482 (mm-40) cc_final: 0.9277 (mm-40) REVERT: b1 399 ARG cc_start: 0.9248 (tpp80) cc_final: 0.8912 (tpp80) REVERT: B2 136 MET cc_start: 0.9430 (ptp) cc_final: 0.9110 (ptp) REVERT: B2 137 MET cc_start: 0.9501 (mmt) cc_final: 0.8810 (mpp) REVERT: B2 144 MET cc_start: 0.9619 (ttp) cc_final: 0.9276 (ttm) REVERT: B2 277 MET cc_start: 0.9198 (tpt) cc_final: 0.8964 (tpp) REVERT: B2 334 MET cc_start: 0.8963 (mmm) cc_final: 0.8726 (mmm) REVERT: B2 458 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9315 (mm) REVERT: b2 75 GLN cc_start: 0.8913 (tp40) cc_final: 0.8688 (tp-100) REVERT: b2 137 MET cc_start: 0.9525 (tpp) cc_final: 0.9081 (tpp) REVERT: b2 260 MET cc_start: 0.9224 (mtm) cc_final: 0.8869 (mtm) REVERT: b2 360 ARG cc_start: 0.9589 (OUTLIER) cc_final: 0.8878 (ttm110) REVERT: b2 372 GLN cc_start: 0.9461 (pt0) cc_final: 0.9110 (pt0) REVERT: b2 397 MET cc_start: 0.8979 (mmm) cc_final: 0.8753 (mmm) REVERT: B3 372 GLN cc_start: 0.9357 (pt0) cc_final: 0.9091 (pp30) REVERT: B3 460 GLU cc_start: 0.8527 (mp0) cc_final: 0.8303 (mp0) REVERT: B3 482 ARG cc_start: 0.9480 (ttm110) cc_final: 0.9150 (mtp180) REVERT: b3 78 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8564 (mm-40) REVERT: b3 144 MET cc_start: 0.9594 (ttp) cc_final: 0.9264 (ttm) REVERT: b3 266 ASN cc_start: 0.9326 (m-40) cc_final: 0.9050 (m110) REVERT: B4 69 TYR cc_start: 0.9573 (m-80) cc_final: 0.9249 (m-80) REVERT: B4 75 GLN cc_start: 0.8839 (tp40) cc_final: 0.8358 (tp-100) REVERT: B4 277 MET cc_start: 0.9234 (mmm) cc_final: 0.9004 (tpp) REVERT: B4 325 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8745 (pp) REVERT: B4 360 ARG cc_start: 0.9500 (OUTLIER) cc_final: 0.8963 (ttm110) REVERT: B4 458 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.8715 (mm) REVERT: b4 69 TYR cc_start: 0.9541 (m-80) cc_final: 0.9339 (m-80) REVERT: b4 75 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8139 (tp-100) REVERT: b4 137 MET cc_start: 0.9419 (ttm) cc_final: 0.9208 (mtt) REVERT: b4 260 MET cc_start: 0.9130 (mtm) cc_final: 0.8778 (mtm) REVERT: b4 270 GLN cc_start: 0.9650 (mm-40) cc_final: 0.9265 (mm-40) REVERT: b4 459 LYS cc_start: 0.9380 (mmmm) cc_final: 0.9118 (mmmm) REVERT: b4 481 LYS cc_start: 0.9226 (mtmm) cc_final: 0.8983 (pttm) REVERT: B5 78 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8679 (mm-40) REVERT: B5 171 MET cc_start: 0.8554 (mmm) cc_final: 0.8303 (mtm) REVERT: B5 258 MET cc_start: 0.9394 (mmm) cc_final: 0.9017 (mmm) REVERT: B5 339 LEU cc_start: 0.9753 (tt) cc_final: 0.9458 (mm) REVERT: B5 360 ARG cc_start: 0.9523 (OUTLIER) cc_final: 0.8774 (ttm110) REVERT: B5 399 ARG cc_start: 0.9408 (tpp80) cc_final: 0.8725 (tpp80) REVERT: B5 453 MET cc_start: 0.7659 (ppp) cc_final: 0.7311 (ppp) REVERT: B5 484 ASP cc_start: 0.9016 (m-30) cc_final: 0.8760 (m-30) REVERT: b5 75 GLN cc_start: 0.8864 (tp40) cc_final: 0.8513 (tp-100) REVERT: b5 137 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.9149 (mmt) REVERT: b5 252 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.8767 (t80) REVERT: b5 334 MET cc_start: 0.9441 (mmm) cc_final: 0.8978 (mmm) REVERT: b5 371 GLU cc_start: 0.8505 (mp0) cc_final: 0.8296 (mp0) outliers start: 193 outliers final: 127 residues processed: 955 average time/residue: 0.5812 time to fit residues: 902.0908 Evaluate side-chains 919 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 780 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 181 ASN Chi-restraints excluded: chain b residue 182 ASN Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 282 ILE Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 384 THR Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 455 ILE Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 250 VAL Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 448 ILE Chi-restraints excluded: chain B1 residue 484 ASP Chi-restraints excluded: chain b1 residue 74 ILE Chi-restraints excluded: chain b1 residue 182 ASN Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 250 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 355 GLU Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 391 GLU Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain b1 residue 484 ASP Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 181 ASN Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 458 LEU Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain b2 residue 45 VAL Chi-restraints excluded: chain b2 residue 46 ASP Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 128 VAL Chi-restraints excluded: chain b2 residue 182 ASN Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 181 ASN Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 250 VAL Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 343 THR Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain b3 residue 63 LEU Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 181 ASN Chi-restraints excluded: chain b3 residue 182 ASN Chi-restraints excluded: chain b3 residue 323 VAL Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 256 GLU Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 182 ASN Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 254 VAL Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 455 ILE Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 181 ASN Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 137 MET Chi-restraints excluded: chain b5 residue 182 ASN Chi-restraints excluded: chain b5 residue 215 MET Chi-restraints excluded: chain b5 residue 240 VAL Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 256 GLU Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 448 ILE Chi-restraints excluded: chain b5 residue 455 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 506 optimal weight: 0.9990 chunk 385 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 344 optimal weight: 7.9990 chunk 514 optimal weight: 5.9990 chunk 545 optimal weight: 2.9990 chunk 269 optimal weight: 10.0000 chunk 488 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 372 GLN b1 356 GLN b1 372 GLN B3 268 GLN B4 194 GLN B4 372 GLN b4 80 HIS ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 45516 Z= 0.306 Angle : 0.641 12.897 61572 Z= 0.335 Chirality : 0.041 0.246 6408 Planarity : 0.005 0.118 8172 Dihedral : 4.494 45.528 6354 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.33 % Favored : 94.39 % Rotamer: Outliers : 4.94 % Allowed : 24.44 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.11), residues: 5664 helix: 1.55 (0.10), residues: 2856 sheet: -0.40 (0.22), residues: 552 loop : -0.06 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPB3 393 HIS 0.004 0.001 HISB4 80 PHE 0.023 0.001 PHEb4 396 TYR 0.021 0.001 TYRB3 395 ARG 0.008 0.000 ARGB2 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 815 time to evaluate : 5.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8793 (tp40) cc_final: 0.8174 (tp40) REVERT: B 270 GLN cc_start: 0.9642 (mm-40) cc_final: 0.9295 (mm-40) REVERT: B 399 ARG cc_start: 0.9108 (tpp80) cc_final: 0.8772 (tpp80) REVERT: B 458 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9373 (mm) REVERT: B 477 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8703 (mtmt) REVERT: B 482 ARG cc_start: 0.9546 (mmm-85) cc_final: 0.9275 (mtp85) REVERT: b 78 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8821 (mm-40) REVERT: b 136 MET cc_start: 0.9059 (pmm) cc_final: 0.8775 (pmm) REVERT: b 144 MET cc_start: 0.9605 (ttp) cc_final: 0.9236 (ttm) REVERT: b 266 ASN cc_start: 0.9557 (m-40) cc_final: 0.9286 (m110) REVERT: b 399 ARG cc_start: 0.9274 (tpp80) cc_final: 0.8859 (tpp80) REVERT: B1 69 TYR cc_start: 0.9574 (m-80) cc_final: 0.9342 (m-80) REVERT: B1 75 GLN cc_start: 0.9058 (tp40) cc_final: 0.8194 (tp-100) REVERT: B1 116 LYS cc_start: 0.9661 (ttpp) cc_final: 0.9458 (pttm) REVERT: B1 238 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8187 (tm-30) REVERT: B1 268 GLN cc_start: 0.9469 (tp40) cc_final: 0.9183 (tp40) REVERT: B1 334 MET cc_start: 0.9045 (mmm) cc_final: 0.8837 (mmm) REVERT: B1 355 GLU cc_start: 0.8944 (pp20) cc_final: 0.8532 (pp20) REVERT: B1 356 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8473 (mm-40) REVERT: B1 360 ARG cc_start: 0.9536 (OUTLIER) cc_final: 0.8921 (ttm110) REVERT: B1 397 MET cc_start: 0.8980 (mmm) cc_final: 0.8710 (mmm) REVERT: b1 75 GLN cc_start: 0.8788 (tp40) cc_final: 0.8186 (tp40) REVERT: b1 79 ASP cc_start: 0.8568 (m-30) cc_final: 0.8071 (m-30) REVERT: b1 147 PHE cc_start: 0.9353 (p90) cc_final: 0.9120 (p90) REVERT: b1 241 GLU cc_start: 0.7527 (pm20) cc_final: 0.7320 (pm20) REVERT: b1 255 MET cc_start: 0.9138 (mtp) cc_final: 0.8734 (mpp) REVERT: b1 277 MET cc_start: 0.9007 (tpp) cc_final: 0.8584 (tpp) REVERT: b1 399 ARG cc_start: 0.9178 (tpp80) cc_final: 0.8654 (tpp80) REVERT: B2 136 MET cc_start: 0.9378 (ptp) cc_final: 0.9138 (ptp) REVERT: B2 137 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.9226 (tpp) REVERT: B2 144 MET cc_start: 0.9597 (ttp) cc_final: 0.9243 (ttm) REVERT: B2 265 GLN cc_start: 0.9493 (mm110) cc_final: 0.9272 (mm-40) REVERT: B2 334 MET cc_start: 0.9106 (mmm) cc_final: 0.8897 (mmm) REVERT: B2 380 MET cc_start: 0.8629 (tpt) cc_final: 0.8311 (tpp) REVERT: B2 458 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9337 (mm) REVERT: b2 75 GLN cc_start: 0.8896 (tp40) cc_final: 0.8631 (tp-100) REVERT: b2 137 MET cc_start: 0.9462 (tpp) cc_final: 0.9017 (tpp) REVERT: b2 266 ASN cc_start: 0.9341 (m110) cc_final: 0.8927 (m110) REVERT: b2 397 MET cc_start: 0.9026 (mmm) cc_final: 0.8780 (mmm) REVERT: B3 43 GLU cc_start: 0.9030 (pm20) cc_final: 0.8187 (pt0) REVERT: B3 144 MET cc_start: 0.9563 (ttm) cc_final: 0.9362 (ttt) REVERT: B3 277 MET cc_start: 0.9307 (mmm) cc_final: 0.8680 (tpt) REVERT: B3 439 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7953 (mmt90) REVERT: B3 460 GLU cc_start: 0.8651 (mp0) cc_final: 0.8413 (mp0) REVERT: B3 482 ARG cc_start: 0.9442 (ttm110) cc_final: 0.9122 (mtp180) REVERT: b3 78 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8744 (mm-40) REVERT: b3 137 MET cc_start: 0.9657 (tpp) cc_final: 0.9303 (mmm) REVERT: b3 144 MET cc_start: 0.9599 (ttp) cc_final: 0.9254 (ttm) REVERT: b3 266 ASN cc_start: 0.9356 (m-40) cc_final: 0.9058 (m110) REVERT: b3 377 TYR cc_start: 0.9204 (m-80) cc_final: 0.8904 (m-80) REVERT: b3 380 MET cc_start: 0.8212 (mmm) cc_final: 0.7903 (tpp) REVERT: B4 75 GLN cc_start: 0.8913 (tp40) cc_final: 0.8325 (tp-100) REVERT: B4 137 MET cc_start: 0.9600 (tpp) cc_final: 0.9311 (mmp) REVERT: B4 325 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8757 (pp) REVERT: B4 360 ARG cc_start: 0.9496 (OUTLIER) cc_final: 0.8982 (ttm110) REVERT: B4 458 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.8743 (mm) REVERT: B4 487 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8669 (mp10) REVERT: b4 75 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8594 (tp40) REVERT: b4 270 GLN cc_start: 0.9652 (mm-40) cc_final: 0.9300 (mm-40) REVERT: b4 371 GLU cc_start: 0.8949 (pm20) cc_final: 0.8662 (pm20) REVERT: b4 377 TYR cc_start: 0.8968 (m-80) cc_final: 0.8707 (m-80) REVERT: b4 380 MET cc_start: 0.8242 (tpp) cc_final: 0.8030 (mmm) REVERT: b4 399 ARG cc_start: 0.9251 (tpp80) cc_final: 0.8916 (tpp80) REVERT: b4 459 LYS cc_start: 0.9302 (mmmm) cc_final: 0.9093 (mmmm) REVERT: b4 479 CYS cc_start: 0.9265 (m) cc_final: 0.8578 (p) REVERT: b4 481 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9093 (pttm) REVERT: B5 78 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8541 (mm-40) REVERT: B5 171 MET cc_start: 0.8544 (mmm) cc_final: 0.8296 (mtm) REVERT: B5 255 MET cc_start: 0.9292 (mtp) cc_final: 0.8783 (tpp) REVERT: B5 258 MET cc_start: 0.9365 (mmm) cc_final: 0.8992 (mmm) REVERT: B5 339 LEU cc_start: 0.9726 (tt) cc_final: 0.9412 (mm) REVERT: B5 360 ARG cc_start: 0.9520 (OUTLIER) cc_final: 0.8776 (ttm110) REVERT: B5 399 ARG cc_start: 0.9403 (tpp80) cc_final: 0.8721 (tpp80) REVERT: B5 453 MET cc_start: 0.7645 (ppp) cc_final: 0.7175 (ppp) REVERT: B5 484 ASP cc_start: 0.9030 (m-30) cc_final: 0.8754 (m-30) REVERT: b5 69 TYR cc_start: 0.9586 (m-80) cc_final: 0.9369 (m-80) REVERT: b5 75 GLN cc_start: 0.9009 (tp40) cc_final: 0.8660 (tp-100) REVERT: b5 136 MET cc_start: 0.9068 (pmm) cc_final: 0.8741 (pmm) REVERT: b5 244 GLN cc_start: 0.8114 (tt0) cc_final: 0.7892 (tt0) REVERT: b5 252 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8764 (t80) REVERT: b5 255 MET cc_start: 0.9165 (pmm) cc_final: 0.8826 (pmm) REVERT: b5 334 MET cc_start: 0.9518 (mmm) cc_final: 0.9008 (mmm) REVERT: b5 371 GLU cc_start: 0.8508 (mp0) cc_final: 0.8150 (mp0) outliers start: 221 outliers final: 153 residues processed: 982 average time/residue: 0.5784 time to fit residues: 916.5299 Evaluate side-chains 949 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 782 time to evaluate : 5.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 77 HIS Chi-restraints excluded: chain b residue 78 GLN Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 181 ASN Chi-restraints excluded: chain b residue 182 ASN Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 282 ILE Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 372 GLN Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 455 ILE Chi-restraints excluded: chain b residue 458 LEU Chi-restraints excluded: chain b residue 489 ILE Chi-restraints excluded: chain B1 residue 34 GLN Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 181 ASN Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 448 ILE Chi-restraints excluded: chain B1 residue 484 ASP Chi-restraints excluded: chain b1 residue 74 ILE Chi-restraints excluded: chain b1 residue 93 SER Chi-restraints excluded: chain b1 residue 182 ASN Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 282 ILE Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 355 GLU Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 368 VAL Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 391 GLU Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain b1 residue 484 ASP Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 137 MET Chi-restraints excluded: chain B2 residue 181 ASN Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 458 LEU Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain b2 residue 45 VAL Chi-restraints excluded: chain b2 residue 46 ASP Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 181 ASN Chi-restraints excluded: chain b2 residue 182 ASN Chi-restraints excluded: chain b2 residue 250 VAL Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 181 ASN Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 250 VAL Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 343 THR Chi-restraints excluded: chain B3 residue 381 SER Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain B3 residue 439 ARG Chi-restraints excluded: chain B3 residue 484 ASP Chi-restraints excluded: chain b3 residue 63 LEU Chi-restraints excluded: chain b3 residue 77 HIS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 181 ASN Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain b3 residue 472 LEU Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 126 ILE Chi-restraints excluded: chain B4 residue 181 ASN Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 256 GLU Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 182 ASN Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 241 GLU Chi-restraints excluded: chain b4 residue 353 VAL Chi-restraints excluded: chain b4 residue 355 GLU Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 476 GLU Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 181 ASN Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 455 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 181 ASN Chi-restraints excluded: chain b5 residue 182 ASN Chi-restraints excluded: chain b5 residue 215 MET Chi-restraints excluded: chain b5 residue 240 VAL Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 256 GLU Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 454 optimal weight: 0.4980 chunk 309 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 405 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 465 optimal weight: 1.9990 chunk 376 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 278 optimal weight: 2.9990 chunk 489 optimal weight: 0.3980 chunk 137 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 372 GLN b1 372 GLN B3 266 ASN B3 372 GLN b3 194 GLN B4 372 GLN b4 80 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45516 Z= 0.207 Angle : 0.630 15.326 61572 Z= 0.321 Chirality : 0.040 0.185 6408 Planarity : 0.005 0.117 8172 Dihedral : 4.394 44.095 6353 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.03 % Favored : 94.69 % Rotamer: Outliers : 3.84 % Allowed : 25.80 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.11), residues: 5664 helix: 1.60 (0.10), residues: 2856 sheet: -0.41 (0.22), residues: 552 loop : -0.02 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPB3 393 HIS 0.003 0.001 HIS B 332 PHE 0.027 0.001 PHE B 147 TYR 0.021 0.001 TYR b 486 ARG 0.007 0.000 ARGB5 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 861 time to evaluate : 5.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8834 (tp40) cc_final: 0.8178 (tp40) REVERT: B 270 GLN cc_start: 0.9628 (mm-40) cc_final: 0.9280 (mm-40) REVERT: B 399 ARG cc_start: 0.9128 (tpp80) cc_final: 0.8740 (tpp80) REVERT: B 458 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9410 (mm) REVERT: B 482 ARG cc_start: 0.9502 (mmm-85) cc_final: 0.9225 (mtp85) REVERT: b 78 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8685 (mm-40) REVERT: b 82 VAL cc_start: 0.9358 (OUTLIER) cc_final: 0.9157 (p) REVERT: b 136 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8610 (pmm) REVERT: b 144 MET cc_start: 0.9605 (ttp) cc_final: 0.9356 (ttt) REVERT: b 266 ASN cc_start: 0.9552 (m-40) cc_final: 0.9276 (m110) REVERT: b 277 MET cc_start: 0.9317 (tpt) cc_final: 0.9068 (tpt) REVERT: b 397 MET cc_start: 0.9137 (mmm) cc_final: 0.8929 (mmm) REVERT: b 399 ARG cc_start: 0.9312 (tpp80) cc_final: 0.8890 (tpp80) REVERT: b 486 TYR cc_start: 0.9117 (p90) cc_final: 0.8863 (p90) REVERT: B1 69 TYR cc_start: 0.9525 (m-80) cc_final: 0.9169 (m-80) REVERT: B1 75 GLN cc_start: 0.8988 (tp40) cc_final: 0.8046 (tp-100) REVERT: B1 116 LYS cc_start: 0.9629 (ttpp) cc_final: 0.9420 (pttm) REVERT: B1 238 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8165 (tm-30) REVERT: B1 268 GLN cc_start: 0.9439 (tp40) cc_final: 0.9204 (tp40) REVERT: B1 355 GLU cc_start: 0.8935 (pp20) cc_final: 0.8559 (pp20) REVERT: B1 356 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8426 (mm-40) REVERT: B1 360 ARG cc_start: 0.9517 (OUTLIER) cc_final: 0.8915 (ttm110) REVERT: B1 397 MET cc_start: 0.9019 (mmm) cc_final: 0.8799 (mmm) REVERT: b1 43 GLU cc_start: 0.8921 (pm20) cc_final: 0.8711 (pm20) REVERT: b1 75 GLN cc_start: 0.8801 (tp40) cc_final: 0.8188 (tp40) REVERT: b1 79 ASP cc_start: 0.8541 (m-30) cc_final: 0.7989 (m-30) REVERT: b1 255 MET cc_start: 0.9130 (mtp) cc_final: 0.8715 (mpp) REVERT: b1 399 ARG cc_start: 0.9222 (tpp80) cc_final: 0.8719 (tpp80) REVERT: B2 116 LYS cc_start: 0.9587 (ptpp) cc_final: 0.9346 (pttm) REVERT: B2 136 MET cc_start: 0.9361 (ptp) cc_final: 0.9122 (ptp) REVERT: B2 137 MET cc_start: 0.9530 (mmt) cc_final: 0.9217 (tpp) REVERT: B2 144 MET cc_start: 0.9611 (ttp) cc_final: 0.9235 (ttm) REVERT: B2 265 GLN cc_start: 0.9470 (mm110) cc_final: 0.9233 (mm-40) REVERT: B2 334 MET cc_start: 0.9118 (mmm) cc_final: 0.8902 (mmm) REVERT: B2 380 MET cc_start: 0.8610 (tpt) cc_final: 0.8245 (tpp) REVERT: B2 458 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9300 (mm) REVERT: b2 75 GLN cc_start: 0.8896 (tp40) cc_final: 0.8623 (tp-100) REVERT: b2 137 MET cc_start: 0.9406 (tpp) cc_final: 0.8833 (tpp) REVERT: b2 171 MET cc_start: 0.8104 (mmm) cc_final: 0.6943 (mtt) REVERT: b2 266 ASN cc_start: 0.9402 (m110) cc_final: 0.8961 (m110) REVERT: B3 116 LYS cc_start: 0.9614 (ptpp) cc_final: 0.9348 (pttm) REVERT: B3 266 ASN cc_start: 0.9422 (m-40) cc_final: 0.9182 (m110) REVERT: B3 277 MET cc_start: 0.9224 (mmm) cc_final: 0.8614 (tpt) REVERT: B3 334 MET cc_start: 0.8942 (tmm) cc_final: 0.8678 (ppp) REVERT: B3 372 GLN cc_start: 0.9344 (pt0) cc_final: 0.9075 (pp30) REVERT: B3 397 MET cc_start: 0.9057 (mmp) cc_final: 0.8854 (mmm) REVERT: B3 460 GLU cc_start: 0.8770 (mp0) cc_final: 0.8551 (mp0) REVERT: b3 78 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8749 (mm-40) REVERT: b3 137 MET cc_start: 0.9586 (tpp) cc_final: 0.9292 (mmp) REVERT: b3 144 MET cc_start: 0.9587 (ttp) cc_final: 0.9248 (ttm) REVERT: b3 266 ASN cc_start: 0.9355 (m-40) cc_final: 0.9050 (m110) REVERT: b3 275 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8773 (mtpt) REVERT: b3 377 TYR cc_start: 0.9194 (m-80) cc_final: 0.8951 (m-80) REVERT: B4 43 GLU cc_start: 0.8811 (pm20) cc_final: 0.8577 (pm20) REVERT: B4 75 GLN cc_start: 0.8868 (tp40) cc_final: 0.8154 (tp-100) REVERT: B4 137 MET cc_start: 0.9571 (tpp) cc_final: 0.9065 (tpp) REVERT: B4 258 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.9176 (mmm) REVERT: B4 325 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8760 (pp) REVERT: B4 360 ARG cc_start: 0.9472 (OUTLIER) cc_final: 0.8946 (ttm110) REVERT: b4 43 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: b4 75 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8519 (tp40) REVERT: b4 144 MET cc_start: 0.9587 (ttm) cc_final: 0.9355 (ttt) REVERT: b4 171 MET cc_start: 0.8671 (mmm) cc_final: 0.8355 (mmm) REVERT: b4 371 GLU cc_start: 0.8915 (pm20) cc_final: 0.8638 (pm20) REVERT: b4 377 TYR cc_start: 0.8931 (m-80) cc_final: 0.8661 (m-80) REVERT: b4 399 ARG cc_start: 0.9274 (tpp80) cc_final: 0.8938 (tpp80) REVERT: b4 458 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9253 (mm) REVERT: b4 479 CYS cc_start: 0.9294 (m) cc_final: 0.8598 (p) REVERT: b4 481 LYS cc_start: 0.9339 (mtmm) cc_final: 0.9078 (pttm) REVERT: B5 78 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8559 (mm-40) REVERT: B5 91 ARG cc_start: 0.9210 (mmm160) cc_final: 0.8944 (mmm160) REVERT: B5 144 MET cc_start: 0.9575 (ttp) cc_final: 0.9202 (ttm) REVERT: B5 171 MET cc_start: 0.8500 (mmm) cc_final: 0.8230 (mtm) REVERT: B5 255 MET cc_start: 0.9240 (mtp) cc_final: 0.8702 (tpp) REVERT: B5 258 MET cc_start: 0.9355 (mmm) cc_final: 0.8987 (mmm) REVERT: B5 360 ARG cc_start: 0.9509 (OUTLIER) cc_final: 0.8734 (ttm110) REVERT: B5 399 ARG cc_start: 0.9401 (tpp80) cc_final: 0.8806 (tpp80) REVERT: B5 484 ASP cc_start: 0.9031 (m-30) cc_final: 0.8758 (m-30) REVERT: b5 69 TYR cc_start: 0.9573 (m-80) cc_final: 0.9358 (m-80) REVERT: b5 75 GLN cc_start: 0.9028 (tp40) cc_final: 0.8603 (tp-100) REVERT: b5 136 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8662 (pmm) REVERT: b5 137 MET cc_start: 0.9473 (mmt) cc_final: 0.9266 (mmp) REVERT: b5 277 MET cc_start: 0.9112 (tpp) cc_final: 0.8832 (tpt) outliers start: 172 outliers final: 117 residues processed: 979 average time/residue: 0.5748 time to fit residues: 911.8932 Evaluate side-chains 936 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 803 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 77 HIS Chi-restraints excluded: chain b residue 78 GLN Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 136 MET Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 455 ILE Chi-restraints excluded: chain b residue 458 LEU Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 484 ASP Chi-restraints excluded: chain b1 residue 93 SER Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 391 GLU Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 383 SER Chi-restraints excluded: chain B2 residue 458 LEU Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 43 GLU Chi-restraints excluded: chain b2 residue 46 ASP Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 163 ARG Chi-restraints excluded: chain B3 residue 181 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 343 THR Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 77 HIS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 275 LYS Chi-restraints excluded: chain b3 residue 323 VAL Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain b3 residue 472 LEU Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 256 GLU Chi-restraints excluded: chain B4 residue 258 MET Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 371 GLU Chi-restraints excluded: chain B4 residue 384 THR Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain b4 residue 43 GLU Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 93 SER Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 241 GLU Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain b4 residue 476 GLU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 137 MET Chi-restraints excluded: chain B5 residue 278 TYR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 455 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 181 ASN Chi-restraints excluded: chain b5 residue 256 GLU Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 359 LEU Chi-restraints excluded: chain b5 residue 360 ARG Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 183 optimal weight: 5.9990 chunk 490 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 320 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 545 optimal weight: 0.8980 chunk 452 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 372 GLN B1 34 GLN B1 372 GLN b1 235 HIS b1 266 ASN b1 372 GLN B4 372 GLN b4 80 HIS b4 266 ASN ** b4 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 72 ASN ** B5 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 45516 Z= 0.299 Angle : 0.662 14.124 61572 Z= 0.340 Chirality : 0.041 0.236 6408 Planarity : 0.005 0.117 8172 Dihedral : 4.428 42.965 6353 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.47 % Favored : 94.24 % Rotamer: Outliers : 4.62 % Allowed : 25.67 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 5664 helix: 1.56 (0.10), residues: 2868 sheet: -0.40 (0.22), residues: 552 loop : -0.08 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPB3 393 HIS 0.004 0.001 HISB4 80 PHE 0.035 0.001 PHE b 396 TYR 0.015 0.001 TYRb4 395 ARG 0.007 0.000 ARGB2 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 817 time to evaluate : 5.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8789 (tp40) cc_final: 0.7788 (tp-100) REVERT: B 270 GLN cc_start: 0.9653 (mm-40) cc_final: 0.9322 (mm-40) REVERT: B 399 ARG cc_start: 0.9165 (tpp80) cc_final: 0.8689 (tpp80) REVERT: B 458 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9419 (mm) REVERT: B 477 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8888 (mtmm) REVERT: B 482 ARG cc_start: 0.9528 (mmm-85) cc_final: 0.8973 (mtm110) REVERT: b 78 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8555 (mm-40) REVERT: b 116 LYS cc_start: 0.9632 (ptpp) cc_final: 0.9420 (ptpp) REVERT: b 136 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8775 (pmm) REVERT: b 144 MET cc_start: 0.9622 (ttp) cc_final: 0.9382 (ttt) REVERT: b 266 ASN cc_start: 0.9560 (m-40) cc_final: 0.9266 (m110) REVERT: b 399 ARG cc_start: 0.9319 (tpp80) cc_final: 0.8899 (tpp80) REVERT: b 462 GLN cc_start: 0.9541 (OUTLIER) cc_final: 0.9338 (mm110) REVERT: b 477 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8637 (mtmt) REVERT: b 486 TYR cc_start: 0.9252 (p90) cc_final: 0.8947 (p90) REVERT: B1 34 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: B1 75 GLN cc_start: 0.9052 (tp40) cc_final: 0.8124 (tp-100) REVERT: B1 136 MET cc_start: 0.9240 (ptp) cc_final: 0.8952 (ptp) REVERT: B1 137 MET cc_start: 0.9602 (tpp) cc_final: 0.9342 (mmp) REVERT: B1 238 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8153 (tm-30) REVERT: B1 268 GLN cc_start: 0.9458 (tp40) cc_final: 0.9210 (tp40) REVERT: B1 277 MET cc_start: 0.9437 (tpt) cc_final: 0.9079 (tpp) REVERT: B1 355 GLU cc_start: 0.8926 (pp20) cc_final: 0.8494 (pp20) REVERT: B1 356 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8456 (mm-40) REVERT: B1 360 ARG cc_start: 0.9551 (OUTLIER) cc_final: 0.8944 (ttm110) REVERT: B1 397 MET cc_start: 0.9038 (mmm) cc_final: 0.8812 (mmm) REVERT: b1 43 GLU cc_start: 0.8952 (pm20) cc_final: 0.8744 (pm20) REVERT: b1 75 GLN cc_start: 0.8804 (tp40) cc_final: 0.8175 (tp40) REVERT: b1 79 ASP cc_start: 0.8608 (m-30) cc_final: 0.8065 (m-30) REVERT: b1 255 MET cc_start: 0.9167 (mtp) cc_final: 0.8745 (mpp) REVERT: b1 277 MET cc_start: 0.9024 (tpp) cc_final: 0.8633 (tpp) REVERT: b1 399 ARG cc_start: 0.9214 (tpp80) cc_final: 0.8615 (tpp80) REVERT: B2 69 TYR cc_start: 0.9622 (m-80) cc_final: 0.9080 (m-80) REVERT: B2 137 MET cc_start: 0.9507 (OUTLIER) cc_final: 0.9190 (tpp) REVERT: B2 144 MET cc_start: 0.9615 (ttp) cc_final: 0.9211 (ttm) REVERT: B2 265 GLN cc_start: 0.9495 (mm110) cc_final: 0.9262 (mm-40) REVERT: B2 380 MET cc_start: 0.8657 (tpt) cc_final: 0.8224 (tpp) REVERT: B2 466 MET cc_start: 0.9608 (mmm) cc_final: 0.8821 (mmm) REVERT: B2 469 GLU cc_start: 0.9240 (pp20) cc_final: 0.8773 (pp20) REVERT: b2 75 GLN cc_start: 0.9019 (tp40) cc_final: 0.8292 (tp-100) REVERT: b2 76 LEU cc_start: 0.9781 (mm) cc_final: 0.9528 (mm) REVERT: b2 137 MET cc_start: 0.9381 (tpp) cc_final: 0.8708 (tpp) REVERT: b2 215 MET cc_start: 0.6139 (pmm) cc_final: 0.5875 (pmm) REVERT: b2 266 ASN cc_start: 0.9413 (m110) cc_final: 0.8974 (m110) REVERT: B3 116 LYS cc_start: 0.9628 (ptpp) cc_final: 0.9369 (pttm) REVERT: B3 266 ASN cc_start: 0.9423 (m-40) cc_final: 0.9196 (m-40) REVERT: B3 277 MET cc_start: 0.9134 (mmm) cc_final: 0.8694 (tpt) REVERT: B3 281 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8438 (t) REVERT: B3 334 MET cc_start: 0.8897 (tmm) cc_final: 0.8657 (ppp) REVERT: B3 397 MET cc_start: 0.9094 (mmp) cc_final: 0.8831 (mmm) REVERT: B3 460 GLU cc_start: 0.8745 (mp0) cc_final: 0.8531 (mp0) REVERT: B3 482 ARG cc_start: 0.9403 (ttm110) cc_final: 0.8943 (mtp180) REVERT: b3 78 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8719 (mm-40) REVERT: b3 137 MET cc_start: 0.9562 (tpp) cc_final: 0.9337 (tpp) REVERT: b3 144 MET cc_start: 0.9595 (ttp) cc_final: 0.9239 (ttm) REVERT: b3 266 ASN cc_start: 0.9365 (m-40) cc_final: 0.9063 (m110) REVERT: b3 275 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8853 (mtpt) REVERT: b3 377 TYR cc_start: 0.9207 (m-80) cc_final: 0.8948 (m-80) REVERT: b3 380 MET cc_start: 0.8364 (mmm) cc_final: 0.8099 (tpp) REVERT: B4 69 TYR cc_start: 0.9584 (m-80) cc_final: 0.9276 (m-80) REVERT: B4 75 GLN cc_start: 0.8974 (tp40) cc_final: 0.8241 (tp-100) REVERT: B4 137 MET cc_start: 0.9558 (tpp) cc_final: 0.9059 (tpp) REVERT: B4 144 MET cc_start: 0.9645 (ttp) cc_final: 0.8869 (tmm) REVERT: B4 258 MET cc_start: 0.9521 (OUTLIER) cc_final: 0.9133 (mmm) REVERT: B4 278 TYR cc_start: 0.7897 (t80) cc_final: 0.7421 (t80) REVERT: B4 325 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8844 (pp) REVERT: B4 360 ARG cc_start: 0.9496 (OUTLIER) cc_final: 0.8962 (ttm110) REVERT: B4 458 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9273 (mm) REVERT: B4 487 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8640 (mp10) REVERT: b4 75 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8532 (tp40) REVERT: b4 266 ASN cc_start: 0.9586 (m-40) cc_final: 0.9176 (m110) REVERT: b4 270 GLN cc_start: 0.9653 (mm-40) cc_final: 0.9295 (mm-40) REVERT: b4 371 GLU cc_start: 0.8954 (pm20) cc_final: 0.8643 (pm20) REVERT: b4 377 TYR cc_start: 0.9065 (m-80) cc_final: 0.8803 (m-80) REVERT: b4 380 MET cc_start: 0.8265 (tpp) cc_final: 0.8026 (mmm) REVERT: b4 399 ARG cc_start: 0.9270 (tpp80) cc_final: 0.8920 (tpp80) REVERT: b4 450 SER cc_start: 0.9665 (OUTLIER) cc_final: 0.9287 (p) REVERT: b4 458 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9254 (mm) REVERT: b4 459 LYS cc_start: 0.9273 (mmtm) cc_final: 0.8963 (mmtm) REVERT: b4 479 CYS cc_start: 0.9298 (m) cc_final: 0.8633 (p) REVERT: b4 481 LYS cc_start: 0.9387 (mtmm) cc_final: 0.9104 (pttm) REVERT: B5 69 TYR cc_start: 0.9672 (m-80) cc_final: 0.9111 (m-80) REVERT: B5 78 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8512 (mm-40) REVERT: B5 144 MET cc_start: 0.9584 (ttp) cc_final: 0.9193 (ttm) REVERT: B5 171 MET cc_start: 0.8636 (mmm) cc_final: 0.8303 (mtm) REVERT: B5 232 SER cc_start: 0.9666 (OUTLIER) cc_final: 0.9217 (p) REVERT: B5 258 MET cc_start: 0.9373 (mmm) cc_final: 0.8977 (mmm) REVERT: B5 285 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8160 (pp20) REVERT: B5 360 ARG cc_start: 0.9516 (OUTLIER) cc_final: 0.8765 (ttm110) REVERT: B5 399 ARG cc_start: 0.9410 (tpp80) cc_final: 0.8790 (tpp80) REVERT: B5 484 ASP cc_start: 0.9020 (m-30) cc_final: 0.8722 (m-30) REVERT: b5 75 GLN cc_start: 0.9099 (tp40) cc_final: 0.8659 (tp-100) REVERT: b5 136 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8675 (pmm) REVERT: b5 137 MET cc_start: 0.9491 (mmt) cc_final: 0.9189 (tpp) REVERT: b5 334 MET cc_start: 0.9638 (mmm) cc_final: 0.8953 (mmm) outliers start: 207 outliers final: 154 residues processed: 971 average time/residue: 0.5667 time to fit residues: 894.4169 Evaluate side-chains 963 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 788 time to evaluate : 5.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 78 GLN Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 136 MET Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 455 ILE Chi-restraints excluded: chain b residue 458 LEU Chi-restraints excluded: chain b residue 462 GLN Chi-restraints excluded: chain b residue 489 ILE Chi-restraints excluded: chain B1 residue 34 GLN Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 484 ASP Chi-restraints excluded: chain b1 residue 93 SER Chi-restraints excluded: chain b1 residue 181 ASN Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 254 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 368 VAL Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 391 GLU Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 137 MET Chi-restraints excluded: chain B2 residue 181 ASN Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 383 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 46 ASP Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 128 VAL Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain b2 residue 487 GLN Chi-restraints excluded: chain B3 residue 163 ARG Chi-restraints excluded: chain B3 residue 181 ASN Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 250 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 281 THR Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 343 THR Chi-restraints excluded: chain B3 residue 368 VAL Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain B3 residue 484 ASP Chi-restraints excluded: chain b3 residue 63 LEU Chi-restraints excluded: chain b3 residue 77 HIS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 181 ASN Chi-restraints excluded: chain b3 residue 182 ASN Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 275 LYS Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 46 ASP Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 256 GLU Chi-restraints excluded: chain B4 residue 258 MET Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 384 THR Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain B4 residue 468 ILE Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 93 SER Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 182 ASN Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 241 GLU Chi-restraints excluded: chain b4 residue 323 VAL Chi-restraints excluded: chain b4 residue 353 VAL Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 369 SER Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain b4 residue 476 GLU Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 181 ASN Chi-restraints excluded: chain B5 residue 232 SER Chi-restraints excluded: chain B5 residue 278 TYR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 163 ARG Chi-restraints excluded: chain b5 residue 181 ASN Chi-restraints excluded: chain b5 residue 182 ASN Chi-restraints excluded: chain b5 residue 240 VAL Chi-restraints excluded: chain b5 residue 256 GLU Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 359 LEU Chi-restraints excluded: chain b5 residue 360 ARG Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 526 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 398 optimal weight: 2.9990 chunk 308 optimal weight: 50.0000 chunk 459 optimal weight: 10.0000 chunk 304 optimal weight: 5.9990 chunk 543 optimal weight: 50.0000 chunk 340 optimal weight: 9.9990 chunk 331 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 372 GLN b1 372 GLN B3 372 GLN B4 372 GLN b4 80 HIS ** B5 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 45516 Z= 0.258 Angle : 0.678 13.573 61572 Z= 0.343 Chirality : 0.042 0.333 6408 Planarity : 0.005 0.117 8172 Dihedral : 4.435 43.043 6353 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.23 % Favored : 94.49 % Rotamer: Outliers : 4.33 % Allowed : 26.41 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.11), residues: 5664 helix: 1.53 (0.10), residues: 2868 sheet: -0.45 (0.22), residues: 552 loop : -0.08 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPb4 115 HIS 0.004 0.001 HISB4 80 PHE 0.023 0.001 PHE B 147 TYR 0.015 0.001 TYRb4 395 ARG 0.007 0.000 ARGb1 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 827 time to evaluate : 4.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8804 (tp40) cc_final: 0.7811 (tp-100) REVERT: B 260 MET cc_start: 0.9143 (mtm) cc_final: 0.8894 (mtm) REVERT: B 270 GLN cc_start: 0.9667 (mm-40) cc_final: 0.9320 (mm-40) REVERT: B 399 ARG cc_start: 0.9186 (tpp80) cc_final: 0.8650 (tpp80) REVERT: B 458 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9048 (mm) REVERT: B 477 LYS cc_start: 0.9173 (mtmm) cc_final: 0.8886 (mtmm) REVERT: B 482 ARG cc_start: 0.9522 (mmm-85) cc_final: 0.8959 (mtm110) REVERT: b 78 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8721 (mm-40) REVERT: b 136 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8754 (pmm) REVERT: b 144 MET cc_start: 0.9613 (ttp) cc_final: 0.9370 (ttt) REVERT: b 266 ASN cc_start: 0.9562 (m-40) cc_final: 0.9269 (m110) REVERT: b 399 ARG cc_start: 0.9326 (tpp80) cc_final: 0.8916 (tpp80) REVERT: b 462 GLN cc_start: 0.9565 (OUTLIER) cc_final: 0.9363 (mm110) REVERT: b 477 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8744 (mtmm) REVERT: B1 75 GLN cc_start: 0.9038 (tp40) cc_final: 0.8029 (tp-100) REVERT: B1 136 MET cc_start: 0.9265 (ptp) cc_final: 0.8952 (ptp) REVERT: B1 137 MET cc_start: 0.9590 (tpp) cc_final: 0.9251 (mmp) REVERT: B1 238 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8162 (tm-30) REVERT: B1 268 GLN cc_start: 0.9468 (tp40) cc_final: 0.9244 (tp40) REVERT: B1 355 GLU cc_start: 0.8863 (pp20) cc_final: 0.8366 (pp20) REVERT: B1 356 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8438 (mm-40) REVERT: B1 360 ARG cc_start: 0.9547 (OUTLIER) cc_final: 0.8922 (ttm110) REVERT: b1 43 GLU cc_start: 0.8961 (pm20) cc_final: 0.8746 (pm20) REVERT: b1 75 GLN cc_start: 0.8887 (tp40) cc_final: 0.8072 (tp40) REVERT: b1 79 ASP cc_start: 0.8604 (m-30) cc_final: 0.8002 (m-30) REVERT: b1 136 MET cc_start: 0.9459 (ptp) cc_final: 0.9106 (pmm) REVERT: b1 151 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9106 (pp) REVERT: b1 255 MET cc_start: 0.9106 (mtp) cc_final: 0.8661 (mpp) REVERT: b1 277 MET cc_start: 0.8997 (tpp) cc_final: 0.8589 (tpp) REVERT: b1 399 ARG cc_start: 0.9243 (tpp80) cc_final: 0.8599 (tpp80) REVERT: B2 69 TYR cc_start: 0.9621 (m-80) cc_final: 0.9025 (m-80) REVERT: B2 116 LYS cc_start: 0.9583 (ptpp) cc_final: 0.9347 (pttm) REVERT: B2 136 MET cc_start: 0.9409 (ptp) cc_final: 0.9206 (ptp) REVERT: B2 137 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9175 (tpp) REVERT: B2 144 MET cc_start: 0.9602 (ttp) cc_final: 0.9244 (ttm) REVERT: B2 232 SER cc_start: 0.9692 (OUTLIER) cc_final: 0.9250 (p) REVERT: B2 258 MET cc_start: 0.9415 (mmm) cc_final: 0.9003 (mpp) REVERT: B2 334 MET cc_start: 0.8918 (mmm) cc_final: 0.8506 (mmm) REVERT: B2 380 MET cc_start: 0.8721 (tpt) cc_final: 0.8314 (tpp) REVERT: B2 399 ARG cc_start: 0.9252 (mmm-85) cc_final: 0.8713 (tpp80) REVERT: B2 469 GLU cc_start: 0.9216 (pp20) cc_final: 0.8859 (pp20) REVERT: b2 75 GLN cc_start: 0.9022 (tp40) cc_final: 0.8345 (tm-30) REVERT: b2 137 MET cc_start: 0.9355 (tpp) cc_final: 0.8594 (tpp) REVERT: b2 171 MET cc_start: 0.8189 (mmm) cc_final: 0.6894 (mtt) REVERT: b2 266 ASN cc_start: 0.9402 (m110) cc_final: 0.8967 (m110) REVERT: b2 277 MET cc_start: 0.9210 (mmm) cc_final: 0.8913 (tpp) REVERT: b2 411 MET cc_start: 0.9559 (mtm) cc_final: 0.9128 (mtm) REVERT: B3 116 LYS cc_start: 0.9625 (ptpp) cc_final: 0.9365 (pttm) REVERT: B3 255 MET cc_start: 0.9210 (mmm) cc_final: 0.8971 (mmm) REVERT: B3 266 ASN cc_start: 0.9423 (m-40) cc_final: 0.9199 (m110) REVERT: B3 277 MET cc_start: 0.9092 (mmm) cc_final: 0.8115 (tpt) REVERT: B3 281 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8480 (t) REVERT: B3 397 MET cc_start: 0.9090 (mmp) cc_final: 0.8817 (mmm) REVERT: B3 460 GLU cc_start: 0.8721 (mp0) cc_final: 0.8491 (mp0) REVERT: b3 78 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8747 (mm-40) REVERT: b3 136 MET cc_start: 0.9402 (ptp) cc_final: 0.9187 (pmm) REVERT: b3 144 MET cc_start: 0.9585 (ttp) cc_final: 0.9234 (ttm) REVERT: b3 266 ASN cc_start: 0.9364 (m-40) cc_final: 0.9058 (m110) REVERT: b3 275 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8771 (mtpt) REVERT: b3 399 ARG cc_start: 0.9222 (mmm-85) cc_final: 0.8702 (tpp80) REVERT: B4 69 TYR cc_start: 0.9593 (m-80) cc_final: 0.9332 (m-80) REVERT: B4 75 GLN cc_start: 0.8988 (tp40) cc_final: 0.8204 (tp-100) REVERT: B4 137 MET cc_start: 0.9531 (tpp) cc_final: 0.8995 (tpp) REVERT: B4 258 MET cc_start: 0.9511 (OUTLIER) cc_final: 0.9147 (mmm) REVERT: B4 278 TYR cc_start: 0.7932 (t80) cc_final: 0.7488 (t80) REVERT: B4 325 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8841 (pp) REVERT: B4 360 ARG cc_start: 0.9467 (OUTLIER) cc_final: 0.8951 (ttm110) REVERT: B4 487 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8629 (mp10) REVERT: b4 69 TYR cc_start: 0.9521 (m-80) cc_final: 0.9225 (m-80) REVERT: b4 75 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8486 (tp40) REVERT: b4 151 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9189 (pp) REVERT: b4 371 GLU cc_start: 0.8962 (pm20) cc_final: 0.8645 (pm20) REVERT: b4 377 TYR cc_start: 0.9060 (m-80) cc_final: 0.8806 (m-80) REVERT: b4 380 MET cc_start: 0.8256 (tpp) cc_final: 0.8028 (mmm) REVERT: b4 399 ARG cc_start: 0.9234 (tpp80) cc_final: 0.8848 (tpp80) REVERT: b4 450 SER cc_start: 0.9669 (OUTLIER) cc_final: 0.9293 (p) REVERT: b4 458 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9225 (mm) REVERT: b4 479 CYS cc_start: 0.9292 (m) cc_final: 0.8508 (p) REVERT: B5 69 TYR cc_start: 0.9667 (m-80) cc_final: 0.9105 (m-80) REVERT: B5 78 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8583 (mm-40) REVERT: B5 144 MET cc_start: 0.9575 (ttp) cc_final: 0.9203 (ttm) REVERT: B5 171 MET cc_start: 0.8645 (mmm) cc_final: 0.8271 (mtm) REVERT: B5 232 SER cc_start: 0.9669 (OUTLIER) cc_final: 0.9227 (p) REVERT: B5 255 MET cc_start: 0.9304 (mtp) cc_final: 0.8737 (tpp) REVERT: B5 258 MET cc_start: 0.9365 (mmm) cc_final: 0.8983 (mmm) REVERT: B5 285 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8153 (pp20) REVERT: B5 360 ARG cc_start: 0.9516 (OUTLIER) cc_final: 0.8756 (ttm110) REVERT: B5 399 ARG cc_start: 0.9461 (tpp80) cc_final: 0.9079 (tpp80) REVERT: B5 484 ASP cc_start: 0.9030 (m-30) cc_final: 0.8741 (m-30) REVERT: b5 69 TYR cc_start: 0.9576 (m-80) cc_final: 0.9182 (m-80) REVERT: b5 75 GLN cc_start: 0.9082 (tp40) cc_final: 0.8603 (tp-100) REVERT: b5 136 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8629 (pmm) REVERT: b5 137 MET cc_start: 0.9459 (mmt) cc_final: 0.9253 (mmt) REVERT: b5 144 MET cc_start: 0.9623 (ttp) cc_final: 0.8726 (tmm) REVERT: b5 334 MET cc_start: 0.9704 (mmm) cc_final: 0.8997 (mmm) outliers start: 194 outliers final: 151 residues processed: 971 average time/residue: 0.5623 time to fit residues: 888.6509 Evaluate side-chains 966 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 793 time to evaluate : 5.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 78 GLN Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 136 MET Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 181 ASN Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 455 ILE Chi-restraints excluded: chain b residue 458 LEU Chi-restraints excluded: chain b residue 462 GLN Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 484 ASP Chi-restraints excluded: chain b1 residue 93 SER Chi-restraints excluded: chain b1 residue 151 LEU Chi-restraints excluded: chain b1 residue 181 ASN Chi-restraints excluded: chain b1 residue 182 ASN Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 254 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 368 VAL Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 391 GLU Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 137 MET Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 232 SER Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 383 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 46 ASP Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 181 ASN Chi-restraints excluded: chain b2 residue 182 ASN Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 163 ARG Chi-restraints excluded: chain B3 residue 181 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 281 THR Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 343 THR Chi-restraints excluded: chain B3 residue 368 VAL Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain B3 residue 484 ASP Chi-restraints excluded: chain b3 residue 77 HIS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 181 ASN Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 275 LYS Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 430 LYS Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 46 ASP Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 126 ILE Chi-restraints excluded: chain B4 residue 181 ASN Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 256 GLU Chi-restraints excluded: chain B4 residue 258 MET Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 384 THR Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 468 ILE Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 77 HIS Chi-restraints excluded: chain b4 residue 93 SER Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 151 LEU Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 241 GLU Chi-restraints excluded: chain b4 residue 254 VAL Chi-restraints excluded: chain b4 residue 323 VAL Chi-restraints excluded: chain b4 residue 353 VAL Chi-restraints excluded: chain b4 residue 355 GLU Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 369 SER Chi-restraints excluded: chain b4 residue 381 SER Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain b4 residue 462 GLN Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 137 MET Chi-restraints excluded: chain B5 residue 181 ASN Chi-restraints excluded: chain B5 residue 232 SER Chi-restraints excluded: chain B5 residue 278 TYR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 163 ARG Chi-restraints excluded: chain b5 residue 181 ASN Chi-restraints excluded: chain b5 residue 256 GLU Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 360 ARG Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 336 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 324 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 chunk 370 optimal weight: 0.9990 chunk 268 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 407 GLN B1 34 GLN B1 372 GLN b1 266 ASN b1 372 GLN b2 372 GLN B4 372 GLN b4 80 HIS b5 145 HIS ** b5 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45516 Z= 0.196 Angle : 0.694 14.468 61572 Z= 0.344 Chirality : 0.042 0.276 6408 Planarity : 0.005 0.117 8172 Dihedral : 4.382 41.669 6353 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.14 % Favored : 94.58 % Rotamer: Outliers : 3.75 % Allowed : 27.26 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.11), residues: 5664 helix: 1.50 (0.10), residues: 2868 sheet: -0.42 (0.22), residues: 552 loop : -0.05 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPb4 115 HIS 0.003 0.001 HIS B 332 PHE 0.025 0.001 PHE B 396 TYR 0.026 0.001 TYRB3 395 ARG 0.006 0.000 ARGb1 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 860 time to evaluate : 5.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8747 (tp40) cc_final: 0.7712 (tp-100) REVERT: B 136 MET cc_start: 0.9514 (ptp) cc_final: 0.9103 (pmm) REVERT: B 270 GLN cc_start: 0.9635 (mm-40) cc_final: 0.9286 (mm-40) REVERT: B 399 ARG cc_start: 0.9142 (tpp80) cc_final: 0.8559 (tpp80) REVERT: B 477 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8856 (mtmm) REVERT: B 482 ARG cc_start: 0.9513 (mmm-85) cc_final: 0.9241 (mtp85) REVERT: b 78 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8729 (mm-40) REVERT: b 79 ASP cc_start: 0.8133 (m-30) cc_final: 0.7892 (m-30) REVERT: b 144 MET cc_start: 0.9600 (ttp) cc_final: 0.9354 (ttt) REVERT: b 266 ASN cc_start: 0.9548 (m-40) cc_final: 0.9244 (m110) REVERT: b 277 MET cc_start: 0.9212 (tpp) cc_final: 0.8884 (tpt) REVERT: b 397 MET cc_start: 0.9009 (mmm) cc_final: 0.8740 (mmp) REVERT: b 399 ARG cc_start: 0.9299 (tpp80) cc_final: 0.8989 (tpp80) REVERT: b 477 LYS cc_start: 0.8956 (mtmm) cc_final: 0.8669 (mtmt) REVERT: b 486 TYR cc_start: 0.9104 (p90) cc_final: 0.8888 (p90) REVERT: B1 75 GLN cc_start: 0.9043 (tp40) cc_final: 0.7969 (tp-100) REVERT: B1 78 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8426 (mm-40) REVERT: B1 136 MET cc_start: 0.9227 (ptp) cc_final: 0.8892 (ptp) REVERT: B1 137 MET cc_start: 0.9610 (tpp) cc_final: 0.9216 (mmp) REVERT: B1 144 MET cc_start: 0.9612 (ttp) cc_final: 0.8718 (tmm) REVERT: B1 238 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B1 277 MET cc_start: 0.9300 (tpt) cc_final: 0.8997 (tpp) REVERT: B1 355 GLU cc_start: 0.8860 (pp20) cc_final: 0.8380 (pp20) REVERT: B1 356 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8560 (mm-40) REVERT: B1 360 ARG cc_start: 0.9544 (OUTLIER) cc_final: 0.8949 (ttm110) REVERT: b1 75 GLN cc_start: 0.8904 (tp40) cc_final: 0.7867 (tp-100) REVERT: b1 76 LEU cc_start: 0.9638 (mt) cc_final: 0.9364 (mt) REVERT: b1 79 ASP cc_start: 0.8602 (m-30) cc_final: 0.7909 (m-30) REVERT: b1 116 LYS cc_start: 0.9622 (ptpp) cc_final: 0.9379 (pttm) REVERT: b1 255 MET cc_start: 0.9074 (mtp) cc_final: 0.8617 (mpp) REVERT: b1 277 MET cc_start: 0.8961 (tpp) cc_final: 0.8570 (tpp) REVERT: b1 380 MET cc_start: 0.8553 (tpp) cc_final: 0.7951 (tpp) REVERT: b1 399 ARG cc_start: 0.9254 (tpp80) cc_final: 0.8568 (tpp80) REVERT: B2 69 TYR cc_start: 0.9615 (m-80) cc_final: 0.9094 (m-80) REVERT: B2 116 LYS cc_start: 0.9581 (ptpp) cc_final: 0.9336 (pttm) REVERT: B2 137 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9172 (tpp) REVERT: B2 144 MET cc_start: 0.9617 (ttp) cc_final: 0.9400 (ttt) REVERT: B2 232 SER cc_start: 0.9706 (OUTLIER) cc_final: 0.9262 (p) REVERT: B2 325 LEU cc_start: 0.8666 (pp) cc_final: 0.8453 (pp) REVERT: B2 334 MET cc_start: 0.9108 (mmm) cc_final: 0.8796 (mmm) REVERT: B2 360 ARG cc_start: 0.8626 (mtp85) cc_final: 0.7831 (mtp85) REVERT: B2 376 ASN cc_start: 0.9573 (t0) cc_final: 0.9186 (t0) REVERT: B2 380 MET cc_start: 0.8593 (tpt) cc_final: 0.8179 (tpp) REVERT: B2 399 ARG cc_start: 0.9256 (mmm-85) cc_final: 0.8738 (tpp80) REVERT: b2 75 GLN cc_start: 0.9062 (tp40) cc_final: 0.8366 (tm-30) REVERT: b2 136 MET cc_start: 0.9459 (ptp) cc_final: 0.9171 (pmm) REVERT: b2 137 MET cc_start: 0.9308 (tpp) cc_final: 0.8646 (tpp) REVERT: b2 171 MET cc_start: 0.8118 (mmm) cc_final: 0.6759 (mtt) REVERT: b2 266 ASN cc_start: 0.9347 (m110) cc_final: 0.8922 (m110) REVERT: b2 489 ILE cc_start: 0.9701 (OUTLIER) cc_final: 0.9500 (mm) REVERT: B3 116 LYS cc_start: 0.9633 (ptpp) cc_final: 0.9366 (pttm) REVERT: B3 255 MET cc_start: 0.9227 (mmm) cc_final: 0.9021 (mmm) REVERT: B3 266 ASN cc_start: 0.9406 (m-40) cc_final: 0.9204 (m110) REVERT: B3 277 MET cc_start: 0.9068 (mmm) cc_final: 0.8093 (tpt) REVERT: B3 334 MET cc_start: 0.8680 (ppp) cc_final: 0.8348 (ppp) REVERT: B3 380 MET cc_start: 0.8152 (tpp) cc_final: 0.7941 (tpp) REVERT: B3 397 MET cc_start: 0.9065 (mmp) cc_final: 0.8776 (mmm) REVERT: B3 399 ARG cc_start: 0.9196 (tpp80) cc_final: 0.8781 (tpp80) REVERT: B3 460 GLU cc_start: 0.8796 (mp0) cc_final: 0.8545 (mp0) REVERT: b3 78 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8659 (mm-40) REVERT: b3 137 MET cc_start: 0.9451 (tpp) cc_final: 0.9069 (tpp) REVERT: b3 144 MET cc_start: 0.9583 (ttp) cc_final: 0.9368 (ttt) REVERT: b3 266 ASN cc_start: 0.9344 (m-40) cc_final: 0.9042 (m110) REVERT: b3 268 GLN cc_start: 0.9468 (tp40) cc_final: 0.9134 (tp40) REVERT: b3 380 MET cc_start: 0.8235 (mmm) cc_final: 0.7910 (tpp) REVERT: b3 399 ARG cc_start: 0.9230 (mmm-85) cc_final: 0.8705 (tpp80) REVERT: B4 69 TYR cc_start: 0.9561 (m-80) cc_final: 0.9294 (m-80) REVERT: B4 75 GLN cc_start: 0.8816 (tp40) cc_final: 0.8102 (tp-100) REVERT: B4 137 MET cc_start: 0.9496 (tpp) cc_final: 0.8983 (tpp) REVERT: B4 144 MET cc_start: 0.9622 (ttp) cc_final: 0.8764 (tmm) REVERT: B4 325 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8850 (pp) REVERT: B4 360 ARG cc_start: 0.9479 (OUTLIER) cc_final: 0.8970 (ttm110) REVERT: B4 487 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8631 (mp10) REVERT: b4 69 TYR cc_start: 0.9490 (m-80) cc_final: 0.9168 (m-80) REVERT: b4 75 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8584 (tp40) REVERT: b4 260 MET cc_start: 0.9193 (mtm) cc_final: 0.8754 (mtm) REVERT: b4 371 GLU cc_start: 0.8866 (pm20) cc_final: 0.8623 (pm20) REVERT: b4 399 ARG cc_start: 0.9260 (tpp80) cc_final: 0.8821 (tpp80) REVERT: b4 458 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9392 (mm) REVERT: B5 69 TYR cc_start: 0.9650 (m-80) cc_final: 0.9085 (m-80) REVERT: B5 75 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8429 (tp-100) REVERT: B5 78 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8627 (mm-40) REVERT: B5 136 MET cc_start: 0.9428 (ptp) cc_final: 0.9215 (ptp) REVERT: B5 171 MET cc_start: 0.8614 (mmm) cc_final: 0.8216 (mtm) REVERT: B5 232 SER cc_start: 0.9668 (OUTLIER) cc_final: 0.9226 (p) REVERT: B5 258 MET cc_start: 0.9351 (mmm) cc_final: 0.8956 (mmm) REVERT: B5 277 MET cc_start: 0.9186 (tpp) cc_final: 0.8982 (tpt) REVERT: B5 285 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8109 (pp20) REVERT: B5 360 ARG cc_start: 0.9504 (OUTLIER) cc_final: 0.8801 (ttm110) REVERT: B5 399 ARG cc_start: 0.9419 (tpp80) cc_final: 0.9036 (tpp80) REVERT: B5 459 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8948 (mmtm) REVERT: B5 484 ASP cc_start: 0.8994 (m-30) cc_final: 0.8705 (m-30) REVERT: b5 75 GLN cc_start: 0.9009 (tp40) cc_final: 0.8461 (tp-100) REVERT: b5 137 MET cc_start: 0.9448 (mmt) cc_final: 0.9196 (mmt) REVERT: b5 334 MET cc_start: 0.9731 (mmm) cc_final: 0.9075 (mmm) outliers start: 168 outliers final: 124 residues processed: 981 average time/residue: 0.5582 time to fit residues: 889.9307 Evaluate side-chains 954 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 817 time to evaluate : 4.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 78 GLN Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 455 ILE Chi-restraints excluded: chain b residue 458 LEU Chi-restraints excluded: chain B1 residue 43 GLU Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 484 ASP Chi-restraints excluded: chain b1 residue 93 SER Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 254 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 368 VAL Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 137 MET Chi-restraints excluded: chain B2 residue 232 SER Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 383 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 43 GLU Chi-restraints excluded: chain b2 residue 46 ASP Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 489 ILE Chi-restraints excluded: chain B3 residue 163 ARG Chi-restraints excluded: chain B3 residue 181 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 281 THR Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 343 THR Chi-restraints excluded: chain B3 residue 368 VAL Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 77 HIS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 275 LYS Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 430 LYS Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain B4 residue 46 ASP Chi-restraints excluded: chain B4 residue 256 GLU Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 371 GLU Chi-restraints excluded: chain B4 residue 384 THR Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 468 ILE Chi-restraints excluded: chain B4 residue 484 ASP Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 77 HIS Chi-restraints excluded: chain b4 residue 93 SER Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 241 GLU Chi-restraints excluded: chain b4 residue 254 VAL Chi-restraints excluded: chain b4 residue 353 VAL Chi-restraints excluded: chain b4 residue 355 GLU Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 381 SER Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain b4 residue 462 GLN Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 137 MET Chi-restraints excluded: chain B5 residue 206 VAL Chi-restraints excluded: chain B5 residue 232 SER Chi-restraints excluded: chain B5 residue 278 TYR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 430 LYS Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 163 ARG Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 494 optimal weight: 7.9990 chunk 520 optimal weight: 4.9990 chunk 475 optimal weight: 9.9990 chunk 506 optimal weight: 0.9980 chunk 304 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 397 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 457 optimal weight: 9.9990 chunk 479 optimal weight: 4.9990 chunk 504 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 372 GLN b1 372 GLN b2 372 GLN B4 372 GLN b4 80 HIS ** b5 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 45516 Z= 0.236 Angle : 0.723 14.509 61572 Z= 0.359 Chirality : 0.043 0.259 6408 Planarity : 0.005 0.118 8172 Dihedral : 4.349 41.377 6350 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.24 % Favored : 94.47 % Rotamer: Outliers : 3.66 % Allowed : 27.79 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.11), residues: 5664 helix: 1.49 (0.10), residues: 2868 sheet: -0.41 (0.22), residues: 552 loop : -0.06 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPb4 115 HIS 0.005 0.001 HISb5 145 PHE 0.036 0.001 PHEB3 396 TYR 0.021 0.001 TYRb2 486 ARG 0.007 0.000 ARGb4 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 830 time to evaluate : 4.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TYR cc_start: 0.9485 (m-80) cc_final: 0.9249 (m-80) REVERT: B 75 GLN cc_start: 0.8724 (tp40) cc_final: 0.7748 (tp-100) REVERT: B 270 GLN cc_start: 0.9676 (mm-40) cc_final: 0.9308 (mm-40) REVERT: B 399 ARG cc_start: 0.9123 (tpp80) cc_final: 0.8497 (tpp80) REVERT: B 477 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8713 (mtmt) REVERT: B 482 ARG cc_start: 0.9470 (mmm-85) cc_final: 0.9160 (mtp85) REVERT: b 78 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8709 (mm-40) REVERT: b 266 ASN cc_start: 0.9555 (m-40) cc_final: 0.9259 (m110) REVERT: b 277 MET cc_start: 0.9231 (tpp) cc_final: 0.8869 (tpt) REVERT: b 371 GLU cc_start: 0.8703 (pm20) cc_final: 0.8455 (pm20) REVERT: b 399 ARG cc_start: 0.9298 (tpp80) cc_final: 0.8923 (tpp80) REVERT: b 477 LYS cc_start: 0.8932 (mtmm) cc_final: 0.8624 (mtmt) REVERT: b 486 TYR cc_start: 0.9128 (p90) cc_final: 0.8910 (p90) REVERT: B1 34 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: B1 75 GLN cc_start: 0.9147 (tp40) cc_final: 0.7712 (tp-100) REVERT: B1 78 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8508 (mm-40) REVERT: B1 79 ASP cc_start: 0.8180 (m-30) cc_final: 0.7973 (p0) REVERT: B1 87 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7404 (mtp180) REVERT: B1 116 LYS cc_start: 0.9557 (pttm) cc_final: 0.9350 (pptt) REVERT: B1 136 MET cc_start: 0.9234 (ptp) cc_final: 0.8899 (ptp) REVERT: B1 137 MET cc_start: 0.9592 (tpp) cc_final: 0.9285 (mmp) REVERT: B1 144 MET cc_start: 0.9620 (ttp) cc_final: 0.8861 (tmm) REVERT: B1 238 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B1 346 ASP cc_start: 0.9274 (m-30) cc_final: 0.9070 (m-30) REVERT: B1 355 GLU cc_start: 0.8889 (pp20) cc_final: 0.8384 (pp20) REVERT: B1 356 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8548 (mm-40) REVERT: B1 360 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.8906 (ttm110) REVERT: b1 75 GLN cc_start: 0.8883 (tp40) cc_final: 0.7859 (tp-100) REVERT: b1 76 LEU cc_start: 0.9646 (mt) cc_final: 0.9373 (mt) REVERT: b1 79 ASP cc_start: 0.8627 (m-30) cc_final: 0.7929 (m-30) REVERT: b1 136 MET cc_start: 0.9472 (ptp) cc_final: 0.9084 (pmm) REVERT: b1 255 MET cc_start: 0.8932 (mtp) cc_final: 0.8507 (mpp) REVERT: b1 277 MET cc_start: 0.8986 (tpp) cc_final: 0.8605 (tpp) REVERT: b1 399 ARG cc_start: 0.9263 (tpp80) cc_final: 0.8597 (tpp80) REVERT: B2 69 TYR cc_start: 0.9626 (m-80) cc_final: 0.9117 (m-80) REVERT: B2 116 LYS cc_start: 0.9580 (ptpp) cc_final: 0.9343 (pttm) REVERT: B2 136 MET cc_start: 0.9467 (ptp) cc_final: 0.9233 (ptp) REVERT: B2 137 MET cc_start: 0.9442 (mmt) cc_final: 0.9055 (tpp) REVERT: B2 144 MET cc_start: 0.9621 (ttp) cc_final: 0.9403 (ttt) REVERT: B2 232 SER cc_start: 0.9713 (OUTLIER) cc_final: 0.9334 (p) REVERT: B2 334 MET cc_start: 0.9112 (mmm) cc_final: 0.8807 (mmm) REVERT: B2 360 ARG cc_start: 0.8609 (mtp85) cc_final: 0.7767 (mtp85) REVERT: B2 380 MET cc_start: 0.8647 (tpt) cc_final: 0.8134 (tpp) REVERT: B2 399 ARG cc_start: 0.9269 (mmm-85) cc_final: 0.8756 (tpp80) REVERT: b2 75 GLN cc_start: 0.9042 (tp40) cc_final: 0.8351 (tm-30) REVERT: b2 137 MET cc_start: 0.9295 (tpp) cc_final: 0.8545 (tpp) REVERT: b2 266 ASN cc_start: 0.9313 (m110) cc_final: 0.8908 (m110) REVERT: b2 277 MET cc_start: 0.9342 (tpp) cc_final: 0.9001 (tpp) REVERT: b2 285 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8991 (tm-30) REVERT: b2 411 MET cc_start: 0.9520 (mtm) cc_final: 0.9097 (mtm) REVERT: B3 76 LEU cc_start: 0.9498 (mt) cc_final: 0.9296 (mt) REVERT: B3 116 LYS cc_start: 0.9623 (ptpp) cc_final: 0.9361 (pttm) REVERT: B3 136 MET cc_start: 0.9517 (ptp) cc_final: 0.9140 (pmm) REVERT: B3 255 MET cc_start: 0.9228 (mmm) cc_final: 0.9002 (mmm) REVERT: B3 266 ASN cc_start: 0.9398 (m-40) cc_final: 0.9147 (m110) REVERT: B3 397 MET cc_start: 0.9031 (mmp) cc_final: 0.8779 (mmm) REVERT: B3 399 ARG cc_start: 0.9167 (tpp80) cc_final: 0.8745 (tpp80) REVERT: B3 460 GLU cc_start: 0.8797 (mp0) cc_final: 0.8570 (mp0) REVERT: b3 78 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8695 (mm-40) REVERT: b3 136 MET cc_start: 0.9403 (ptp) cc_final: 0.9059 (pmm) REVERT: b3 144 MET cc_start: 0.9581 (ttp) cc_final: 0.9358 (ttt) REVERT: b3 266 ASN cc_start: 0.9352 (m-40) cc_final: 0.8908 (m110) REVERT: b3 268 GLN cc_start: 0.9483 (tp40) cc_final: 0.9136 (tp40) REVERT: b3 380 MET cc_start: 0.8349 (mmm) cc_final: 0.7980 (tpp) REVERT: b3 399 ARG cc_start: 0.9209 (mmm-85) cc_final: 0.8662 (tpp80) REVERT: B4 69 TYR cc_start: 0.9564 (m-80) cc_final: 0.9335 (m-80) REVERT: B4 74 ILE cc_start: 0.9692 (tp) cc_final: 0.9492 (tp) REVERT: B4 75 GLN cc_start: 0.8916 (tp40) cc_final: 0.8228 (tp-100) REVERT: B4 144 MET cc_start: 0.9630 (ttp) cc_final: 0.8732 (tmm) REVERT: B4 232 SER cc_start: 0.9751 (OUTLIER) cc_final: 0.9449 (p) REVERT: B4 258 MET cc_start: 0.9539 (OUTLIER) cc_final: 0.9183 (mmm) REVERT: B4 268 GLN cc_start: 0.9529 (tp40) cc_final: 0.9324 (tp40) REVERT: B4 278 TYR cc_start: 0.7955 (t80) cc_final: 0.7515 (t80) REVERT: B4 325 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8787 (pp) REVERT: B4 360 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.8973 (ttm110) REVERT: B4 397 MET cc_start: 0.8964 (mmm) cc_final: 0.8646 (mmp) REVERT: B4 487 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8688 (mp10) REVERT: b4 69 TYR cc_start: 0.9510 (m-80) cc_final: 0.9177 (m-80) REVERT: b4 75 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8615 (tp40) REVERT: b4 399 ARG cc_start: 0.9239 (tpp80) cc_final: 0.8802 (tpp80) REVERT: b4 458 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9253 (mm) REVERT: B5 69 TYR cc_start: 0.9658 (m-80) cc_final: 0.9095 (m-80) REVERT: B5 75 GLN cc_start: 0.9021 (tp-100) cc_final: 0.8480 (tp-100) REVERT: B5 78 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8452 (mm-40) REVERT: B5 136 MET cc_start: 0.9409 (ptp) cc_final: 0.9199 (ptp) REVERT: B5 171 MET cc_start: 0.8643 (mmm) cc_final: 0.8205 (mtm) REVERT: B5 232 SER cc_start: 0.9663 (OUTLIER) cc_final: 0.9220 (p) REVERT: B5 258 MET cc_start: 0.9382 (mmm) cc_final: 0.8968 (mmm) REVERT: B5 277 MET cc_start: 0.9313 (tpp) cc_final: 0.9103 (tpt) REVERT: B5 285 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8148 (pp20) REVERT: B5 360 ARG cc_start: 0.9441 (OUTLIER) cc_final: 0.8859 (ttm110) REVERT: B5 399 ARG cc_start: 0.9447 (tpp80) cc_final: 0.9071 (tpp80) REVERT: B5 484 ASP cc_start: 0.8982 (m-30) cc_final: 0.8685 (m-30) REVERT: b5 69 TYR cc_start: 0.9546 (m-80) cc_final: 0.9127 (m-80) REVERT: b5 75 GLN cc_start: 0.9082 (tp40) cc_final: 0.8525 (tp-100) REVERT: b5 136 MET cc_start: 0.9415 (ptp) cc_final: 0.9109 (ptp) REVERT: b5 137 MET cc_start: 0.9442 (mmt) cc_final: 0.9134 (tpp) REVERT: b5 144 MET cc_start: 0.9619 (ttp) cc_final: 0.8709 (tmm) REVERT: b5 277 MET cc_start: 0.9270 (tpt) cc_final: 0.9065 (tpp) REVERT: b5 334 MET cc_start: 0.9728 (mmm) cc_final: 0.8958 (mmm) REVERT: b5 397 MET cc_start: 0.9003 (mmm) cc_final: 0.8768 (mmp) outliers start: 164 outliers final: 141 residues processed: 955 average time/residue: 0.5617 time to fit residues: 873.1549 Evaluate side-chains 972 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 817 time to evaluate : 5.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 78 GLN Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 181 ASN Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 458 LEU Chi-restraints excluded: chain B1 residue 34 GLN Chi-restraints excluded: chain B1 residue 43 GLU Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 181 ASN Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 484 ASP Chi-restraints excluded: chain b1 residue 93 SER Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 254 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 368 VAL Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 181 ASN Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 232 SER Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 383 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 43 GLU Chi-restraints excluded: chain b2 residue 46 ASP Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 405 SER Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 163 ARG Chi-restraints excluded: chain B3 residue 181 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 281 THR Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 343 THR Chi-restraints excluded: chain B3 residue 368 VAL Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 77 HIS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 275 LYS Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 430 LYS Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain b3 residue 467 LEU Chi-restraints excluded: chain B4 residue 46 ASP Chi-restraints excluded: chain B4 residue 232 SER Chi-restraints excluded: chain B4 residue 256 GLU Chi-restraints excluded: chain B4 residue 258 MET Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 346 ASP Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 371 GLU Chi-restraints excluded: chain B4 residue 384 THR Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 468 ILE Chi-restraints excluded: chain B4 residue 484 ASP Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 77 HIS Chi-restraints excluded: chain b4 residue 93 SER Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 241 GLU Chi-restraints excluded: chain b4 residue 254 VAL Chi-restraints excluded: chain b4 residue 355 GLU Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 381 SER Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain b4 residue 462 GLN Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 137 MET Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 232 SER Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 430 LYS Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 163 ARG Chi-restraints excluded: chain b5 residue 181 ASN Chi-restraints excluded: chain b5 residue 240 VAL Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 332 optimal weight: 2.9990 chunk 535 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 chunk 372 optimal weight: 5.9990 chunk 561 optimal weight: 5.9990 chunk 517 optimal weight: 4.9990 chunk 447 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 345 optimal weight: 0.0970 chunk 274 optimal weight: 10.0000 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 372 GLN b1 372 GLN b1 376 ASN b2 372 GLN ** B3 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 266 ASN B4 372 GLN b5 268 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45516 Z= 0.204 Angle : 0.743 15.520 61572 Z= 0.364 Chirality : 0.043 0.281 6408 Planarity : 0.005 0.118 8172 Dihedral : 4.335 40.375 6350 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.28 % Favored : 94.44 % Rotamer: Outliers : 3.35 % Allowed : 28.28 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.11), residues: 5664 helix: 1.38 (0.10), residues: 2868 sheet: -0.42 (0.22), residues: 552 loop : -0.11 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPb4 115 HIS 0.004 0.001 HISb5 145 PHE 0.025 0.001 PHEB5 147 TYR 0.026 0.001 TYR B 486 ARG 0.007 0.000 ARGb2 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 842 time to evaluate : 5.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8757 (tp40) cc_final: 0.7782 (tp-100) REVERT: B 116 LYS cc_start: 0.9670 (mtmm) cc_final: 0.9381 (pttm) REVERT: B 270 GLN cc_start: 0.9661 (mm-40) cc_final: 0.9313 (mm-40) REVERT: B 399 ARG cc_start: 0.9169 (tpp80) cc_final: 0.8554 (tpp80) REVERT: B 458 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9359 (mm) REVERT: B 477 LYS cc_start: 0.9158 (mtmm) cc_final: 0.8742 (mtmt) REVERT: B 482 ARG cc_start: 0.9472 (mmm-85) cc_final: 0.9187 (mtp85) REVERT: b 78 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8788 (mm-40) REVERT: b 136 MET cc_start: 0.9288 (ptp) cc_final: 0.8886 (pmm) REVERT: b 266 ASN cc_start: 0.9546 (m-40) cc_final: 0.9254 (m110) REVERT: b 277 MET cc_start: 0.9218 (tpp) cc_final: 0.8872 (tpt) REVERT: b 399 ARG cc_start: 0.9312 (tpp80) cc_final: 0.8972 (tpp80) REVERT: b 486 TYR cc_start: 0.9081 (p90) cc_final: 0.8828 (p90) REVERT: B1 75 GLN cc_start: 0.9124 (tp40) cc_final: 0.7655 (tp-100) REVERT: B1 78 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8533 (mm-40) REVERT: B1 87 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7323 (mtp180) REVERT: B1 116 LYS cc_start: 0.9564 (pttm) cc_final: 0.9324 (pptt) REVERT: B1 136 MET cc_start: 0.9227 (ptp) cc_final: 0.8889 (ptp) REVERT: B1 137 MET cc_start: 0.9586 (tpp) cc_final: 0.9265 (mmt) REVERT: B1 144 MET cc_start: 0.9620 (ttp) cc_final: 0.8812 (tmm) REVERT: B1 238 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B1 346 ASP cc_start: 0.9285 (m-30) cc_final: 0.9081 (m-30) REVERT: B1 355 GLU cc_start: 0.8874 (pp20) cc_final: 0.8318 (pp20) REVERT: B1 356 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8507 (mm-40) REVERT: B1 360 ARG cc_start: 0.9539 (OUTLIER) cc_final: 0.8952 (ttm110) REVERT: B1 397 MET cc_start: 0.8853 (mmp) cc_final: 0.8622 (mmm) REVERT: B1 411 MET cc_start: 0.9519 (mtm) cc_final: 0.9204 (mtm) REVERT: b1 75 GLN cc_start: 0.8894 (tp40) cc_final: 0.8024 (tp-100) REVERT: b1 76 LEU cc_start: 0.9600 (mt) cc_final: 0.9321 (mt) REVERT: b1 79 ASP cc_start: 0.8609 (m-30) cc_final: 0.7897 (m-30) REVERT: b1 136 MET cc_start: 0.9461 (ptp) cc_final: 0.9076 (pmm) REVERT: b1 255 MET cc_start: 0.8973 (mtp) cc_final: 0.8654 (mpp) REVERT: b1 260 MET cc_start: 0.9052 (mtm) cc_final: 0.8647 (ptp) REVERT: b1 277 MET cc_start: 0.9073 (tpp) cc_final: 0.8688 (tpt) REVERT: b1 399 ARG cc_start: 0.9266 (tpp80) cc_final: 0.8611 (tpp80) REVERT: B2 69 TYR cc_start: 0.9625 (m-80) cc_final: 0.9112 (m-80) REVERT: B2 116 LYS cc_start: 0.9577 (ptpp) cc_final: 0.9335 (pttm) REVERT: B2 136 MET cc_start: 0.9456 (ptp) cc_final: 0.9249 (ptp) REVERT: B2 144 MET cc_start: 0.9617 (ttp) cc_final: 0.9395 (ttt) REVERT: B2 232 SER cc_start: 0.9724 (OUTLIER) cc_final: 0.9339 (p) REVERT: B2 334 MET cc_start: 0.9188 (mmm) cc_final: 0.8911 (mmm) REVERT: B2 376 ASN cc_start: 0.9573 (t0) cc_final: 0.9185 (t0) REVERT: B2 380 MET cc_start: 0.8557 (tpt) cc_final: 0.8102 (tpp) REVERT: B2 482 ARG cc_start: 0.9523 (mtp85) cc_final: 0.9194 (mtm110) REVERT: b2 75 GLN cc_start: 0.8937 (tp40) cc_final: 0.8273 (tm-30) REVERT: b2 78 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8677 (mm-40) REVERT: b2 171 MET cc_start: 0.8331 (mmm) cc_final: 0.6989 (mtt) REVERT: b2 266 ASN cc_start: 0.9308 (m110) cc_final: 0.8920 (m110) REVERT: b2 277 MET cc_start: 0.9350 (tpp) cc_final: 0.9093 (tpp) REVERT: b2 285 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8946 (tm-30) REVERT: b2 411 MET cc_start: 0.9510 (mtm) cc_final: 0.9114 (mtm) REVERT: b2 489 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9494 (mm) REVERT: B3 76 LEU cc_start: 0.9436 (mt) cc_final: 0.9107 (mt) REVERT: B3 80 HIS cc_start: 0.9153 (m-70) cc_final: 0.8648 (m-70) REVERT: B3 116 LYS cc_start: 0.9628 (ptpp) cc_final: 0.9359 (pttm) REVERT: B3 265 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8880 (mm-40) REVERT: B3 266 ASN cc_start: 0.9368 (m-40) cc_final: 0.9132 (m110) REVERT: B3 277 MET cc_start: 0.9301 (tpt) cc_final: 0.8889 (mmm) REVERT: B3 346 ASP cc_start: 0.7690 (t0) cc_final: 0.6964 (t0) REVERT: B3 397 MET cc_start: 0.8931 (mmp) cc_final: 0.8695 (mmm) REVERT: B3 460 GLU cc_start: 0.8802 (mp0) cc_final: 0.8580 (mp0) REVERT: b3 78 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8508 (mm-40) REVERT: b3 136 MET cc_start: 0.9369 (ptp) cc_final: 0.9066 (pmm) REVERT: b3 144 MET cc_start: 0.9586 (ttp) cc_final: 0.9364 (ttt) REVERT: b3 175 LYS cc_start: 0.9565 (mtmm) cc_final: 0.9186 (pttt) REVERT: b3 266 ASN cc_start: 0.9333 (m-40) cc_final: 0.9018 (m110) REVERT: b3 268 GLN cc_start: 0.9471 (tp40) cc_final: 0.9116 (tp40) REVERT: b3 380 MET cc_start: 0.8328 (mmm) cc_final: 0.7879 (tpp) REVERT: b3 399 ARG cc_start: 0.9222 (mmm-85) cc_final: 0.8734 (tpp80) REVERT: B4 69 TYR cc_start: 0.9546 (m-80) cc_final: 0.9323 (m-80) REVERT: B4 75 GLN cc_start: 0.8888 (tp40) cc_final: 0.8216 (tp-100) REVERT: B4 136 MET cc_start: 0.9285 (ptp) cc_final: 0.8860 (ptp) REVERT: B4 137 MET cc_start: 0.9545 (tpp) cc_final: 0.9058 (tpp) REVERT: B4 144 MET cc_start: 0.9622 (ttp) cc_final: 0.8715 (tmm) REVERT: B4 258 MET cc_start: 0.9530 (OUTLIER) cc_final: 0.9185 (mmm) REVERT: B4 266 ASN cc_start: 0.9344 (m-40) cc_final: 0.9081 (m110) REVERT: B4 278 TYR cc_start: 0.7919 (t80) cc_final: 0.7476 (t80) REVERT: B4 325 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8661 (pp) REVERT: B4 360 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.8972 (ttm110) REVERT: B4 487 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8711 (mp10) REVERT: b4 69 TYR cc_start: 0.9515 (m-80) cc_final: 0.9160 (m-80) REVERT: b4 75 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8489 (tp40) REVERT: b4 277 MET cc_start: 0.9105 (tpp) cc_final: 0.8686 (tpt) REVERT: b4 334 MET cc_start: 0.8772 (mmm) cc_final: 0.8461 (mmm) REVERT: b4 399 ARG cc_start: 0.9239 (tpp80) cc_final: 0.8778 (tpp80) REVERT: B5 43 GLU cc_start: 0.9085 (pm20) cc_final: 0.8831 (pm20) REVERT: B5 69 TYR cc_start: 0.9643 (m-80) cc_final: 0.9079 (m-80) REVERT: B5 75 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8427 (tp-100) REVERT: B5 78 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8502 (mm-40) REVERT: B5 91 ARG cc_start: 0.9223 (mmm160) cc_final: 0.8946 (mmm160) REVERT: B5 136 MET cc_start: 0.9397 (ptp) cc_final: 0.9189 (ptp) REVERT: B5 171 MET cc_start: 0.8609 (mmm) cc_final: 0.8163 (mtm) REVERT: B5 232 SER cc_start: 0.9674 (OUTLIER) cc_final: 0.9288 (p) REVERT: B5 258 MET cc_start: 0.9348 (mmm) cc_final: 0.8980 (mmm) REVERT: B5 277 MET cc_start: 0.9314 (tpp) cc_final: 0.9112 (tpt) REVERT: B5 285 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8041 (pp20) REVERT: B5 360 ARG cc_start: 0.9451 (OUTLIER) cc_final: 0.8864 (ttm110) REVERT: B5 399 ARG cc_start: 0.9435 (tpp80) cc_final: 0.9035 (tpp80) REVERT: B5 459 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8912 (mmtm) REVERT: B5 484 ASP cc_start: 0.8963 (m-30) cc_final: 0.8671 (m-30) REVERT: b5 69 TYR cc_start: 0.9531 (m-80) cc_final: 0.9074 (m-80) REVERT: b5 75 GLN cc_start: 0.9081 (tp40) cc_final: 0.8484 (tp-100) REVERT: b5 136 MET cc_start: 0.9422 (ptp) cc_final: 0.9136 (ptp) REVERT: b5 137 MET cc_start: 0.9425 (mmt) cc_final: 0.9116 (tpp) REVERT: b5 144 MET cc_start: 0.9637 (ttp) cc_final: 0.8770 (tmm) REVERT: b5 270 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8856 (mm-40) REVERT: b5 334 MET cc_start: 0.9752 (mmm) cc_final: 0.9082 (mmm) outliers start: 150 outliers final: 122 residues processed: 954 average time/residue: 0.5582 time to fit residues: 868.0905 Evaluate side-chains 960 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 825 time to evaluate : 5.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 77 HIS Chi-restraints excluded: chain b residue 78 GLN Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 458 LEU Chi-restraints excluded: chain B1 residue 43 GLU Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 484 ASP Chi-restraints excluded: chain b1 residue 93 SER Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 254 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 368 VAL Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 181 ASN Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 232 SER Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 43 GLU Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 489 ILE Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 181 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 281 THR Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 343 THR Chi-restraints excluded: chain B3 residue 368 VAL Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 77 HIS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 430 LYS Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 467 LEU Chi-restraints excluded: chain B4 residue 256 GLU Chi-restraints excluded: chain B4 residue 258 MET Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 371 GLU Chi-restraints excluded: chain B4 residue 384 THR Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 468 ILE Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 77 HIS Chi-restraints excluded: chain b4 residue 93 SER Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 241 GLU Chi-restraints excluded: chain b4 residue 254 VAL Chi-restraints excluded: chain b4 residue 355 GLU Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 381 SER Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 462 GLN Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 232 SER Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 163 ARG Chi-restraints excluded: chain b5 residue 268 GLN Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 360 ARG Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 355 optimal weight: 9.9990 chunk 476 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 412 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 448 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 460 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 372 GLN b1 372 GLN b2 372 GLN ** B3 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 372 GLN ** b5 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.071960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.058643 restraints weight = 175179.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.060352 restraints weight = 100740.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.061492 restraints weight = 69096.825| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 45516 Z= 0.252 Angle : 0.800 59.185 61572 Z= 0.411 Chirality : 0.045 0.968 6408 Planarity : 0.005 0.118 8172 Dihedral : 4.332 40.451 6350 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.23 % Favored : 94.49 % Rotamer: Outliers : 3.28 % Allowed : 28.71 % Favored : 68.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.11), residues: 5664 helix: 1.37 (0.10), residues: 2868 sheet: -0.42 (0.22), residues: 552 loop : -0.11 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRPb5 393 HIS 0.006 0.001 HISB3 80 PHE 0.024 0.001 PHEB5 147 TYR 0.031 0.001 TYRB3 395 ARG 0.008 0.000 ARGb4 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12723.20 seconds wall clock time: 227 minutes 3.64 seconds (13623.64 seconds total)