Starting phenix.real_space_refine on Sat May 24 11:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i51_35190/05_2025/8i51_35190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i51_35190/05_2025/8i51_35190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i51_35190/05_2025/8i51_35190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i51_35190/05_2025/8i51_35190.map" model { file = "/net/cci-nas-00/data/ceres_data/8i51_35190/05_2025/8i51_35190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i51_35190/05_2025/8i51_35190_neut.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.141 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 6 5.21 5 S 108 5.16 5 C 16266 2.51 5 N 4254 2.21 5 O 4776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25416 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 14.93, per 1000 atoms: 0.59 Number of scatterers: 25416 At special positions: 0 Unit cell: (169.338, 158.184, 94.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 6 15.00 Mg 6 11.99 O 4776 8.00 N 4254 7.00 C 16266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.54 Conformation dependent library (CDL) restraints added in 3.4 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 36.4% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 3.750A pdb=" N LEU A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 59 removed outlier: 3.574A pdb=" N GLY A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.524A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 3.547A pdb=" N GLY A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.572A pdb=" N GLN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.924A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.525A pdb=" N THR A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.545A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.591A pdb=" N LEU A 337 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.567A pdb=" N LYS A 399 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.622A pdb=" N ALA A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.524A pdb=" N LYS A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.750A pdb=" N LEU B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 59 removed outlier: 3.574A pdb=" N GLY B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.523A pdb=" N LEU B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.547A pdb=" N GLY B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.572A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.924A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.525A pdb=" N THR B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.545A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.591A pdb=" N LEU B 337 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 349 Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.567A pdb=" N LYS B 399 " --> pdb=" O ASN B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 Processing helix chain 'B' and resid 440 through 447 Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.622A pdb=" N ALA B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.524A pdb=" N LYS B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.750A pdb=" N LEU C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 59 removed outlier: 3.575A pdb=" N GLY C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.524A pdb=" N LEU C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.546A pdb=" N GLY C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.572A pdb=" N GLN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.924A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 removed outlier: 3.525A pdb=" N THR C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.545A pdb=" N ASN C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.591A pdb=" N LEU C 337 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 349 Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.568A pdb=" N LYS C 399 " --> pdb=" O ASN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 406 Processing helix chain 'C' and resid 440 through 447 Processing helix chain 'C' and resid 483 through 493 removed outlier: 3.623A pdb=" N ALA C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 493 " --> pdb=" O GLY C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.525A pdb=" N LYS C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.749A pdb=" N LEU D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 59 removed outlier: 3.574A pdb=" N GLY D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.524A pdb=" N LEU D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.547A pdb=" N GLY D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.573A pdb=" N GLN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.924A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 removed outlier: 3.525A pdb=" N THR D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.545A pdb=" N ASN D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.591A pdb=" N LEU D 337 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 349 Processing helix chain 'D' and resid 395 through 402 removed outlier: 3.567A pdb=" N LYS D 399 " --> pdb=" O ASN D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 406 Processing helix chain 'D' and resid 440 through 447 Processing helix chain 'D' and resid 483 through 493 removed outlier: 3.623A pdb=" N ALA D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.524A pdb=" N LYS D 530 " --> pdb=" O LYS D 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.750A pdb=" N LEU E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 59 removed outlier: 3.575A pdb=" N GLY E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 removed outlier: 3.524A pdb=" N LEU E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix removed outlier: 3.546A pdb=" N GLY E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.572A pdb=" N GLN E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.924A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.524A pdb=" N THR E 202 " --> pdb=" O GLY E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 230 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.545A pdb=" N ASN E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.591A pdb=" N LEU E 337 " --> pdb=" O PRO E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 349 Processing helix chain 'E' and resid 395 through 402 removed outlier: 3.566A pdb=" N LYS E 399 " --> pdb=" O ASN E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 406 Processing helix chain 'E' and resid 440 through 447 Processing helix chain 'E' and resid 483 through 493 removed outlier: 3.622A pdb=" N ALA E 491 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP E 493 " --> pdb=" O GLY E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 532 removed outlier: 3.524A pdb=" N LYS E 530 " --> pdb=" O LYS E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 21 removed outlier: 3.750A pdb=" N LEU F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 59 removed outlier: 3.574A pdb=" N GLY F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 87 removed outlier: 3.524A pdb=" N LEU F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix removed outlier: 3.546A pdb=" N GLY F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.572A pdb=" N GLN F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.924A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 204 removed outlier: 3.525A pdb=" N THR F 202 " --> pdb=" O GLY F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 230 Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.546A pdb=" N ASN F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 333 through 337 removed outlier: 3.591A pdb=" N LEU F 337 " --> pdb=" O PRO F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 349 Processing helix chain 'F' and resid 395 through 402 removed outlier: 3.567A pdb=" N LYS F 399 " --> pdb=" O ASN F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 406 Processing helix chain 'F' and resid 440 through 447 Processing helix chain 'F' and resid 483 through 493 removed outlier: 3.622A pdb=" N ALA F 491 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP F 493 " --> pdb=" O GLY F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 532 removed outlier: 3.524A pdb=" N LYS F 530 " --> pdb=" O LYS F 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 5.806A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER A 266 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 292 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY A 317 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 294 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLY A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA A 316 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE A 329 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR A 318 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.416A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.367A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 463 removed outlier: 3.817A pdb=" N GLU A 455 " --> pdb=" O THR A 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 40 removed outlier: 5.807A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER B 266 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL B 292 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY B 317 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 294 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLY B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA B 316 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE B 329 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR B 318 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.415A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.367A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 430 through 431 Processing sheet with id=AB1, first strand: chain 'B' and resid 453 through 463 removed outlier: 3.817A pdb=" N GLU B 455 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 40 removed outlier: 5.805A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER C 266 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL C 292 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY C 317 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 294 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N GLY C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA C 316 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE C 329 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR C 318 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.416A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C 66 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.366A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AB6, first strand: chain 'C' and resid 453 through 463 removed outlier: 3.817A pdb=" N GLU C 455 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 37 through 40 removed outlier: 5.806A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER D 266 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL D 292 " --> pdb=" O PHE D 315 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY D 317 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 294 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLY D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA D 316 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE D 329 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR D 318 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.416A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 66 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.367A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 430 through 431 Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 463 removed outlier: 3.817A pdb=" N GLU D 455 " --> pdb=" O THR D 475 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 37 through 40 removed outlier: 5.807A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SER E 266 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL E 292 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY E 317 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE E 294 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLY E 319 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA E 316 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE E 329 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR E 318 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.415A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL E 66 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 361 through 363 removed outlier: 5.366A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 430 through 431 Processing sheet with id=AC7, first strand: chain 'E' and resid 453 through 463 removed outlier: 3.818A pdb=" N GLU E 455 " --> pdb=" O THR E 475 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 37 through 40 removed outlier: 5.806A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SER F 266 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL F 292 " --> pdb=" O PHE F 315 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY F 317 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE F 294 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLY F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA F 316 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE F 329 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR F 318 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.416A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL F 66 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 361 through 363 removed outlier: 5.367A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 430 through 431 Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 463 removed outlier: 3.817A pdb=" N GLU F 455 " --> pdb=" O THR F 475 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2340 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: 10.06 Time building geometry restraints manager: 7.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4266 1.27 - 1.41: 6367 1.41 - 1.54: 15005 1.54 - 1.68: 150 1.68 - 1.81: 192 Bond restraints: 25980 Sorted by residual: bond pdb=" CA ASP F 72 " pdb=" C ASP F 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.96e+01 bond pdb=" CA ASP C 72 " pdb=" C ASP C 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.95e+01 bond pdb=" CA ASP A 72 " pdb=" C ASP A 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.95e+01 bond pdb=" CA ASP B 72 " pdb=" C ASP B 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.93e+01 bond pdb=" CA ASP E 72 " pdb=" C ASP E 72 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.23e-02 6.61e+03 7.87e+01 ... (remaining 25975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 33916 2.72 - 5.44: 1064 5.44 - 8.15: 210 8.15 - 10.87: 30 10.87 - 13.59: 18 Bond angle restraints: 35238 Sorted by residual: angle pdb=" N HIS C 448 " pdb=" CA HIS C 448 " pdb=" C HIS C 448 " ideal model delta sigma weight residual 114.04 100.45 13.59 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS D 448 " pdb=" CA HIS D 448 " pdb=" C HIS D 448 " ideal model delta sigma weight residual 114.04 100.46 13.58 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS B 448 " pdb=" CA HIS B 448 " pdb=" C HIS B 448 " ideal model delta sigma weight residual 114.04 100.47 13.57 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS A 448 " pdb=" CA HIS A 448 " pdb=" C HIS A 448 " ideal model delta sigma weight residual 114.04 100.48 13.56 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS E 448 " pdb=" CA HIS E 448 " pdb=" C HIS E 448 " ideal model delta sigma weight residual 114.04 100.49 13.55 1.24e+00 6.50e-01 1.19e+02 ... (remaining 35233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 15060 35.53 - 71.06: 477 71.06 - 106.59: 30 106.59 - 142.12: 0 142.12 - 177.65: 3 Dihedral angle restraints: 15570 sinusoidal: 6342 harmonic: 9228 Sorted by residual: dihedral pdb=" C5' AMP A 602 " pdb=" O5' AMP A 602 " pdb=" P AMP A 602 " pdb=" O3P AMP A 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.35 177.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' AMP C 602 " pdb=" O5' AMP C 602 " pdb=" P AMP C 602 " pdb=" O3P AMP C 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.36 177.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' AMP E 602 " pdb=" O5' AMP E 602 " pdb=" P AMP E 602 " pdb=" O3P AMP E 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.36 177.65 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 15567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3649 0.129 - 0.258: 185 0.258 - 0.388: 84 0.388 - 0.517: 42 0.517 - 0.646: 24 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CB VAL D 253 " pdb=" CA VAL D 253 " pdb=" CG1 VAL D 253 " pdb=" CG2 VAL D 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.98 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CB VAL B 253 " pdb=" CA VAL B 253 " pdb=" CG1 VAL B 253 " pdb=" CG2 VAL B 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CB VAL E 253 " pdb=" CA VAL E 253 " pdb=" CG1 VAL E 253 " pdb=" CG2 VAL E 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 3981 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 338 " 0.022 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C GLU D 338 " -0.082 2.00e-02 2.50e+03 pdb=" O GLU D 338 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU D 339 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 338 " 0.022 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C GLU B 338 " -0.082 2.00e-02 2.50e+03 pdb=" O GLU B 338 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU B 339 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 338 " -0.022 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C GLU A 338 " 0.082 2.00e-02 2.50e+03 pdb=" O GLU A 338 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU A 339 " -0.028 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 714 2.68 - 3.24: 23538 3.24 - 3.79: 39035 3.79 - 4.35: 56172 4.35 - 4.90: 91490 Nonbonded interactions: 210949 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O3P AMP B 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3P AMP D 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1P AMP A 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1P AMP C 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG E 601 " pdb=" O1P AMP E 602 " model vdw 2.130 2.170 ... (remaining 210944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.440 Check model and map are aligned: 0.000 Set scattering table: 0.200 Process input model: 59.040 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.120 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:15.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.013 0.258 25986 Z= 0.957 Angle : 1.104 13.588 35238 Z= 0.685 Chirality : 0.100 0.646 3984 Planarity : 0.007 0.048 4470 Dihedral : 16.675 177.648 9630 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.49 % Favored : 91.32 % Rotamer: Outliers : 0.69 % Allowed : 20.01 % Favored : 79.30 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.14), residues: 3156 helix: -0.50 (0.16), residues: 1062 sheet: -0.60 (0.24), residues: 522 loop : -2.00 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 437 HIS 0.013 0.001 HIS F 408 PHE 0.007 0.001 PHE E 315 TYR 0.020 0.002 TYR F 174 ARG 0.007 0.000 ARG C 426 Details of bonding type rmsd hydrogen bonds : bond 0.22578 ( 846) hydrogen bonds : angle 7.51124 ( 2340) covalent geometry : bond 0.01212 (25980) covalent geometry : angle 1.10415 (35238) Misc. bond : bond 0.25722 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 2.930 Fit side-chains REVERT: A 367 MET cc_start: 0.8170 (mmm) cc_final: 0.7935 (mmm) REVERT: C 58 MET cc_start: 0.8321 (mtt) cc_final: 0.8055 (mtt) REVERT: C 224 MET cc_start: 0.8407 (ttt) cc_final: 0.7925 (ttt) REVERT: C 343 GLN cc_start: 0.8054 (tt0) cc_final: 0.7761 (mp10) REVERT: D 58 MET cc_start: 0.8302 (mtt) cc_final: 0.8035 (mtt) REVERT: D 224 MET cc_start: 0.8491 (ttt) cc_final: 0.7811 (ttt) REVERT: D 275 LEU cc_start: 0.8395 (mt) cc_final: 0.8093 (mp) REVERT: D 343 GLN cc_start: 0.8234 (tt0) cc_final: 0.7905 (mp10) REVERT: E 96 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7991 (mpt-90) REVERT: E 224 MET cc_start: 0.8355 (ttt) cc_final: 0.7990 (ttt) REVERT: F 342 ASP cc_start: 0.7504 (t0) cc_final: 0.7279 (t0) REVERT: F 343 GLN cc_start: 0.8027 (tt0) cc_final: 0.7733 (mm-40) REVERT: F 367 MET cc_start: 0.8176 (mmm) cc_final: 0.7957 (mmm) outliers start: 19 outliers final: 3 residues processed: 252 average time/residue: 1.3276 time to fit residues: 389.6718 Evaluate side-chains 193 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 29 GLN A 117 HIS A 206 ASN A 209 GLN A 213 HIS A 226 HIS A 256 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN B 29 GLN B 117 HIS B 206 ASN B 209 GLN B 213 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN C 29 GLN C 117 HIS C 206 ASN C 209 GLN C 213 HIS C 226 HIS C 256 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN D 29 GLN D 117 HIS D 206 ASN D 209 GLN D 213 HIS D 256 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 29 GLN E 117 HIS E 206 ASN E 209 GLN E 213 HIS E 226 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 GLN F 29 GLN F 117 HIS F 206 ASN F 209 GLN F 213 HIS F 226 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117032 restraints weight = 29894.617| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.98 r_work: 0.3266 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25986 Z= 0.142 Angle : 0.631 8.064 35238 Z= 0.320 Chirality : 0.048 0.160 3984 Planarity : 0.004 0.037 4470 Dihedral : 6.969 130.474 3522 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.05 % Favored : 91.76 % Rotamer: Outliers : 2.47 % Allowed : 19.68 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3156 helix: 0.24 (0.16), residues: 1050 sheet: -0.79 (0.22), residues: 570 loop : -1.59 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 466 HIS 0.004 0.001 HIS B 213 PHE 0.008 0.001 PHE E 81 TYR 0.010 0.001 TYR D 174 ARG 0.002 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 846) hydrogen bonds : angle 5.19740 ( 2340) covalent geometry : bond 0.00324 (25980) covalent geometry : angle 0.63139 (35238) Misc. bond : bond 0.00020 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 3.114 Fit side-chains REVERT: A 281 LYS cc_start: 0.7491 (tttm) cc_final: 0.7107 (tttm) REVERT: A 461 MET cc_start: 0.3925 (ppp) cc_final: 0.3307 (tmm) REVERT: A 530 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6101 (mtpt) REVERT: B 461 MET cc_start: 0.4617 (ppp) cc_final: 0.3726 (tmm) REVERT: B 530 LYS cc_start: 0.6287 (OUTLIER) cc_final: 0.5980 (mtpp) REVERT: C 346 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: C 461 MET cc_start: 0.4677 (ppp) cc_final: 0.3996 (tpp) REVERT: C 530 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5951 (mtpt) REVERT: D 275 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8078 (mp) REVERT: D 346 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: D 461 MET cc_start: 0.4495 (ppp) cc_final: 0.3802 (tpp) REVERT: D 530 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.6140 (mtpt) REVERT: E 530 LYS cc_start: 0.6266 (OUTLIER) cc_final: 0.5949 (mtpt) REVERT: F 395 ASN cc_start: 0.8293 (m110) cc_final: 0.8057 (m-40) REVERT: F 461 MET cc_start: 0.4478 (ppp) cc_final: 0.4042 (tpp) REVERT: F 530 LYS cc_start: 0.6444 (OUTLIER) cc_final: 0.6049 (mtpt) outliers start: 68 outliers final: 28 residues processed: 274 average time/residue: 1.3227 time to fit residues: 424.2337 Evaluate side-chains 231 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 530 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 530 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 289 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 91 optimal weight: 0.0470 chunk 169 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 254 optimal weight: 20.0000 chunk 236 optimal weight: 0.7980 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 HIS ** C 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 226 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 HIS F 226 HIS F 256 ASN ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.169034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118737 restraints weight = 29789.842| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.34 r_work: 0.3259 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25986 Z= 0.131 Angle : 0.588 7.420 35238 Z= 0.297 Chirality : 0.047 0.154 3984 Planarity : 0.004 0.043 4470 Dihedral : 6.485 98.313 3520 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.64 % Favored : 92.17 % Rotamer: Outliers : 3.56 % Allowed : 18.66 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.15), residues: 3156 helix: 0.54 (0.16), residues: 1050 sheet: -0.88 (0.21), residues: 570 loop : -1.52 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 402 HIS 0.003 0.001 HIS C 36 PHE 0.011 0.001 PHE A 225 TYR 0.009 0.001 TYR D 174 ARG 0.003 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 846) hydrogen bonds : angle 4.86676 ( 2340) covalent geometry : bond 0.00299 (25980) covalent geometry : angle 0.58766 (35238) Misc. bond : bond 0.00039 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 213 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8402 (m) REVERT: A 343 GLN cc_start: 0.8343 (mp10) cc_final: 0.7850 (mp10) REVERT: A 416 ASP cc_start: 0.7748 (t0) cc_final: 0.7265 (t0) REVERT: A 417 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: A 461 MET cc_start: 0.4015 (ppp) cc_final: 0.3541 (tmm) REVERT: A 531 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5902 (mp) REVERT: B 343 GLN cc_start: 0.7889 (mp10) cc_final: 0.7575 (mp10) REVERT: B 461 MET cc_start: 0.4391 (ppp) cc_final: 0.3929 (tmm) REVERT: C 43 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8411 (m) REVERT: C 224 MET cc_start: 0.8585 (ttt) cc_final: 0.8147 (ttt) REVERT: C 346 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: C 417 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: D 43 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8401 (m) REVERT: D 275 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8016 (mp) REVERT: D 346 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: D 417 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: E 340 ASP cc_start: 0.7302 (p0) cc_final: 0.7042 (p0) REVERT: E 343 GLN cc_start: 0.7859 (mt0) cc_final: 0.7528 (mp-120) REVERT: F 43 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8449 (m) REVERT: F 395 ASN cc_start: 0.8300 (m110) cc_final: 0.8069 (m-40) REVERT: F 417 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7367 (m-30) outliers start: 98 outliers final: 46 residues processed: 294 average time/residue: 1.2373 time to fit residues: 425.6645 Evaluate side-chains 250 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 154 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 239 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.169191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119709 restraints weight = 30167.591| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.51 r_work: 0.3268 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25986 Z= 0.115 Angle : 0.574 8.920 35238 Z= 0.289 Chirality : 0.047 0.148 3984 Planarity : 0.004 0.044 4470 Dihedral : 6.258 68.829 3520 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.14 % Favored : 91.67 % Rotamer: Outliers : 3.41 % Allowed : 19.32 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3156 helix: 0.60 (0.17), residues: 1044 sheet: -0.72 (0.22), residues: 564 loop : -1.50 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 402 HIS 0.003 0.001 HIS B 36 PHE 0.009 0.001 PHE F 225 TYR 0.007 0.001 TYR C 148 ARG 0.005 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 846) hydrogen bonds : angle 4.70815 ( 2340) covalent geometry : bond 0.00259 (25980) covalent geometry : angle 0.57371 (35238) Misc. bond : bond 0.00035 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 213 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8417 (m) REVERT: A 343 GLN cc_start: 0.8199 (mp10) cc_final: 0.7839 (mp10) REVERT: A 416 ASP cc_start: 0.7771 (t0) cc_final: 0.7307 (t0) REVERT: A 461 MET cc_start: 0.3764 (ppp) cc_final: 0.3530 (tmm) REVERT: A 531 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5853 (mp) REVERT: B 337 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7656 (mp) REVERT: B 343 GLN cc_start: 0.7881 (mp10) cc_final: 0.7616 (mp10) REVERT: B 452 SER cc_start: 0.4328 (OUTLIER) cc_final: 0.3849 (t) REVERT: B 461 MET cc_start: 0.4385 (ppp) cc_final: 0.4006 (tmm) REVERT: B 531 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5917 (mp) REVERT: C 172 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8392 (p) REVERT: C 224 MET cc_start: 0.8508 (ttt) cc_final: 0.8147 (ttt) REVERT: C 346 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: C 452 SER cc_start: 0.3635 (OUTLIER) cc_final: 0.3117 (t) REVERT: C 461 MET cc_start: 0.4029 (ppp) cc_final: 0.3742 (tmm) REVERT: D 172 THR cc_start: 0.8754 (m) cc_final: 0.8427 (p) REVERT: D 224 MET cc_start: 0.8618 (ttt) cc_final: 0.8151 (ttt) REVERT: D 275 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8030 (mp) REVERT: D 461 MET cc_start: 0.4018 (ppp) cc_final: 0.3469 (tpp) REVERT: E 337 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7720 (mp) REVERT: E 340 ASP cc_start: 0.7397 (p0) cc_final: 0.7042 (p0) REVERT: E 343 GLN cc_start: 0.7909 (mt0) cc_final: 0.7367 (mp10) REVERT: F 43 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8459 (m) REVERT: F 58 MET cc_start: 0.8104 (mtt) cc_final: 0.7858 (mtt) REVERT: F 417 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7373 (m-30) outliers start: 94 outliers final: 34 residues processed: 282 average time/residue: 1.2543 time to fit residues: 415.4777 Evaluate side-chains 243 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 449 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 308 optimal weight: 20.0000 chunk 231 optimal weight: 1.9990 chunk 296 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 119 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 257 optimal weight: 0.0370 chunk 214 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 198 optimal weight: 0.0670 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 HIS F 226 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS F 532 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118995 restraints weight = 30106.867| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.18 r_work: 0.3268 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25986 Z= 0.112 Angle : 0.571 8.175 35238 Z= 0.289 Chirality : 0.047 0.163 3984 Planarity : 0.004 0.044 4470 Dihedral : 6.079 56.756 3520 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.60 % Favored : 92.21 % Rotamer: Outliers : 3.38 % Allowed : 19.86 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 3156 helix: 0.55 (0.17), residues: 1080 sheet: -0.63 (0.22), residues: 564 loop : -1.53 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 402 HIS 0.003 0.001 HIS B 267 PHE 0.009 0.001 PHE F 225 TYR 0.007 0.001 TYR C 148 ARG 0.006 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 846) hydrogen bonds : angle 4.60310 ( 2340) covalent geometry : bond 0.00250 (25980) covalent geometry : angle 0.57130 (35238) Misc. bond : bond 0.00035 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 211 time to evaluate : 2.772 Fit side-chains revert: symmetry clash REVERT: A 343 GLN cc_start: 0.8175 (mp10) cc_final: 0.7723 (mp10) REVERT: A 416 ASP cc_start: 0.7844 (t0) cc_final: 0.7382 (t0) REVERT: A 461 MET cc_start: 0.3896 (ppp) cc_final: 0.3635 (tmm) REVERT: A 531 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5904 (mp) REVERT: B 76 TYR cc_start: 0.9241 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: B 337 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7628 (mp) REVERT: B 343 GLN cc_start: 0.7884 (mp10) cc_final: 0.7633 (mp10) REVERT: B 452 SER cc_start: 0.4366 (OUTLIER) cc_final: 0.3970 (t) REVERT: B 461 MET cc_start: 0.4561 (ppp) cc_final: 0.4072 (tmm) REVERT: B 531 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5843 (mp) REVERT: C 141 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8066 (mtp85) REVERT: C 172 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8379 (p) REVERT: C 224 MET cc_start: 0.8548 (ttt) cc_final: 0.8220 (ttt) REVERT: C 452 SER cc_start: 0.3485 (OUTLIER) cc_final: 0.2980 (t) REVERT: C 461 MET cc_start: 0.4030 (ppp) cc_final: 0.3746 (tmm) REVERT: D 172 THR cc_start: 0.8725 (m) cc_final: 0.8415 (p) REVERT: D 224 MET cc_start: 0.8566 (ttt) cc_final: 0.8191 (ttt) REVERT: D 275 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7994 (mp) REVERT: D 461 MET cc_start: 0.4254 (ppp) cc_final: 0.3833 (tpp) REVERT: E 76 TYR cc_start: 0.9251 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: E 337 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7678 (mp) REVERT: E 340 ASP cc_start: 0.7287 (p0) cc_final: 0.7041 (p0) REVERT: E 343 GLN cc_start: 0.7905 (mt0) cc_final: 0.7555 (mp-120) REVERT: E 452 SER cc_start: 0.4512 (OUTLIER) cc_final: 0.3998 (t) REVERT: F 58 MET cc_start: 0.8139 (mtt) cc_final: 0.7897 (mtt) REVERT: F 461 MET cc_start: 0.4386 (ppp) cc_final: 0.3965 (tmm) outliers start: 93 outliers final: 35 residues processed: 280 average time/residue: 1.2540 time to fit residues: 412.1613 Evaluate side-chains 242 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 244 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 69 optimal weight: 0.0170 chunk 111 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.164609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.117222 restraints weight = 28742.928| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.87 r_work: 0.3124 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25986 Z= 0.141 Angle : 0.594 9.152 35238 Z= 0.301 Chirality : 0.048 0.209 3984 Planarity : 0.004 0.050 4470 Dihedral : 6.017 57.800 3518 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.24 % Favored : 91.57 % Rotamer: Outliers : 3.20 % Allowed : 20.23 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3156 helix: 0.57 (0.17), residues: 1080 sheet: -0.62 (0.22), residues: 564 loop : -1.54 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 402 HIS 0.004 0.001 HIS B 39 PHE 0.010 0.001 PHE F 225 TYR 0.008 0.001 TYR F 318 ARG 0.006 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 846) hydrogen bonds : angle 4.64898 ( 2340) covalent geometry : bond 0.00330 (25980) covalent geometry : angle 0.59405 (35238) Misc. bond : bond 0.00036 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 202 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.8310 (mp10) cc_final: 0.7843 (mp10) REVERT: A 416 ASP cc_start: 0.7946 (t0) cc_final: 0.7528 (t0) REVERT: A 429 ASP cc_start: 0.7138 (m-30) cc_final: 0.6583 (m-30) REVERT: A 531 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5813 (mp) REVERT: B 337 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 343 GLN cc_start: 0.7983 (mp10) cc_final: 0.7689 (mp10) REVERT: B 452 SER cc_start: 0.4362 (OUTLIER) cc_final: 0.3970 (t) REVERT: B 461 MET cc_start: 0.4059 (ppp) cc_final: 0.3573 (tmm) REVERT: B 531 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6070 (mp) REVERT: C 224 MET cc_start: 0.8666 (ttt) cc_final: 0.8233 (ttt) REVERT: C 346 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: C 452 SER cc_start: 0.3610 (OUTLIER) cc_final: 0.3076 (t) REVERT: C 461 MET cc_start: 0.4045 (ppp) cc_final: 0.3749 (tmm) REVERT: D 224 MET cc_start: 0.8650 (ttt) cc_final: 0.8332 (ttt) REVERT: D 275 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8120 (mp) REVERT: D 461 MET cc_start: 0.4190 (ppp) cc_final: 0.3770 (tpp) REVERT: E 76 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: E 337 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7904 (mp) REVERT: E 343 GLN cc_start: 0.7963 (mt0) cc_final: 0.7546 (mp10) REVERT: E 452 SER cc_start: 0.4759 (OUTLIER) cc_final: 0.4200 (t) REVERT: F 58 MET cc_start: 0.8303 (mtt) cc_final: 0.8077 (mtt) REVERT: F 461 MET cc_start: 0.4403 (ppp) cc_final: 0.3836 (tmm) outliers start: 88 outliers final: 45 residues processed: 267 average time/residue: 1.2401 time to fit residues: 388.5506 Evaluate side-chains 248 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 121 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 302 optimal weight: 0.0020 chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 290 optimal weight: 4.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119302 restraints weight = 29608.553| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.97 r_work: 0.3137 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25986 Z= 0.129 Angle : 0.583 7.379 35238 Z= 0.295 Chirality : 0.047 0.151 3984 Planarity : 0.004 0.047 4470 Dihedral : 5.960 59.524 3518 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.64 % Favored : 92.17 % Rotamer: Outliers : 3.05 % Allowed : 20.81 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3156 helix: 0.61 (0.17), residues: 1080 sheet: -0.60 (0.22), residues: 564 loop : -1.49 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 402 HIS 0.004 0.001 HIS E 267 PHE 0.009 0.001 PHE F 225 TYR 0.007 0.001 TYR B 104 ARG 0.007 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 846) hydrogen bonds : angle 4.61584 ( 2340) covalent geometry : bond 0.00298 (25980) covalent geometry : angle 0.58295 (35238) Misc. bond : bond 0.00033 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 204 time to evaluate : 3.142 Fit side-chains REVERT: A 343 GLN cc_start: 0.8342 (mp10) cc_final: 0.7865 (mp10) REVERT: A 416 ASP cc_start: 0.7974 (t0) cc_final: 0.7543 (t0) REVERT: A 452 SER cc_start: 0.3343 (OUTLIER) cc_final: 0.2979 (t) REVERT: A 531 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5771 (mp) REVERT: B 76 TYR cc_start: 0.9273 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: B 337 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7820 (mp) REVERT: B 343 GLN cc_start: 0.8034 (mp10) cc_final: 0.7722 (mp10) REVERT: B 452 SER cc_start: 0.4373 (OUTLIER) cc_final: 0.3961 (t) REVERT: B 461 MET cc_start: 0.3991 (ppp) cc_final: 0.3554 (tmm) REVERT: B 531 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6096 (mp) REVERT: C 172 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8536 (p) REVERT: C 452 SER cc_start: 0.3923 (OUTLIER) cc_final: 0.3361 (t) REVERT: C 461 MET cc_start: 0.3998 (ppp) cc_final: 0.3749 (tmm) REVERT: D 172 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8550 (p) REVERT: D 224 MET cc_start: 0.8665 (ttt) cc_final: 0.8206 (ttt) REVERT: D 275 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8149 (tp) REVERT: D 461 MET cc_start: 0.4078 (ppp) cc_final: 0.3808 (tpp) REVERT: E 76 TYR cc_start: 0.9290 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: E 337 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7914 (mp) REVERT: E 343 GLN cc_start: 0.7922 (mt0) cc_final: 0.7631 (mp10) REVERT: E 452 SER cc_start: 0.4688 (OUTLIER) cc_final: 0.4121 (t) REVERT: E 530 LYS cc_start: 0.5978 (OUTLIER) cc_final: 0.5339 (mttp) REVERT: F 58 MET cc_start: 0.8260 (mtt) cc_final: 0.8032 (mtt) REVERT: F 452 SER cc_start: 0.3471 (OUTLIER) cc_final: 0.3187 (t) REVERT: F 461 MET cc_start: 0.4298 (ppp) cc_final: 0.3557 (tmm) outliers start: 84 outliers final: 38 residues processed: 263 average time/residue: 1.2649 time to fit residues: 389.9535 Evaluate side-chains 244 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 311 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 61 optimal weight: 0.0870 chunk 276 optimal weight: 0.9990 chunk 118 optimal weight: 0.0570 chunk 43 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 overall best weight: 1.2280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.165018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117869 restraints weight = 29367.138| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.03 r_work: 0.3149 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25986 Z= 0.145 Angle : 0.604 14.747 35238 Z= 0.304 Chirality : 0.048 0.154 3984 Planarity : 0.004 0.041 4470 Dihedral : 5.958 59.062 3518 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.08 % Favored : 91.73 % Rotamer: Outliers : 3.05 % Allowed : 20.92 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3156 helix: 0.58 (0.17), residues: 1080 sheet: -0.58 (0.22), residues: 564 loop : -1.48 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 290 HIS 0.004 0.001 HIS E 39 PHE 0.010 0.001 PHE F 225 TYR 0.009 0.001 TYR F 174 ARG 0.006 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 846) hydrogen bonds : angle 4.64540 ( 2340) covalent geometry : bond 0.00341 (25980) covalent geometry : angle 0.60415 (35238) Misc. bond : bond 0.00033 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 190 time to evaluate : 3.189 Fit side-chains REVERT: A 343 GLN cc_start: 0.8325 (mp10) cc_final: 0.7823 (mp10) REVERT: A 416 ASP cc_start: 0.8015 (t0) cc_final: 0.7595 (t0) REVERT: A 452 SER cc_start: 0.3482 (OUTLIER) cc_final: 0.3121 (t) REVERT: A 461 MET cc_start: 0.3821 (ppp) cc_final: 0.3454 (tmm) REVERT: A 531 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5757 (mp) REVERT: B 76 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.6769 (m-80) REVERT: B 337 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 343 GLN cc_start: 0.8031 (mp10) cc_final: 0.7787 (mp10) REVERT: B 452 SER cc_start: 0.4331 (OUTLIER) cc_final: 0.3943 (t) REVERT: B 461 MET cc_start: 0.3969 (ppp) cc_final: 0.3547 (tmm) REVERT: B 531 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6123 (mp) REVERT: C 346 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: C 452 SER cc_start: 0.3925 (OUTLIER) cc_final: 0.3361 (t) REVERT: C 461 MET cc_start: 0.4226 (ppp) cc_final: 0.3917 (tmm) REVERT: D 275 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8151 (tp) REVERT: D 461 MET cc_start: 0.4062 (ppp) cc_final: 0.3792 (tpp) REVERT: E 76 TYR cc_start: 0.9292 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: E 337 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7954 (mp) REVERT: E 343 GLN cc_start: 0.7939 (mt0) cc_final: 0.7609 (mp10) REVERT: E 452 SER cc_start: 0.4540 (OUTLIER) cc_final: 0.4049 (t) REVERT: E 530 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5335 (mttp) REVERT: F 58 MET cc_start: 0.8264 (mtt) cc_final: 0.8057 (mtt) REVERT: F 281 LYS cc_start: 0.7517 (tttm) cc_final: 0.7237 (tttm) REVERT: F 452 SER cc_start: 0.3481 (OUTLIER) cc_final: 0.3246 (t) REVERT: F 461 MET cc_start: 0.4343 (ppp) cc_final: 0.3864 (tmm) outliers start: 84 outliers final: 44 residues processed: 253 average time/residue: 1.2366 time to fit residues: 368.5123 Evaluate side-chains 246 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 130 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 289 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.165028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117430 restraints weight = 29486.869| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.10 r_work: 0.3151 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25986 Z= 0.143 Angle : 0.604 14.607 35238 Z= 0.304 Chirality : 0.048 0.189 3984 Planarity : 0.004 0.042 4470 Dihedral : 5.916 57.261 3518 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.89 % Rotamer: Outliers : 2.83 % Allowed : 21.35 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3156 helix: 0.77 (0.17), residues: 1044 sheet: -0.58 (0.22), residues: 564 loop : -1.41 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 402 HIS 0.004 0.001 HIS E 267 PHE 0.010 0.001 PHE F 225 TYR 0.008 0.001 TYR F 318 ARG 0.006 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 846) hydrogen bonds : angle 4.64782 ( 2340) covalent geometry : bond 0.00334 (25980) covalent geometry : angle 0.60378 (35238) Misc. bond : bond 0.00031 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 193 time to evaluate : 3.196 Fit side-chains REVERT: A 343 GLN cc_start: 0.8247 (mp10) cc_final: 0.7737 (mp10) REVERT: A 452 SER cc_start: 0.3784 (OUTLIER) cc_final: 0.3412 (t) REVERT: A 461 MET cc_start: 0.3779 (ppp) cc_final: 0.3233 (tmm) REVERT: A 531 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5687 (mp) REVERT: B 76 TYR cc_start: 0.9282 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: B 337 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7820 (mp) REVERT: B 343 GLN cc_start: 0.8011 (mp10) cc_final: 0.7756 (mp10) REVERT: B 452 SER cc_start: 0.4207 (OUTLIER) cc_final: 0.3866 (t) REVERT: B 461 MET cc_start: 0.4011 (ppp) cc_final: 0.3594 (tmm) REVERT: B 531 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6019 (mp) REVERT: C 346 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: C 452 SER cc_start: 0.4034 (OUTLIER) cc_final: 0.3540 (t) REVERT: C 461 MET cc_start: 0.4243 (ppp) cc_final: 0.3935 (tmm) REVERT: D 172 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8562 (p) REVERT: D 275 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8076 (mp) REVERT: D 461 MET cc_start: 0.4150 (ppp) cc_final: 0.3826 (tpp) REVERT: E 76 TYR cc_start: 0.9265 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: E 337 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7921 (mp) REVERT: E 343 GLN cc_start: 0.7928 (mt0) cc_final: 0.7588 (mp10) REVERT: E 452 SER cc_start: 0.4497 (OUTLIER) cc_final: 0.4026 (t) REVERT: E 530 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5289 (mttp) REVERT: F 58 MET cc_start: 0.8237 (mtt) cc_final: 0.7919 (mtt) REVERT: F 281 LYS cc_start: 0.7558 (tttm) cc_final: 0.7289 (tttm) REVERT: F 452 SER cc_start: 0.3452 (OUTLIER) cc_final: 0.3228 (t) REVERT: F 461 MET cc_start: 0.4320 (ppp) cc_final: 0.3875 (tmm) outliers start: 78 outliers final: 46 residues processed: 249 average time/residue: 1.2424 time to fit residues: 363.0874 Evaluate side-chains 246 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 139 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 271 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 177 optimal weight: 0.0000 chunk 153 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.166823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119929 restraints weight = 29330.993| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.05 r_work: 0.3188 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25986 Z= 0.112 Angle : 0.578 14.417 35238 Z= 0.290 Chirality : 0.047 0.146 3984 Planarity : 0.004 0.040 4470 Dihedral : 5.739 54.263 3518 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 2.21 % Allowed : 22.08 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 3156 helix: 0.68 (0.17), residues: 1080 sheet: -0.52 (0.22), residues: 564 loop : -1.39 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 402 HIS 0.003 0.001 HIS A 408 PHE 0.008 0.001 PHE F 225 TYR 0.007 0.001 TYR F 234 ARG 0.007 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 846) hydrogen bonds : angle 4.52206 ( 2340) covalent geometry : bond 0.00253 (25980) covalent geometry : angle 0.57751 (35238) Misc. bond : bond 0.00030 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 3.100 Fit side-chains REVERT: A 343 GLN cc_start: 0.8215 (mp10) cc_final: 0.7713 (mp10) REVERT: A 452 SER cc_start: 0.4011 (OUTLIER) cc_final: 0.3675 (t) REVERT: A 461 MET cc_start: 0.3744 (ppp) cc_final: 0.3244 (tmm) REVERT: A 531 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5726 (mp) REVERT: B 76 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: B 337 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7832 (mp) REVERT: B 343 GLN cc_start: 0.8009 (mp10) cc_final: 0.7744 (mp10) REVERT: B 452 SER cc_start: 0.4394 (OUTLIER) cc_final: 0.4061 (t) REVERT: B 461 MET cc_start: 0.4028 (ppp) cc_final: 0.3613 (tmm) REVERT: B 531 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5930 (mp) REVERT: C 172 THR cc_start: 0.8735 (m) cc_final: 0.8524 (p) REVERT: C 346 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: C 461 MET cc_start: 0.4236 (ppp) cc_final: 0.3917 (tmm) REVERT: D 172 THR cc_start: 0.8744 (m) cc_final: 0.8533 (p) REVERT: D 275 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8105 (tp) REVERT: D 461 MET cc_start: 0.4128 (ppp) cc_final: 0.3802 (tpp) REVERT: E 76 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: E 337 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7910 (mp) REVERT: E 343 GLN cc_start: 0.7886 (mt0) cc_final: 0.7592 (mp10) REVERT: E 452 SER cc_start: 0.4330 (OUTLIER) cc_final: 0.3914 (t) REVERT: E 530 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5266 (mttp) REVERT: F 281 LYS cc_start: 0.7580 (tttm) cc_final: 0.7355 (tttm) REVERT: F 452 SER cc_start: 0.3939 (OUTLIER) cc_final: 0.3688 (t) REVERT: F 461 MET cc_start: 0.4455 (ppp) cc_final: 0.4057 (tmm) outliers start: 61 outliers final: 34 residues processed: 234 average time/residue: 1.2948 time to fit residues: 356.6756 Evaluate side-chains 233 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 298 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 61 optimal weight: 0.0060 chunk 265 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 281 optimal weight: 0.4980 chunk 198 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120344 restraints weight = 29436.355| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.97 r_work: 0.3188 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25986 Z= 0.109 Angle : 0.576 14.279 35238 Z= 0.288 Chirality : 0.046 0.146 3984 Planarity : 0.004 0.041 4470 Dihedral : 5.644 51.107 3518 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 2.03 % Allowed : 22.37 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3156 helix: 0.72 (0.17), residues: 1080 sheet: -0.58 (0.22), residues: 570 loop : -1.33 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 402 HIS 0.004 0.001 HIS D 267 PHE 0.009 0.001 PHE F 225 TYR 0.006 0.001 TYR C 148 ARG 0.007 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 846) hydrogen bonds : angle 4.46908 ( 2340) covalent geometry : bond 0.00244 (25980) covalent geometry : angle 0.57562 (35238) Misc. bond : bond 0.00027 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18299.54 seconds wall clock time: 315 minutes 39.87 seconds (18939.87 seconds total)