Starting phenix.real_space_refine on Sun Jun 22 00:08:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i51_35190/06_2025/8i51_35190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i51_35190/06_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_35190/06_2025/8i51_35190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i51_35190/06_2025/8i51_35190.map" model { file = "/net/cci-nas-00/data/ceres_data/8i51_35190/06_2025/8i51_35190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i51_35190/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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, 'AMP%rna3p': 1, 'OP3': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'OP3': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'OP3': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'OP3': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'OP3': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'OP3': 1} Classifications: {'RNA_mixed': 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: 14.83, per 1000 atoms: 0.58 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: 6.32 Conformation dependent library (CDL) restraints added in 3.2 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: 3.86 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: 12.15 Time building geometry restraints manager: 7.48 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: 33910 2.72 - 5.44: 1058 5.44 - 8.15: 210 8.15 - 10.87: 42 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: 3655 0.129 - 0.258: 179 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: 0.21 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: 1.920 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: 0.030 Extract box with map and model: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 61.440 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables: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= 0.956 Angle : 1.116 13.588 35238 Z= 0.678 Chirality : 0.099 0.646 3984 Planarity : 0.007 0.048 4470 Dihedral : 16.681 177.648 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 1.11552 (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 : 3.622 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: 1.6332 time to fit residues: 477.4712 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 : 4.425 ------------------------------------------------------------------------------- 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** 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 = 0.4002 r_free = 0.4002 target = 0.169074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116985 restraints weight = 29888.434| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.98 r_work: 0.3260 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1268 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= 0.143 Angle : 0.641 7.787 35238 Z= 0.321 Chirality : 0.048 0.160 3984 Planarity : 0.004 0.038 4470 Dihedral : 6.699 124.378 3522 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.02 % Favored : 91.79 % Rotamer: Outliers : 2.47 % Allowed : 19.54 % Favored : 78.00 % 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: -1.26 (0.15), residues: 3156 helix: 0.23 (0.16), residues: 1050 sheet: -0.80 (0.22), residues: 570 loop : -1.59 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 402 HIS 0.004 0.001 HIS B 213 PHE 0.007 0.001 PHE E 81 TYR 0.011 0.001 TYR D 174 ARG 0.001 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 846) hydrogen bonds : angle 5.22469 ( 2340) covalent geometry : bond 0.00325 (25980) covalent geometry : angle 0.64142 (35238) Misc. bond : bond 0.00073 ( 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 289 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 221 time to evaluate : 4.008 Fit side-chains REVERT: A 281 LYS cc_start: 0.7495 (tttm) cc_final: 0.7119 (tttm) REVERT: A 461 MET cc_start: 0.3895 (ppp) cc_final: 0.3252 (tmm) REVERT: A 530 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.6115 (mtpt) REVERT: B 461 MET cc_start: 0.4643 (ppp) cc_final: 0.3628 (tmm) REVERT: B 530 LYS cc_start: 0.6337 (OUTLIER) cc_final: 0.6017 (mtpp) REVERT: C 346 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: C 469 VAL cc_start: 0.4452 (OUTLIER) cc_final: 0.4182 (t) REVERT: C 530 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.6015 (mtpt) REVERT: D 275 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8032 (mp) REVERT: D 346 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: D 461 MET cc_start: 0.4526 (ppp) cc_final: 0.3815 (tpp) REVERT: D 530 LYS cc_start: 0.6536 (OUTLIER) cc_final: 0.6162 (mtpt) REVERT: E 461 MET cc_start: 0.4320 (ppp) cc_final: 0.4070 (tpp) REVERT: E 530 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.6033 (mtpt) REVERT: F 395 ASN cc_start: 0.8263 (m110) cc_final: 0.8015 (m-40) REVERT: F 461 MET cc_start: 0.4489 (ppp) cc_final: 0.4109 (tpp) REVERT: F 530 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6061 (mtpt) outliers start: 68 outliers final: 27 residues processed: 273 average time/residue: 1.4270 time to fit residues: 458.4134 Evaluate side-chains 229 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 2.763 ------------------------------------------------------------------------------- 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: 0.9980 chunk 91 optimal weight: 0.0870 chunk 169 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 chunk 236 optimal weight: 0.7980 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.169874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119796 restraints weight = 29793.468| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.39 r_work: 0.3265 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25986 Z= 0.119 Angle : 0.592 7.709 35238 Z= 0.294 Chirality : 0.047 0.152 3984 Planarity : 0.004 0.038 4470 Dihedral : 6.058 75.321 3520 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.54 % Favored : 92.27 % Rotamer: Outliers : 3.45 % Allowed : 18.88 % Favored : 77.67 % 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: -1.04 (0.15), residues: 3156 helix: 0.52 (0.16), residues: 1056 sheet: -0.88 (0.21), residues: 570 loop : -1.47 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 402 HIS 0.003 0.001 HIS B 36 PHE 0.011 0.001 PHE A 225 TYR 0.008 0.001 TYR D 174 ARG 0.003 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 846) hydrogen bonds : angle 4.82237 ( 2340) covalent geometry : bond 0.00267 (25980) covalent geometry : angle 0.59189 (35238) Misc. bond : bond 0.00049 ( 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: 95 poor density : 216 time to evaluate : 2.863 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: 0.8629 (OUTLIER) cc_final: 0.8385 (m) REVERT: A 343 GLN cc_start: 0.8377 (mp10) cc_final: 0.7880 (mp10) REVERT: A 416 ASP cc_start: 0.7746 (t0) cc_final: 0.7266 (t0) REVERT: A 417 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: A 461 MET cc_start: 0.4037 (ppp) cc_final: 0.3544 (tmm) REVERT: A 531 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5761 (mp) REVERT: B 343 GLN cc_start: 0.7868 (mp10) cc_final: 0.7553 (mp10) REVERT: B 461 MET cc_start: 0.4410 (ppp) cc_final: 0.4007 (tmm) REVERT: C 224 MET cc_start: 0.8557 (ttt) cc_final: 0.8147 (ttt) REVERT: C 346 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: C 417 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: C 461 MET cc_start: 0.4614 (ppp) cc_final: 0.4165 (tpp) REVERT: D 43 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8405 (m) REVERT: D 275 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7948 (mp) REVERT: D 346 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: D 417 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: E 343 GLN cc_start: 0.7879 (mt0) cc_final: 0.7575 (mp-120) REVERT: F 43 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8435 (m) REVERT: F 58 MET cc_start: 0.8162 (mtt) cc_final: 0.7855 (mtt) REVERT: F 395 ASN cc_start: 0.8305 (m110) cc_final: 0.8070 (m-40) REVERT: F 417 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7360 (m-30) outliers start: 95 outliers final: 41 residues processed: 293 average time/residue: 1.5034 time to fit residues: 513.4396 Evaluate side-chains 245 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 3.458 ------------------------------------------------------------------------------- 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 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 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 417 ASP Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 469 VAL 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 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 449 GLN 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 293 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 449 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 154 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 264 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 267 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 226 HIS ** 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 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117122 restraints weight = 30232.415| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.40 r_work: 0.3194 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25986 Z= 0.219 Angle : 0.669 7.902 35238 Z= 0.337 Chirality : 0.051 0.177 3984 Planarity : 0.005 0.044 4470 Dihedral : 6.059 57.326 3518 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.90 % Favored : 90.91 % Rotamer: Outliers : 4.18 % Allowed : 18.59 % Favored : 77.23 % 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: -1.16 (0.14), residues: 3156 helix: 0.53 (0.17), residues: 1032 sheet: -0.89 (0.21), residues: 570 loop : -1.63 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 290 HIS 0.005 0.001 HIS A 226 PHE 0.013 0.002 PHE B 315 TYR 0.013 0.002 TYR D 174 ARG 0.005 0.001 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 846) hydrogen bonds : angle 4.97455 ( 2340) covalent geometry : bond 0.00530 (25980) covalent geometry : angle 0.66863 (35238) Misc. bond : bond 0.00044 ( 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 304 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 189 time to evaluate : 4.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.8276 (mp10) cc_final: 0.7927 (mp10) REVERT: A 416 ASP cc_start: 0.7888 (t0) cc_final: 0.7446 (t0) REVERT: A 417 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: A 461 MET cc_start: 0.3761 (ppp) cc_final: 0.3463 (tmm) REVERT: A 531 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5878 (mp) REVERT: B 226 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.6161 (m170) REVERT: B 337 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7807 (mp) REVERT: B 343 GLN cc_start: 0.8079 (mp10) cc_final: 0.7764 (mp10) REVERT: B 452 SER cc_start: 0.4069 (OUTLIER) cc_final: 0.3557 (t) REVERT: B 461 MET cc_start: 0.4372 (ppp) cc_final: 0.4000 (tmm) REVERT: C 224 MET cc_start: 0.8587 (ttt) cc_final: 0.8040 (ttt) REVERT: C 346 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: C 417 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: C 461 MET cc_start: 0.4543 (ppp) cc_final: 0.4121 (tpp) REVERT: D 224 MET cc_start: 0.8608 (ttt) cc_final: 0.8018 (ttt) REVERT: D 275 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8165 (mp) REVERT: D 346 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: D 417 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: D 461 MET cc_start: 0.4003 (ppp) cc_final: 0.3482 (tpp) REVERT: E 337 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7867 (mp) REVERT: E 343 GLN cc_start: 0.8008 (mt0) cc_final: 0.7492 (mp10) REVERT: E 469 VAL cc_start: 0.5352 (OUTLIER) cc_final: 0.4309 (t) REVERT: F 417 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7392 (m-30) outliers start: 115 outliers final: 53 residues processed: 282 average time/residue: 1.8533 time to fit residues: 618.5499 Evaluate side-chains 251 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 3.270 ------------------------------------------------------------------------------- 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 275 LEU 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 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 226 HIS 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 417 ASP Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 469 VAL 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 C residue 469 VAL 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 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 D residue 469 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 337 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 E residue 469 VAL Chi-restraints excluded: chain F residue 43 THR 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 417 ASP Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 452 SER 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: 0.6980 chunk 296 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 257 optimal weight: 0.7980 chunk 214 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 198 optimal weight: 0.0070 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** ** A 532 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** ** C 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120455 restraints weight = 30148.370| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.43 r_work: 0.3241 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25986 Z= 0.116 Angle : 0.592 8.297 35238 Z= 0.295 Chirality : 0.047 0.201 3984 Planarity : 0.004 0.044 4470 Dihedral : 5.666 57.511 3518 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 3.34 % Allowed : 19.39 % 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: -1.00 (0.15), residues: 3156 helix: 0.63 (0.17), residues: 1044 sheet: -0.77 (0.21), residues: 570 loop : -1.53 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 290 HIS 0.003 0.001 HIS A 408 PHE 0.009 0.001 PHE F 225 TYR 0.007 0.001 TYR D 174 ARG 0.006 0.000 ARG F 96 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 846) hydrogen bonds : angle 4.73564 ( 2340) covalent geometry : bond 0.00261 (25980) covalent geometry : angle 0.59183 (35238) Misc. bond : bond 0.00040 ( 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 298 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 206 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8440 (m) REVERT: A 343 GLN cc_start: 0.8254 (mp10) cc_final: 0.7861 (mp10) REVERT: A 416 ASP cc_start: 0.7868 (t0) cc_final: 0.7398 (t0) REVERT: A 461 MET cc_start: 0.3919 (ppp) cc_final: 0.3611 (tmm) REVERT: B 337 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7773 (mp) REVERT: B 343 GLN cc_start: 0.7969 (mp10) cc_final: 0.7688 (mp10) REVERT: B 417 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: B 452 SER cc_start: 0.4320 (OUTLIER) cc_final: 0.3844 (t) REVERT: B 461 MET cc_start: 0.4197 (ppp) cc_final: 0.3753 (tmm) REVERT: C 172 THR cc_start: 0.8745 (m) cc_final: 0.8454 (p) REVERT: C 224 MET cc_start: 0.8596 (ttt) cc_final: 0.8138 (ttt) REVERT: C 346 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: C 452 SER cc_start: 0.3496 (OUTLIER) cc_final: 0.2985 (t) REVERT: C 461 MET cc_start: 0.4246 (ppp) cc_final: 0.3969 (tpp) REVERT: D 43 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8434 (m) REVERT: D 172 THR cc_start: 0.8761 (m) cc_final: 0.8484 (p) REVERT: D 224 MET cc_start: 0.8605 (ttt) cc_final: 0.8241 (ttt) REVERT: D 275 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8100 (mp) REVERT: D 461 MET cc_start: 0.4221 (ppp) cc_final: 0.3730 (tpp) REVERT: E 337 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7850 (mp) REVERT: E 343 GLN cc_start: 0.7945 (mt0) cc_final: 0.7634 (mp10) REVERT: F 43 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8464 (m) REVERT: F 461 MET cc_start: 0.4264 (ppp) cc_final: 0.3981 (tpp) outliers start: 92 outliers final: 42 residues processed: 273 average time/residue: 1.3875 time to fit residues: 445.4903 Evaluate side-chains 243 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 3.347 ------------------------------------------------------------------------------- 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 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 409 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 505 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 417 ASP Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 70 ASP 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 452 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 70 ASP 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 E residue 70 ASP 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 F residue 43 THR Chi-restraints excluded: chain F residue 70 ASP 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 424 THR Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 449 GLN 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: 0.9980 chunk 151 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** A 532 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 HIS ** 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** F 532 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.166443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114357 restraints weight = 30179.713| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.99 r_work: 0.3187 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25986 Z= 0.170 Angle : 0.633 7.622 35238 Z= 0.318 Chirality : 0.049 0.213 3984 Planarity : 0.004 0.043 4470 Dihedral : 5.683 58.630 3518 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.46 % Favored : 91.35 % Rotamer: Outliers : 3.52 % Allowed : 19.61 % Favored : 76.87 % 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: -1.01 (0.15), residues: 3156 helix: 0.62 (0.17), residues: 1044 sheet: -0.77 (0.21), residues: 570 loop : -1.55 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 290 HIS 0.004 0.001 HIS D 36 PHE 0.011 0.001 PHE F 225 TYR 0.010 0.001 TYR A 174 ARG 0.006 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 846) hydrogen bonds : angle 4.79419 ( 2340) covalent geometry : bond 0.00404 (25980) covalent geometry : angle 0.63257 (35238) Misc. bond : bond 0.00041 ( 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 288 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 191 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8404 (m) REVERT: A 343 GLN cc_start: 0.8186 (mp10) cc_final: 0.7724 (mp10) REVERT: A 416 ASP cc_start: 0.7812 (t0) cc_final: 0.7330 (t0) REVERT: A 461 MET cc_start: 0.3720 (ppp) cc_final: 0.3489 (tmm) REVERT: B 337 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 425 ASP cc_start: 0.7818 (t0) cc_final: 0.7604 (t0) REVERT: B 452 SER cc_start: 0.4422 (OUTLIER) cc_final: 0.4001 (t) REVERT: B 461 MET cc_start: 0.4202 (ppp) cc_final: 0.3732 (tmm) REVERT: C 141 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7946 (mtp85) REVERT: C 224 MET cc_start: 0.8625 (ttt) cc_final: 0.8184 (ttt) REVERT: C 346 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: C 452 SER cc_start: 0.3808 (OUTLIER) cc_final: 0.3250 (t) REVERT: D 43 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8408 (m) REVERT: D 224 MET cc_start: 0.8616 (ttt) cc_final: 0.8132 (ttt) REVERT: D 275 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8040 (mp) REVERT: D 461 MET cc_start: 0.4265 (ppp) cc_final: 0.3851 (tpp) REVERT: E 76 TYR cc_start: 0.9268 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: E 337 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7684 (mp) REVERT: E 343 GLN cc_start: 0.7862 (mt0) cc_final: 0.7480 (mp-120) REVERT: E 452 SER cc_start: 0.4653 (OUTLIER) cc_final: 0.4096 (t) REVERT: E 530 LYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5438 (mttp) REVERT: F 43 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8428 (m) REVERT: F 461 MET cc_start: 0.4295 (ppp) cc_final: 0.3698 (tmm) outliers start: 97 outliers final: 50 residues processed: 269 average time/residue: 1.3048 time to fit residues: 410.7675 Evaluate side-chains 247 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR 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 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 449 GLN Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 141 ARG 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 447 LEU 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 70 ASP 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 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 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 449 GLN Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain F residue 43 THR 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 449 GLN 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: 5.9990 chunk 276 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 64 optimal weight: 0.0470 chunk 13 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 302 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 290 optimal weight: 6.9990 overall best weight: 1.9882 ------------------------------------------------------------------------------- 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 226 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** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.167743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121964 restraints weight = 30237.513| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.05 r_work: 0.3258 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25986 Z= 0.203 Angle : 0.658 8.400 35238 Z= 0.333 Chirality : 0.051 0.193 3984 Planarity : 0.005 0.045 4470 Dihedral : 5.801 59.340 3518 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.62 % Favored : 91.19 % Rotamer: Outliers : 4.14 % Allowed : 19.61 % Favored : 76.25 % 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: -1.05 (0.15), residues: 3156 helix: 0.64 (0.17), residues: 1032 sheet: -0.76 (0.21), residues: 570 loop : -1.61 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 290 HIS 0.004 0.001 HIS B 39 PHE 0.012 0.002 PHE F 225 TYR 0.013 0.002 TYR D 174 ARG 0.007 0.001 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 846) hydrogen bonds : angle 4.89123 ( 2340) covalent geometry : bond 0.00488 (25980) covalent geometry : angle 0.65834 (35238) Misc. bond : bond 0.00043 ( 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 304 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 190 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.8210 (mp10) cc_final: 0.7755 (mp10) REVERT: A 416 ASP cc_start: 0.7909 (t0) cc_final: 0.7428 (t0) REVERT: A 452 SER cc_start: 0.3434 (OUTLIER) cc_final: 0.3080 (t) REVERT: A 461 MET cc_start: 0.3632 (ppp) cc_final: 0.3399 (tmm) REVERT: A 530 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6216 (mtpt) REVERT: B 154 GLN cc_start: 0.7635 (pt0) cc_final: 0.7433 (pt0) REVERT: B 337 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7753 (mp) REVERT: B 343 GLN cc_start: 0.7866 (mp10) cc_final: 0.7553 (mp10) REVERT: B 452 SER cc_start: 0.4385 (OUTLIER) cc_final: 0.3979 (t) REVERT: B 461 MET cc_start: 0.4277 (ppp) cc_final: 0.3686 (tmm) REVERT: C 141 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8005 (mtp85) REVERT: C 226 HIS cc_start: 0.6109 (OUTLIER) cc_final: 0.5653 (m170) REVERT: C 346 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: C 452 SER cc_start: 0.3713 (OUTLIER) cc_final: 0.3187 (t) REVERT: D 275 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8097 (mp) REVERT: D 461 MET cc_start: 0.4133 (ppp) cc_final: 0.3740 (tpp) REVERT: E 337 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7815 (mp) REVERT: E 343 GLN cc_start: 0.7853 (mt0) cc_final: 0.7336 (mp10) REVERT: E 452 SER cc_start: 0.4678 (OUTLIER) cc_final: 0.4103 (t) REVERT: E 530 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5333 (mttp) REVERT: E 531 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5991 (mp) REVERT: F 461 MET cc_start: 0.4243 (ppp) cc_final: 0.3602 (tmm) outliers start: 114 outliers final: 54 residues processed: 284 average time/residue: 1.2877 time to fit residues: 426.7589 Evaluate side-chains 253 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 2.916 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 505 LEU 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 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 417 ASP Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 226 HIS 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 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 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 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 449 GLN Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 43 THR 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 424 THR Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 311 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** 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 226 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.162243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115497 restraints weight = 28685.575| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.99 r_work: 0.3057 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25986 Z= 0.168 Angle : 0.635 9.131 35238 Z= 0.320 Chirality : 0.049 0.179 3984 Planarity : 0.004 0.045 4470 Dihedral : 5.689 57.479 3518 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.17 % Favored : 91.63 % Rotamer: Outliers : 3.45 % Allowed : 20.62 % Favored : 75.93 % 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: -1.13 (0.15), residues: 3156 helix: 0.60 (0.17), residues: 1044 sheet: -1.24 (0.20), residues: 660 loop : -1.48 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 402 HIS 0.004 0.001 HIS B 226 PHE 0.011 0.001 PHE F 225 TYR 0.009 0.001 TYR D 174 ARG 0.006 0.000 ARG F 96 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 846) hydrogen bonds : angle 4.81410 ( 2340) covalent geometry : bond 0.00401 (25980) covalent geometry : angle 0.63504 (35238) Misc. bond : bond 0.00040 ( 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 285 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 190 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.8224 (mp10) cc_final: 0.7757 (mp10) REVERT: A 452 SER cc_start: 0.3777 (OUTLIER) cc_final: 0.3398 (t) REVERT: A 531 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5845 (mp) REVERT: B 337 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7833 (mp) REVERT: B 343 GLN cc_start: 0.7942 (mp10) cc_final: 0.7499 (mp10) REVERT: B 452 SER cc_start: 0.4214 (OUTLIER) cc_final: 0.3852 (t) REVERT: B 461 MET cc_start: 0.4251 (ppp) cc_final: 0.3575 (tmm) REVERT: C 346 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: C 452 SER cc_start: 0.3845 (OUTLIER) cc_final: 0.3299 (t) REVERT: C 461 MET cc_start: 0.3874 (ppp) cc_final: 0.3537 (tmm) REVERT: D 275 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8188 (mp) REVERT: D 461 MET cc_start: 0.4051 (ppp) cc_final: 0.3777 (tpp) REVERT: E 226 HIS cc_start: 0.6284 (OUTLIER) cc_final: 0.5905 (m170) REVERT: E 337 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7910 (mp) REVERT: E 343 GLN cc_start: 0.7994 (mt0) cc_final: 0.7501 (mp10) REVERT: E 452 SER cc_start: 0.4510 (OUTLIER) cc_final: 0.4024 (t) REVERT: E 530 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5227 (mttp) REVERT: E 531 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5993 (mp) REVERT: F 396 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7745 (mttt) REVERT: F 461 MET cc_start: 0.4278 (ppp) cc_final: 0.3899 (tmm) outliers start: 95 outliers final: 53 residues processed: 269 average time/residue: 1.2407 time to fit residues: 390.4336 Evaluate side-chains 245 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 2.912 ------------------------------------------------------------------------------- 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 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 70 ASP 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 293 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 SER 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 447 LEU 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 70 ASP 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 424 THR Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 226 HIS 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 449 GLN Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 43 THR 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 396 LYS Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 130 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 150 optimal weight: 30.0000 chunk 3 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 179 optimal weight: 0.6980 chunk 260 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 289 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.166231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120213 restraints weight = 29531.871| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.95 r_work: 0.3154 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25986 Z= 0.113 Angle : 0.590 8.141 35238 Z= 0.295 Chirality : 0.047 0.154 3984 Planarity : 0.004 0.044 4470 Dihedral : 5.328 44.534 3516 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.26 % Favored : 92.55 % Rotamer: Outliers : 2.43 % Allowed : 22.00 % Favored : 75.56 % 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: -0.84 (0.15), residues: 3156 helix: 0.74 (0.17), residues: 1044 sheet: -0.60 (0.22), residues: 564 loop : -1.45 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 290 HIS 0.004 0.001 HIS A 408 PHE 0.008 0.001 PHE F 225 TYR 0.007 0.001 TYR E 148 ARG 0.010 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 846) hydrogen bonds : angle 4.62194 ( 2340) covalent geometry : bond 0.00254 (25980) covalent geometry : angle 0.59032 (35238) Misc. bond : bond 0.00032 ( 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 272 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 2.820 Fit side-chains REVERT: A 343 GLN cc_start: 0.8279 (mp10) cc_final: 0.7787 (mp10) REVERT: A 531 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5791 (mp) REVERT: B 337 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 452 SER cc_start: 0.4304 (OUTLIER) cc_final: 0.3978 (t) REVERT: B 461 MET cc_start: 0.4326 (ppp) cc_final: 0.3621 (tmm) REVERT: C 172 THR cc_start: 0.8709 (m) cc_final: 0.8462 (p) REVERT: C 346 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: C 461 MET cc_start: 0.3949 (ppp) cc_final: 0.3610 (tmm) REVERT: D 172 THR cc_start: 0.8740 (m) cc_final: 0.8495 (p) REVERT: D 275 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8108 (mp) REVERT: D 461 MET cc_start: 0.3988 (ppp) cc_final: 0.3736 (tpp) REVERT: E 76 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.6760 (m-80) REVERT: E 337 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7986 (mp) REVERT: E 343 GLN cc_start: 0.7938 (mt0) cc_final: 0.7546 (mp10) REVERT: E 452 SER cc_start: 0.4530 (OUTLIER) cc_final: 0.4041 (t) REVERT: E 531 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6202 (mp) REVERT: F 172 THR cc_start: 0.8480 (m) cc_final: 0.8269 (p) REVERT: F 281 LYS cc_start: 0.7614 (tttm) cc_final: 0.7373 (tttm) REVERT: F 452 SER cc_start: 0.3957 (OUTLIER) cc_final: 0.3700 (t) REVERT: F 461 MET cc_start: 0.4185 (ppp) cc_final: 0.3858 (tmm) outliers start: 67 outliers final: 34 residues processed: 255 average time/residue: 1.3312 time to fit residues: 397.0290 Evaluate side-chains 234 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 3.149 ------------------------------------------------------------------------------- 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 409 THR 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 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 C residue 70 ASP Chi-restraints excluded: chain C residue 221 ILE 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 D residue 221 ILE 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 362 ILE 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 179 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 531 LEU 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 Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 139 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 119 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.164207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117297 restraints weight = 29325.698| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.02 r_work: 0.3144 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25986 Z= 0.155 Angle : 0.629 8.127 35238 Z= 0.315 Chirality : 0.049 0.168 3984 Planarity : 0.004 0.044 4470 Dihedral : 5.364 43.949 3516 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.02 % Favored : 91.79 % Rotamer: Outliers : 2.07 % Allowed : 22.33 % 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: -0.86 (0.15), residues: 3156 helix: 0.72 (0.17), residues: 1044 sheet: -0.59 (0.22), residues: 564 loop : -1.47 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 402 HIS 0.003 0.001 HIS E 39 PHE 0.010 0.001 PHE F 225 TYR 0.010 0.001 TYR B 174 ARG 0.007 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 846) hydrogen bonds : angle 4.67038 ( 2340) covalent geometry : bond 0.00367 (25980) covalent geometry : angle 0.62905 (35238) Misc. bond : bond 0.00038 ( 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 243 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 3.410 Fit side-chains REVERT: A 58 MET cc_start: 0.8144 (mtt) cc_final: 0.7942 (mtt) REVERT: A 452 SER cc_start: 0.3937 (OUTLIER) cc_final: 0.3604 (t) REVERT: A 461 MET cc_start: 0.3955 (ppp) cc_final: 0.3589 (tmm) REVERT: B 337 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7844 (mp) REVERT: B 452 SER cc_start: 0.4355 (OUTLIER) cc_final: 0.4009 (t) REVERT: B 461 MET cc_start: 0.4307 (ppp) cc_final: 0.3657 (tmm) REVERT: C 346 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: C 461 MET cc_start: 0.4057 (ppp) cc_final: 0.3746 (tmm) REVERT: D 275 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8084 (mp) REVERT: D 461 MET cc_start: 0.3970 (ppp) cc_final: 0.3742 (tpp) REVERT: E 76 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: E 337 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7889 (mp) REVERT: E 343 GLN cc_start: 0.7877 (mt0) cc_final: 0.7453 (mp10) REVERT: E 452 SER cc_start: 0.4423 (OUTLIER) cc_final: 0.3976 (t) REVERT: E 530 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5250 (mttp) REVERT: E 531 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6197 (mp) REVERT: F 58 MET cc_start: 0.8213 (mtt) cc_final: 0.7965 (mtt) REVERT: F 281 LYS cc_start: 0.7545 (tttm) cc_final: 0.7295 (tttm) REVERT: F 452 SER cc_start: 0.3944 (OUTLIER) cc_final: 0.3687 (t) REVERT: F 461 MET cc_start: 0.4230 (ppp) cc_final: 0.3977 (tmm) outliers start: 57 outliers final: 32 residues processed: 226 average time/residue: 1.5839 time to fit residues: 418.3759 Evaluate side-chains 226 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 2.830 ------------------------------------------------------------------------------- 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 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 B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL 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 C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU 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 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 E residue 76 TYR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 179 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 362 ILE Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain E residue 531 LEU 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 424 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 298 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 259 optimal weight: 0.6980 chunk 153 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 281 optimal weight: 0.0670 chunk 198 optimal weight: 5.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- 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 ** 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 = 0.3925 r_free = 0.3925 target = 0.164050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117709 restraints weight = 29412.094| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.96 r_work: 0.3138 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25986 Z= 0.157 Angle : 0.639 14.425 35238 Z= 0.320 Chirality : 0.049 0.177 3984 Planarity : 0.004 0.045 4470 Dihedral : 5.379 44.409 3516 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.89 % Favored : 91.92 % Rotamer: Outliers : 1.92 % Allowed : 22.44 % Favored : 75.64 % 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: -0.88 (0.15), residues: 3156 helix: 0.70 (0.17), residues: 1044 sheet: -0.61 (0.22), residues: 564 loop : -1.48 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 402 HIS 0.004 0.001 HIS A 408 PHE 0.010 0.001 PHE F 225 TYR 0.010 0.001 TYR D 174 ARG 0.007 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 846) hydrogen bonds : angle 4.71198 ( 2340) covalent geometry : bond 0.00372 (25980) covalent geometry : angle 0.63893 (35238) Misc. bond : bond 0.00036 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21104.09 seconds wall clock time: 374 minutes 27.04 seconds (22467.04 seconds total)