Starting phenix.real_space_refine on Sat Aug 8 02:27:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i51_35190/08_2026/8i51_35190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i51_35190/08_2026/8i51_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i51_35190/08_2026/8i51_35190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i51_35190/08_2026/8i51_35190_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i51_35190/08_2026/8i51_35190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i51_35190/08_2026/8i51_35190.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.141 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 5.52, per 1000 atoms: 0.22 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: 2.57 Conformation dependent library (CDL) restraints added in 1.4 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 36.4% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 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: 4.45 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4266 1.27 - 1.41: 6367 1.41 - 1.54: 15005 1.54 - 1.68: 150 1.68 - 1.81: 192 Bond restraints: 25980 Sorted by residual: bond pdb=" CA ASP F 72 " pdb=" C ASP F 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.96e+01 bond pdb=" CA ASP C 72 " pdb=" C ASP C 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.95e+01 bond pdb=" CA ASP A 72 " pdb=" C ASP A 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.95e+01 bond pdb=" CA ASP B 72 " pdb=" C ASP B 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.93e+01 bond pdb=" CA ASP E 72 " pdb=" C ASP E 72 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.23e-02 6.61e+03 7.87e+01 ... (remaining 25975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 33916 2.72 - 5.44: 1064 5.44 - 8.15: 210 8.15 - 10.87: 30 10.87 - 13.59: 18 Bond angle restraints: 35238 Sorted by residual: angle pdb=" N HIS C 448 " pdb=" CA HIS C 448 " pdb=" C HIS C 448 " ideal model delta sigma weight residual 114.04 100.45 13.59 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS D 448 " pdb=" CA HIS D 448 " pdb=" C HIS D 448 " ideal model delta sigma weight residual 114.04 100.46 13.58 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS B 448 " pdb=" CA HIS B 448 " pdb=" C HIS B 448 " ideal model delta sigma weight residual 114.04 100.47 13.57 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS A 448 " pdb=" CA HIS A 448 " pdb=" C HIS A 448 " ideal model delta sigma weight residual 114.04 100.48 13.56 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS E 448 " pdb=" CA HIS E 448 " pdb=" C HIS E 448 " ideal model delta sigma weight residual 114.04 100.49 13.55 1.24e+00 6.50e-01 1.19e+02 ... (remaining 35233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 15060 35.53 - 71.06: 477 71.06 - 106.59: 30 106.59 - 142.12: 0 142.12 - 177.65: 3 Dihedral angle restraints: 15570 sinusoidal: 6342 harmonic: 9228 Sorted by residual: dihedral pdb=" C5' AMP A 602 " pdb=" O5' AMP A 602 " pdb=" P AMP A 602 " pdb=" O3P AMP A 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.35 177.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' AMP C 602 " pdb=" O5' AMP C 602 " pdb=" P AMP C 602 " pdb=" O3P AMP C 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.36 177.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' AMP E 602 " pdb=" O5' AMP E 602 " pdb=" P AMP E 602 " pdb=" O3P AMP E 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.36 177.65 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 15567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3649 0.129 - 0.258: 185 0.258 - 0.388: 84 0.388 - 0.517: 42 0.517 - 0.646: 24 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CB VAL D 253 " pdb=" CA VAL D 253 " pdb=" CG1 VAL D 253 " pdb=" CG2 VAL D 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.98 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CB VAL B 253 " pdb=" CA VAL B 253 " pdb=" CG1 VAL B 253 " pdb=" CG2 VAL B 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CB VAL E 253 " pdb=" CA VAL E 253 " pdb=" CG1 VAL E 253 " pdb=" CG2 VAL E 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 3981 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 338 " 0.022 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C GLU D 338 " -0.082 2.00e-02 2.50e+03 pdb=" O GLU D 338 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU D 339 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 338 " 0.022 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C GLU B 338 " -0.082 2.00e-02 2.50e+03 pdb=" O GLU B 338 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU B 339 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 338 " -0.022 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C GLU A 338 " 0.082 2.00e-02 2.50e+03 pdb=" O GLU A 338 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU A 339 " -0.028 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 714 2.68 - 3.24: 23538 3.24 - 3.79: 39035 3.79 - 4.35: 56172 4.35 - 4.90: 91490 Nonbonded interactions: 210949 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O3P AMP B 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3P AMP D 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1P AMP A 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1P AMP C 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG E 601 " pdb=" O1P AMP E 602 " model vdw 2.130 2.170 ... (remaining 210944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.380 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.258 25986 Z= 0.957 Angle : 1.104 13.588 35238 Z= 0.685 Chirality : 0.100 0.646 3984 Planarity : 0.007 0.048 4470 Dihedral : 16.675 177.648 9630 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.007 0.000 ARG C 426 TYR 0.020 0.002 TYR F 174 PHE 0.007 0.001 PHE E 315 TRP 0.015 0.002 TRP D 437 HIS 0.013 0.001 HIS F 408 Details of bonding type rmsd/Z covalent geometry : bond 0.01212 / 0.87 (25980) covalent geometry : angle 1.10415 / 0.69 (35238) hydrogen bonds : bond 0.22578 / 14.91 ( 846) hydrogen bonds : angle 7.51124 / 5.34 ( 2340) Misc. bond : bond 0.25722 / 13.13 ( 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 : 0.813 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: 0.5777 time to fit residues: 169.1448 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 : 0.875 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.3980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 29 GLN A 117 HIS A 206 ASN A 209 GLN A 213 HIS A 226 HIS A 256 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN B 29 GLN B 117 HIS B 206 ASN B 209 GLN B 213 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 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 532 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** ** D 532 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** ** E 532 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 = 0.4017 r_free = 0.4017 target = 0.170475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118575 restraints weight = 30074.618| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.99 r_work: 0.3277 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1280 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= 0.122 Angle : 0.617 8.422 35238 Z= 0.311 Chirality : 0.047 0.159 3984 Planarity : 0.004 0.036 4470 Dihedral : 6.910 131.331 3522 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.89 % Rotamer: Outliers : 2.21 % Allowed : 19.57 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3156 helix: 0.26 (0.16), residues: 1050 sheet: -0.80 (0.24), residues: 492 loop : -1.52 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 96 TYR 0.008 0.001 TYR D 234 PHE 0.007 0.001 PHE D 120 TRP 0.007 0.001 TRP F 290 HIS 0.003 0.001 HIS B 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (25980) covalent geometry : angle 0.61718 / 0.31 (35238) hydrogen bonds : bond 0.03991 / 2.68 ( 846) hydrogen bonds : angle 5.16384 / 3.63 ( 2340) Misc. bond : bond 0.00030 / 0.02 ( 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: 61 poor density : 228 time to evaluate : 0.627 Fit side-chains REVERT: A 281 LYS cc_start: 0.7494 (tttm) cc_final: 0.7122 (tttm) REVERT: A 395 ASN cc_start: 0.8283 (m110) cc_final: 0.8037 (m-40) REVERT: A 461 MET cc_start: 0.3985 (ppp) cc_final: 0.3384 (tmm) REVERT: A 530 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6092 (mtpt) REVERT: B 461 MET cc_start: 0.4585 (ppp) cc_final: 0.3784 (tmm) REVERT: B 530 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5983 (mtpp) REVERT: C 346 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: C 461 MET cc_start: 0.4666 (ppp) cc_final: 0.3995 (tpp) REVERT: C 530 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5931 (mtpt) REVERT: D 275 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8030 (mp) REVERT: D 346 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: D 461 MET cc_start: 0.4456 (ppp) cc_final: 0.3749 (tpp) REVERT: D 530 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6109 (mtpt) REVERT: E 530 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5909 (mtpt) REVERT: F 395 ASN cc_start: 0.8209 (m110) cc_final: 0.7966 (m-40) REVERT: F 461 MET cc_start: 0.4474 (ppp) cc_final: 0.4061 (tpp) REVERT: F 530 LYS cc_start: 0.6354 (OUTLIER) cc_final: 0.6000 (mtpt) outliers start: 61 outliers final: 21 residues processed: 272 average time/residue: 0.5479 time to fit residues: 174.5714 Evaluate side-chains 225 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 469 VAL Chi-restraints excluded: chain A residue 530 LYS 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 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 176 THR 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 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 105 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 chunk 17 optimal weight: 0.0020 chunk 161 optimal weight: 2.9990 chunk 308 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 184 optimal weight: 0.0980 chunk 158 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 0.0470 overall best weight: 0.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS A 532 HIS B 226 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS B 532 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 HIS C 532 HIS D 226 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS D 532 HIS E 226 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 HIS E 532 HIS F 226 HIS F 256 ASN ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS F 532 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.173279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124785 restraints weight = 30382.160| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.34 r_work: 0.3335 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25986 Z= 0.098 Angle : 0.552 7.127 35238 Z= 0.276 Chirality : 0.046 0.151 3984 Planarity : 0.004 0.041 4470 Dihedral : 6.176 92.120 3518 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.32 % Favored : 92.49 % Rotamer: Outliers : 2.87 % Allowed : 19.24 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3156 helix: 0.43 (0.16), residues: 1092 sheet: -1.00 (0.24), residues: 486 loop : -1.40 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.007 0.001 TYR B 361 PHE 0.011 0.001 PHE A 225 TRP 0.009 0.001 TRP A 290 HIS 0.003 0.001 HIS E 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (25980) covalent geometry : angle 0.55203 / 0.28 (35238) hydrogen bonds : bond 0.03145 / 2.11 ( 846) hydrogen bonds : angle 4.68457 / 3.28 ( 2340) Misc. bond : bond 0.00045 / 0.02 ( 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 323 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 244 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8082 (mtt) cc_final: 0.7780 (mtt) REVERT: A 416 ASP cc_start: 0.7775 (t0) cc_final: 0.7320 (t0) REVERT: A 417 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: A 461 MET cc_start: 0.3881 (ppp) cc_final: 0.3445 (tmm) REVERT: B 343 GLN cc_start: 0.7955 (mp10) cc_final: 0.7722 (mp10) REVERT: B 461 MET cc_start: 0.4311 (ppp) cc_final: 0.3952 (tmm) REVERT: C 172 THR cc_start: 0.8610 (m) cc_final: 0.8332 (p) REVERT: C 224 MET cc_start: 0.8381 (ttt) cc_final: 0.8018 (ttt) REVERT: C 417 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: D 172 THR cc_start: 0.8642 (m) cc_final: 0.8363 (p) REVERT: D 275 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8063 (mp) REVERT: E 343 GLN cc_start: 0.7904 (mt0) cc_final: 0.7670 (mp-120) REVERT: F 172 THR cc_start: 0.8373 (m) cc_final: 0.8106 (p) outliers start: 79 outliers final: 28 residues processed: 305 average time/residue: 0.5360 time to fit residues: 190.0672 Evaluate side-chains 235 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 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 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 449 GLN 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 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 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 449 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 248 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 309 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 256 ASN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.166499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118363 restraints weight = 30206.693| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.36 r_work: 0.3216 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25986 Z= 0.187 Angle : 0.640 10.711 35238 Z= 0.324 Chirality : 0.050 0.235 3984 Planarity : 0.004 0.041 4470 Dihedral : 6.293 65.143 3516 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.52 % Favored : 91.29 % Rotamer: Outliers : 4.03 % Allowed : 19.24 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 3156 helix: 0.57 (0.17), residues: 1038 sheet: -0.81 (0.21), residues: 570 loop : -1.53 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 141 TYR 0.012 0.002 TYR D 174 PHE 0.013 0.002 PHE E 315 TRP 0.012 0.002 TRP C 290 HIS 0.005 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (25980) covalent geometry : angle 0.63961 / 0.32 (35238) hydrogen bonds : bond 0.04249 / 2.84 ( 846) hydrogen bonds : angle 4.87131 / 3.41 ( 2340) Misc. bond : bond 0.00037 / 0.02 ( 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 306 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 195 time to evaluate : 0.859 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: 0.8753 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 281 LYS cc_start: 0.7608 (tttm) cc_final: 0.7388 (tttm) REVERT: A 343 GLN cc_start: 0.8177 (mp10) cc_final: 0.7961 (mp10) REVERT: A 416 ASP cc_start: 0.7849 (t0) cc_final: 0.7409 (t0) REVERT: A 417 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: A 461 MET cc_start: 0.3853 (ppp) cc_final: 0.3519 (tmm) REVERT: B 43 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8551 (m) REVERT: B 337 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7763 (mp) REVERT: B 343 GLN cc_start: 0.8070 (mp10) cc_final: 0.7682 (mp10) REVERT: B 461 MET cc_start: 0.4241 (ppp) cc_final: 0.3887 (tmm) REVERT: B 531 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5928 (mp) REVERT: C 43 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8464 (m) REVERT: C 224 MET cc_start: 0.8604 (ttt) cc_final: 0.8189 (ttt) REVERT: C 346 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: C 452 SER cc_start: 0.3647 (OUTLIER) cc_final: 0.3126 (t) REVERT: C 461 MET cc_start: 0.3960 (ppp) cc_final: 0.3679 (tmm) REVERT: D 224 MET cc_start: 0.8586 (ttt) cc_final: 0.8278 (ttt) REVERT: D 275 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8128 (mp) REVERT: D 461 MET cc_start: 0.4100 (ppp) cc_final: 0.3551 (tpp) REVERT: E 76 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: E 337 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7867 (mp) REVERT: E 340 ASP cc_start: 0.7780 (p0) cc_final: 0.7394 (p0) REVERT: E 343 GLN cc_start: 0.7954 (mt0) cc_final: 0.7610 (mp-120) REVERT: F 43 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8506 (m) REVERT: F 417 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7406 (m-30) outliers start: 111 outliers final: 45 residues processed: 283 average time/residue: 0.5675 time to fit residues: 189.6385 Evaluate side-chains 246 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 B residue 43 THR 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 531 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 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 449 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 293 VAL 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 F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 179 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 225 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 131 optimal weight: 0.0020 chunk 14 optimal weight: 0.8980 chunk 301 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 290 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.167564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118472 restraints weight = 30046.799| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.37 r_work: 0.3245 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25986 Z= 0.143 Angle : 0.600 7.779 35238 Z= 0.304 Chirality : 0.048 0.159 3984 Planarity : 0.004 0.045 4470 Dihedral : 6.096 51.288 3516 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.89 % Favored : 91.92 % Rotamer: Outliers : 3.56 % Allowed : 19.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 3156 helix: 0.61 (0.17), residues: 1044 sheet: -0.77 (0.21), residues: 570 loop : -1.51 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 141 TYR 0.010 0.001 TYR D 174 PHE 0.009 0.001 PHE F 225 TRP 0.007 0.001 TRP E 402 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (25980) covalent geometry : angle 0.59960 / 0.30 (35238) hydrogen bonds : bond 0.03709 / 2.48 ( 846) hydrogen bonds : angle 4.76896 / 3.33 ( 2340) Misc. bond : bond 0.00036 / 0.02 ( 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: 98 poor density : 200 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8455 (m) REVERT: A 343 GLN cc_start: 0.8236 (mp10) cc_final: 0.7966 (mp10) REVERT: A 416 ASP cc_start: 0.7877 (t0) cc_final: 0.7432 (t0) REVERT: A 461 MET cc_start: 0.3899 (ppp) cc_final: 0.3590 (tmm) REVERT: A 531 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5816 (mp) REVERT: B 76 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.6698 (m-80) REVERT: B 337 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7807 (mp) REVERT: B 343 GLN cc_start: 0.7984 (mp10) cc_final: 0.7636 (mp10) REVERT: B 452 SER cc_start: 0.4322 (OUTLIER) cc_final: 0.3847 (t) REVERT: B 531 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5911 (mp) REVERT: C 224 MET cc_start: 0.8504 (ttt) cc_final: 0.8251 (ttt) REVERT: C 346 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: C 461 MET cc_start: 0.4019 (ppp) cc_final: 0.3746 (tmm) REVERT: D 43 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8424 (m) REVERT: D 275 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8125 (mp) REVERT: D 461 MET cc_start: 0.4339 (ppp) cc_final: 0.3814 (tpp) REVERT: E 76 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.6737 (m-80) REVERT: E 238 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8916 (ttt) REVERT: E 337 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7899 (mp) REVERT: E 343 GLN cc_start: 0.7927 (mt0) cc_final: 0.7603 (mp-120) REVERT: E 530 LYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5363 (mttp) REVERT: F 58 MET cc_start: 0.8297 (mtt) cc_final: 0.7943 (mtt) REVERT: F 417 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: F 461 MET cc_start: 0.4238 (ppp) cc_final: 0.3904 (tpp) outliers start: 98 outliers final: 49 residues processed: 275 average time/residue: 0.6116 time to fit residues: 197.7756 Evaluate side-chains 251 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 469 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 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 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 E residue 70 ASP Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 238 MET 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 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 179 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 29 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 223 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 302 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4021 r_free = 0.4021 target = 0.169501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123530 restraints weight = 30104.860| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.20 r_work: 0.3284 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1967 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= 0.155 Angle : 0.606 7.512 35238 Z= 0.308 Chirality : 0.048 0.232 3984 Planarity : 0.004 0.041 4470 Dihedral : 6.021 47.846 3516 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.43 % Favored : 91.38 % Rotamer: Outliers : 3.78 % Allowed : 19.50 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 3156 helix: 0.64 (0.17), residues: 1044 sheet: -0.72 (0.21), residues: 570 loop : -1.50 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.011 0.001 TYR D 174 PHE 0.010 0.001 PHE F 225 TRP 0.007 0.001 TRP E 402 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (25980) covalent geometry : angle 0.60614 / 0.31 (35238) hydrogen bonds : bond 0.03796 / 2.53 ( 846) hydrogen bonds : angle 4.75791 / 3.32 ( 2340) Misc. bond : bond 0.00036 / 0.02 ( 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 300 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 196 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8391 (m) REVERT: A 343 GLN cc_start: 0.8166 (mp10) cc_final: 0.7820 (mp10) REVERT: A 416 ASP cc_start: 0.7813 (t0) cc_final: 0.7356 (t0) REVERT: A 461 MET cc_start: 0.3714 (ppp) cc_final: 0.3477 (tmm) REVERT: A 531 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5800 (mp) REVERT: B 76 TYR cc_start: 0.9248 (OUTLIER) cc_final: 0.6597 (m-80) REVERT: B 337 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7785 (mp) REVERT: B 343 GLN cc_start: 0.7882 (mp10) cc_final: 0.7632 (mp10) REVERT: B 452 SER cc_start: 0.4358 (OUTLIER) cc_final: 0.3962 (t) REVERT: B 531 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5985 (mp) REVERT: C 43 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8396 (m) REVERT: C 224 MET cc_start: 0.8514 (ttt) cc_final: 0.8122 (ttt) REVERT: C 346 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: C 452 SER cc_start: 0.3738 (OUTLIER) cc_final: 0.3212 (t) REVERT: C 461 MET cc_start: 0.4061 (ppp) cc_final: 0.3783 (tmm) REVERT: D 43 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8375 (m) REVERT: D 275 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8038 (mp) REVERT: D 461 MET cc_start: 0.4263 (ppp) cc_final: 0.3852 (tpp) REVERT: E 76 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.6559 (m-80) REVERT: E 337 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7838 (mp) REVERT: E 343 GLN cc_start: 0.7861 (mt0) cc_final: 0.7379 (mp10) REVERT: E 452 SER cc_start: 0.4642 (OUTLIER) cc_final: 0.4101 (t) REVERT: E 530 LYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5173 (mttp) REVERT: F 43 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8395 (m) REVERT: F 58 MET cc_start: 0.8215 (mtt) cc_final: 0.7894 (mtt) REVERT: F 461 MET cc_start: 0.4470 (ppp) cc_final: 0.3868 (tmm) outliers start: 104 outliers final: 51 residues processed: 278 average time/residue: 0.6157 time to fit residues: 201.2794 Evaluate side-chains 256 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 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 70 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 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 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 179 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 269 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 293 optimal weight: 7.9990 chunk 307 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113003 restraints weight = 28838.018| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.86 r_work: 0.3060 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 25986 Z= 0.238 Angle : 0.678 9.604 35238 Z= 0.348 Chirality : 0.052 0.203 3984 Planarity : 0.005 0.044 4470 Dihedral : 6.245 49.359 3516 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.16 % Favored : 90.65 % Rotamer: Outliers : 4.10 % Allowed : 19.75 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3156 helix: 0.59 (0.17), residues: 1032 sheet: -1.31 (0.20), residues: 660 loop : -1.52 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.013 0.002 TYR D 174 PHE 0.013 0.002 PHE F 225 TRP 0.017 0.002 TRP C 290 HIS 0.005 0.001 HIS B 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (25980) covalent geometry : angle 0.67783 / 0.35 (35238) hydrogen bonds : bond 0.04574 / 3.07 ( 846) hydrogen bonds : angle 4.95103 / 3.46 ( 2340) Misc. bond : bond 0.00043 / 0.02 ( 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 302 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 189 time to evaluate : 0.995 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: 0.8328 (mp10) cc_final: 0.7981 (mp10) REVERT: A 461 MET cc_start: 0.3717 (ppp) cc_final: 0.3477 (tmm) REVERT: B 337 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7956 (mp) REVERT: B 343 GLN cc_start: 0.8131 (mp10) cc_final: 0.7883 (mp10) REVERT: B 425 ASP cc_start: 0.8102 (t0) cc_final: 0.7880 (t0) REVERT: B 452 SER cc_start: 0.4322 (OUTLIER) cc_final: 0.3917 (t) REVERT: B 461 MET cc_start: 0.3831 (ppp) cc_final: 0.3090 (tmm) REVERT: B 531 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6103 (mp) REVERT: C 452 SER cc_start: 0.3794 (OUTLIER) cc_final: 0.3245 (t) REVERT: D 275 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8227 (mp) REVERT: D 461 MET cc_start: 0.4007 (ppp) cc_final: 0.3761 (tpp) REVERT: E 226 HIS cc_start: 0.6357 (OUTLIER) cc_final: 0.5994 (m170) REVERT: E 337 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8052 (mp) REVERT: E 343 GLN cc_start: 0.8071 (mt0) cc_final: 0.7569 (mp10) REVERT: E 452 SER cc_start: 0.4635 (OUTLIER) cc_final: 0.4018 (t) REVERT: E 530 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5437 (mttp) REVERT: F 226 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.6250 (m170) REVERT: F 417 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: F 461 MET cc_start: 0.4365 (ppp) cc_final: 0.3829 (tmm) outliers start: 113 outliers final: 59 residues processed: 281 average time/residue: 0.5652 time to fit residues: 188.5415 Evaluate side-chains 250 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 283 LYS 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 452 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 505 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 449 GLN Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 341 VAL 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 341 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 447 LEU 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 70 ASP 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 F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 226 HIS 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 417 ASP 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 109 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.163969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116248 restraints weight = 28848.899| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.92 r_work: 0.3116 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25986 Z= 0.129 Angle : 0.597 7.734 35238 Z= 0.302 Chirality : 0.047 0.165 3984 Planarity : 0.004 0.043 4470 Dihedral : 5.934 52.314 3516 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 2.98 % Allowed : 21.06 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 3156 helix: 0.64 (0.17), residues: 1044 sheet: -0.67 (0.22), residues: 564 loop : -1.52 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.007 0.001 TYR C 148 PHE 0.009 0.001 PHE F 225 TRP 0.007 0.001 TRP E 402 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (25980) covalent geometry : angle 0.59676 / 0.30 (35238) hydrogen bonds : bond 0.03493 / 2.34 ( 846) hydrogen bonds : angle 4.73094 / 3.30 ( 2340) Misc. bond : bond 0.00032 / 0.02 ( 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 278 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 196 time to evaluate : 0.829 Fit side-chains REVERT: A 343 GLN cc_start: 0.8168 (mp10) cc_final: 0.7784 (mp10) REVERT: A 461 MET cc_start: 0.3730 (ppp) cc_final: 0.3455 (tmm) REVERT: B 337 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7915 (mp) REVERT: B 452 SER cc_start: 0.4141 (OUTLIER) cc_final: 0.3814 (t) REVERT: B 461 MET cc_start: 0.3993 (ppp) cc_final: 0.3162 (tmm) REVERT: B 531 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6110 (mp) REVERT: C 43 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8428 (m) REVERT: C 452 SER cc_start: 0.3862 (OUTLIER) cc_final: 0.3338 (t) REVERT: D 275 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8163 (mp) REVERT: D 461 MET cc_start: 0.4170 (ppp) cc_final: 0.3920 (tpp) REVERT: E 76 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: E 337 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7991 (mp) REVERT: E 343 GLN cc_start: 0.7995 (mt0) cc_final: 0.7539 (mp10) REVERT: E 452 SER cc_start: 0.4525 (OUTLIER) cc_final: 0.4037 (t) REVERT: E 530 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5334 (mttp) REVERT: F 43 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8443 (m) REVERT: F 196 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8794 (m) REVERT: F 461 MET cc_start: 0.4347 (ppp) cc_final: 0.3873 (tmm) outliers start: 82 outliers final: 41 residues processed: 257 average time/residue: 0.5800 time to fit residues: 176.0155 Evaluate side-chains 235 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 182 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 293 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 409 THR 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 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 43 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 362 ILE Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 269 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 303 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 231 optimal weight: 0.4980 chunk 281 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3922 r_free = 0.3922 target = 0.163504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115807 restraints weight = 28741.433| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.90 r_work: 0.3107 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2156 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= 0.146 Angle : 0.616 14.263 35238 Z= 0.311 Chirality : 0.048 0.165 3984 Planarity : 0.004 0.043 4470 Dihedral : 5.891 52.019 3516 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.30 % Favored : 91.51 % Rotamer: Outliers : 2.58 % Allowed : 21.64 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3156 helix: 0.66 (0.17), residues: 1044 sheet: -0.67 (0.22), residues: 564 loop : -1.49 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.008 0.001 TYR D 174 PHE 0.010 0.001 PHE F 225 TRP 0.007 0.001 TRP D 402 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (25980) covalent geometry : angle 0.61553 / 0.31 (35238) hydrogen bonds : bond 0.03632 / 2.43 ( 846) hydrogen bonds : angle 4.73745 / 3.31 ( 2340) Misc. bond : bond 0.00035 / 0.02 ( 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 255 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 184 time to evaluate : 0.998 Fit side-chains REVERT: A 343 GLN cc_start: 0.8131 (mp10) cc_final: 0.7688 (mp10) REVERT: A 452 SER cc_start: 0.4042 (OUTLIER) cc_final: 0.3688 (t) REVERT: A 461 MET cc_start: 0.3815 (ppp) cc_final: 0.3563 (tmm) REVERT: B 76 TYR cc_start: 0.9289 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: B 337 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 343 GLN cc_start: 0.7886 (mp10) cc_final: 0.7556 (mp10) REVERT: B 452 SER cc_start: 0.4351 (OUTLIER) cc_final: 0.4022 (t) REVERT: B 461 MET cc_start: 0.3952 (ppp) cc_final: 0.3154 (tmm) REVERT: B 531 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6087 (mp) REVERT: C 43 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8474 (m) REVERT: C 346 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: C 452 SER cc_start: 0.3848 (OUTLIER) cc_final: 0.3337 (t) REVERT: D 275 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8162 (mp) REVERT: D 461 MET cc_start: 0.4001 (ppp) cc_final: 0.3765 (tpp) REVERT: E 76 TYR cc_start: 0.9263 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: E 337 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7973 (mp) REVERT: E 343 GLN cc_start: 0.7938 (mt0) cc_final: 0.7477 (mp10) REVERT: E 452 SER cc_start: 0.4439 (OUTLIER) cc_final: 0.3992 (t) REVERT: E 530 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5319 (mttp) REVERT: F 43 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8478 (m) REVERT: F 196 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8788 (m) REVERT: F 281 LYS cc_start: 0.7565 (tttm) cc_final: 0.7321 (tttm) REVERT: F 452 SER cc_start: 0.3981 (OUTLIER) cc_final: 0.3716 (t) REVERT: F 461 MET cc_start: 0.4316 (ppp) cc_final: 0.3887 (tmm) outliers start: 71 outliers final: 41 residues processed: 238 average time/residue: 0.6196 time to fit residues: 172.8415 Evaluate side-chains 237 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 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 76 TYR 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 B residue 531 LEU Chi-restraints excluded: chain C residue 43 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 362 ILE Chi-restraints excluded: chain C residue 452 SER 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 417 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain F residue 43 THR 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 179 THR Chi-restraints excluded: chain F residue 196 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 59 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 267 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3951 r_free = 0.3951 target = 0.166508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120549 restraints weight = 29480.860| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.96 r_work: 0.3172 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25986 Z= 0.113 Angle : 0.581 14.911 35238 Z= 0.291 Chirality : 0.047 0.155 3984 Planarity : 0.004 0.041 4470 Dihedral : 5.697 51.547 3516 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.88 % Favored : 92.93 % Rotamer: Outliers : 2.03 % Allowed : 22.15 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 3156 helix: 0.78 (0.17), residues: 1044 sheet: -0.63 (0.22), residues: 564 loop : -1.37 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.008 0.001 TYR E 361 PHE 0.009 0.001 PHE F 225 TRP 0.009 0.001 TRP D 290 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (25980) covalent geometry : angle 0.58120 / 0.29 (35238) hydrogen bonds : bond 0.03125 / 2.09 ( 846) hydrogen bonds : angle 4.57301 / 3.19 ( 2340) Misc. bond : bond 0.00029 / 0.02 ( 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 263 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 0.812 Fit side-chains REVERT: A 343 GLN cc_start: 0.8148 (mp10) cc_final: 0.7702 (mp10) REVERT: A 461 MET cc_start: 0.3741 (ppp) cc_final: 0.3482 (tmm) REVERT: B 76 TYR cc_start: 0.9261 (OUTLIER) cc_final: 0.6768 (m-80) REVERT: B 337 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7900 (mp) REVERT: B 343 GLN cc_start: 0.7956 (mp10) cc_final: 0.7474 (mp10) REVERT: B 452 SER cc_start: 0.4419 (OUTLIER) cc_final: 0.4074 (t) REVERT: B 461 MET cc_start: 0.3951 (ppp) cc_final: 0.3143 (tmm) REVERT: B 531 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5994 (mp) REVERT: C 172 THR cc_start: 0.8705 (m) cc_final: 0.8442 (p) REVERT: C 452 SER cc_start: 0.3709 (OUTLIER) cc_final: 0.3371 (t) REVERT: D 172 THR cc_start: 0.8742 (m) cc_final: 0.8479 (p) REVERT: D 275 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8153 (tp) REVERT: D 461 MET cc_start: 0.4035 (ppp) cc_final: 0.3784 (tpp) REVERT: E 76 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: E 337 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7950 (mp) REVERT: E 343 GLN cc_start: 0.7888 (mt0) cc_final: 0.7476 (mp10) REVERT: E 452 SER cc_start: 0.4389 (OUTLIER) cc_final: 0.3963 (t) REVERT: E 530 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5323 (mttp) REVERT: F 172 THR cc_start: 0.8428 (m) cc_final: 0.8205 (p) REVERT: F 281 LYS cc_start: 0.7599 (tttm) cc_final: 0.7364 (tttm) REVERT: F 452 SER cc_start: 0.3884 (OUTLIER) cc_final: 0.3644 (t) REVERT: F 461 MET cc_start: 0.4478 (ppp) cc_final: 0.4068 (tmm) outliers start: 56 outliers final: 37 residues processed: 244 average time/residue: 0.6006 time to fit residues: 171.3257 Evaluate side-chains 240 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 283 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 76 TYR 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 B residue 531 LEU 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 293 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 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 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 F residue 95 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 179 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 181 optimal weight: 4.9990 chunk 88 optimal weight: 0.0170 chunk 278 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 74 optimal weight: 0.0980 chunk 138 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 237 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120771 restraints weight = 29419.245| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.07 r_work: 0.3204 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25986 Z= 0.102 Angle : 0.578 14.965 35238 Z= 0.288 Chirality : 0.046 0.167 3984 Planarity : 0.004 0.041 4470 Dihedral : 5.580 50.459 3516 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.13 % Favored : 92.68 % Rotamer: Outliers : 1.82 % Allowed : 22.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 3156 helix: 0.95 (0.17), residues: 1038 sheet: -0.64 (0.22), residues: 570 loop : -1.24 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 141 TYR 0.007 0.001 TYR E 148 PHE 0.009 0.001 PHE D 225 TRP 0.011 0.001 TRP D 290 HIS 0.003 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (25980) covalent geometry : angle 0.57813 / 0.29 (35238) hydrogen bonds : bond 0.02902 / 1.94 ( 846) hydrogen bonds : angle 4.44566 / 3.10 ( 2340) Misc. bond : bond 0.00024 / 0.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8590.53 seconds wall clock time: 147 minutes 11.34 seconds (8831.34 seconds total)