Starting phenix.real_space_refine on Mon Aug 25 04:51:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i51_35190/08_2025/8i51_35190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i51_35190/08_2025/8i51_35190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i51_35190/08_2025/8i51_35190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i51_35190/08_2025/8i51_35190_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i51_35190/08_2025/8i51_35190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i51_35190/08_2025/8i51_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.19, per 1000 atoms: 0.20 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: 1.81 Conformation dependent library (CDL) restraints added in 691.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.83 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: 4.67 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4266 1.27 - 1.41: 6367 1.41 - 1.54: 15005 1.54 - 1.68: 150 1.68 - 1.81: 192 Bond restraints: 25980 Sorted by residual: bond pdb=" CA ASP F 72 " pdb=" C ASP F 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.96e+01 bond pdb=" CA ASP C 72 " pdb=" C ASP C 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.95e+01 bond pdb=" CA ASP A 72 " pdb=" C ASP A 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.95e+01 bond pdb=" CA ASP B 72 " pdb=" C ASP B 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.93e+01 bond pdb=" CA ASP E 72 " pdb=" C ASP E 72 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.23e-02 6.61e+03 7.87e+01 ... (remaining 25975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 33910 2.72 - 5.44: 1058 5.44 - 8.15: 210 8.15 - 10.87: 42 10.87 - 13.59: 18 Bond angle restraints: 35238 Sorted by residual: angle pdb=" N HIS C 448 " pdb=" CA HIS C 448 " pdb=" C HIS C 448 " ideal model delta sigma weight residual 114.04 100.45 13.59 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS D 448 " pdb=" CA HIS D 448 " pdb=" C HIS D 448 " ideal model delta sigma weight residual 114.04 100.46 13.58 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS B 448 " pdb=" CA HIS B 448 " pdb=" C HIS B 448 " ideal model delta sigma weight residual 114.04 100.47 13.57 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS A 448 " pdb=" CA HIS A 448 " pdb=" C HIS A 448 " ideal model delta sigma weight residual 114.04 100.48 13.56 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS E 448 " pdb=" CA HIS E 448 " pdb=" C HIS E 448 " ideal model delta sigma weight residual 114.04 100.49 13.55 1.24e+00 6.50e-01 1.19e+02 ... (remaining 35233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 15060 35.53 - 71.06: 477 71.06 - 106.59: 30 106.59 - 142.12: 0 142.12 - 177.65: 3 Dihedral angle restraints: 15570 sinusoidal: 6342 harmonic: 9228 Sorted by residual: dihedral pdb=" C5' AMP A 602 " pdb=" O5' AMP A 602 " pdb=" P AMP A 602 " pdb=" O3P AMP A 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.35 177.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' AMP C 602 " pdb=" O5' AMP C 602 " pdb=" P AMP C 602 " pdb=" O3P AMP C 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.36 177.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' AMP E 602 " pdb=" O5' AMP E 602 " pdb=" P AMP E 602 " pdb=" O3P AMP E 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.36 177.65 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 15567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3655 0.129 - 0.258: 179 0.258 - 0.388: 84 0.388 - 0.517: 42 0.517 - 0.646: 24 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CB VAL D 253 " pdb=" CA VAL D 253 " pdb=" CG1 VAL D 253 " pdb=" CG2 VAL D 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.98 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CB VAL B 253 " pdb=" CA VAL B 253 " pdb=" CG1 VAL B 253 " pdb=" CG2 VAL B 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CB VAL E 253 " pdb=" CA VAL E 253 " pdb=" CG1 VAL E 253 " pdb=" CG2 VAL E 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 3981 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 338 " 0.022 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C GLU D 338 " -0.082 2.00e-02 2.50e+03 pdb=" O GLU D 338 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU D 339 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 338 " 0.022 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C GLU B 338 " -0.082 2.00e-02 2.50e+03 pdb=" O GLU B 338 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU B 339 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 338 " -0.022 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C GLU A 338 " 0.082 2.00e-02 2.50e+03 pdb=" O GLU A 338 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU A 339 " -0.028 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 714 2.68 - 3.24: 23538 3.24 - 3.79: 39035 3.79 - 4.35: 56172 4.35 - 4.90: 91490 Nonbonded interactions: 210949 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O3P AMP B 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3P AMP D 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1P AMP A 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1P AMP C 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG E 601 " pdb=" O1P AMP E 602 " model vdw 2.130 2.170 ... (remaining 210944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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: 1.770 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.420 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.258 25986 Z= 0.956 Angle : 1.116 13.588 35238 Z= 0.678 Chirality : 0.099 0.646 3984 Planarity : 0.007 0.048 4470 Dihedral : 16.681 177.648 9630 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 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 aren 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 covalent geometry : bond 0.01212 (25980) covalent geometry : angle 1.11552 (35238) hydrogen bonds : bond 0.22578 ( 846) hydrogen bonds : angle 7.51124 ( 2340) Misc. bond : bond 0.25722 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.796 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: 0.5871 time to fit residues: 171.2190 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 : 1.006 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 29 GLN A 117 HIS A 206 ASN A 209 GLN A 213 HIS A 226 HIS A 256 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN B 29 GLN B 117 HIS B 206 ASN B 209 GLN B 213 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4018 r_free = 0.4018 target = 0.170490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123051 restraints weight = 29956.028| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.23 r_work: 0.3293 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1310 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= 0.121 Angle : 0.628 8.337 35238 Z= 0.312 Chirality : 0.047 0.159 3984 Planarity : 0.004 0.036 4470 Dihedral : 6.605 120.930 3522 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.02 % Favored : 91.79 % Rotamer: Outliers : 2.29 % Allowed : 19.32 % Favored : 78.40 % 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 aren not related in a simple way. whole: -1.20 (0.15), residues: 3156 helix: 0.28 (0.16), residues: 1050 sheet: -0.81 (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 0.007 0.001 TYR D 174 PHE 0.007 0.001 PHE D 120 TRP 0.007 0.001 TRP E 466 HIS 0.003 0.001 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00267 (25980) covalent geometry : angle 0.62774 (35238) hydrogen bonds : bond 0.03856 ( 846) hydrogen bonds : angle 5.13898 ( 2340) Misc. bond : bond 0.00017 ( 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 292 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 229 time to evaluate : 0.941 Fit side-chains REVERT: A 281 LYS cc_start: 0.7502 (tttm) cc_final: 0.7128 (tttm) REVERT: A 395 ASN cc_start: 0.8306 (m110) cc_final: 0.8074 (m-40) REVERT: A 461 MET cc_start: 0.3997 (ppp) cc_final: 0.3408 (tmm) REVERT: A 530 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.6126 (mtpt) REVERT: B 461 MET cc_start: 0.4596 (ppp) cc_final: 0.3722 (tmm) REVERT: B 530 LYS cc_start: 0.6349 (OUTLIER) cc_final: 0.6031 (mtpp) REVERT: C 346 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: C 461 MET cc_start: 0.4544 (ppp) cc_final: 0.3943 (tpp) REVERT: C 530 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.5960 (mtpt) REVERT: D 275 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8077 (mp) REVERT: D 346 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: D 417 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: D 461 MET cc_start: 0.4316 (ppp) cc_final: 0.3734 (tpp) REVERT: D 530 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6155 (mtpt) REVERT: E 461 MET cc_start: 0.4461 (ppp) cc_final: 0.4199 (tpp) REVERT: E 530 LYS cc_start: 0.6215 (OUTLIER) cc_final: 0.5990 (mtpt) REVERT: F 395 ASN cc_start: 0.8235 (m110) cc_final: 0.8024 (m-40) REVERT: F 461 MET cc_start: 0.4322 (ppp) cc_final: 0.3936 (tpp) REVERT: F 530 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.6038 (mtpt) outliers start: 63 outliers final: 21 residues processed: 275 average time/residue: 0.5507 time to fit residues: 176.8424 Evaluate side-chains 228 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 417 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 530 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 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: 0.9990 chunk 135 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 161 optimal weight: 0.0170 chunk 308 optimal weight: 20.0000 chunk 276 optimal weight: 4.9990 chunk 269 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 0.0370 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS A 532 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.172187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123651 restraints weight = 30337.796| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.23 r_work: 0.3282 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25986 Z= 0.106 Angle : 0.571 7.169 35238 Z= 0.282 Chirality : 0.046 0.150 3984 Planarity : 0.004 0.035 4470 Dihedral : 5.796 66.939 3518 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.38 % Favored : 92.43 % Rotamer: Outliers : 3.01 % Allowed : 19.24 % Favored : 77.74 % 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 aren not related in a simple way. whole: -1.07 (0.15), residues: 3156 helix: 0.39 (0.16), residues: 1098 sheet: -0.90 (0.24), residues: 480 loop : -1.44 (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 E 148 PHE 0.010 0.001 PHE F 225 TRP 0.007 0.001 TRP D 402 HIS 0.003 0.001 HIS E 414 Details of bonding type rmsd covalent geometry : bond 0.00222 (25980) covalent geometry : angle 0.57065 (35238) hydrogen bonds : bond 0.03264 ( 846) hydrogen bonds : angle 4.69675 ( 2340) Misc. bond : bond 0.00049 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 228 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8145 (mtt) cc_final: 0.7840 (mtt) REVERT: A 118 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: A 141 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7654 (mtp85) REVERT: A 343 GLN cc_start: 0.8392 (mp10) cc_final: 0.7921 (mp10) REVERT: A 416 ASP cc_start: 0.7806 (t0) cc_final: 0.7344 (t0) REVERT: A 417 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: A 461 MET cc_start: 0.3927 (ppp) cc_final: 0.3539 (tmm) REVERT: B 343 GLN cc_start: 0.7951 (mp10) cc_final: 0.7592 (mp10) REVERT: B 461 MET cc_start: 0.4397 (ppp) cc_final: 0.3966 (tmm) REVERT: C 172 THR cc_start: 0.8656 (m) cc_final: 0.8365 (p) REVERT: C 346 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: C 417 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: D 172 THR cc_start: 0.8661 (m) cc_final: 0.8383 (p) REVERT: D 275 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8094 (mp) REVERT: D 461 MET cc_start: 0.4165 (ppp) cc_final: 0.3863 (tpp) REVERT: E 340 ASP cc_start: 0.7257 (p0) cc_final: 0.7047 (p0) REVERT: E 343 GLN cc_start: 0.7928 (mt0) cc_final: 0.7636 (mp-120) REVERT: F 58 MET cc_start: 0.8124 (mtt) cc_final: 0.7825 (mtt) REVERT: F 118 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: F 141 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7673 (mtp85) REVERT: F 172 THR cc_start: 0.8417 (m) cc_final: 0.8179 (p) outliers start: 83 outliers final: 34 residues processed: 294 average time/residue: 0.6022 time to fit residues: 205.5433 Evaluate side-chains 242 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 141 ARG 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 469 VAL 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 362 ILE Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 141 ARG 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 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 293 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 141 ARG 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: 3.9990 chunk 29 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 207 optimal weight: 0.0470 chunk 215 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 309 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.169093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.120364 restraints weight = 30083.769| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.42 r_work: 0.3227 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25986 Z= 0.137 Angle : 0.595 7.398 35238 Z= 0.296 Chirality : 0.048 0.154 3984 Planarity : 0.004 0.040 4470 Dihedral : 5.544 48.859 3516 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.17 % Favored : 91.63 % Rotamer: Outliers : 4.10 % Allowed : 18.92 % Favored : 76.98 % 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 aren not related in a simple way. whole: -1.07 (0.15), residues: 3156 helix: 0.45 (0.16), residues: 1080 sheet: -0.78 (0.22), residues: 570 loop : -1.52 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.008 0.001 TYR F 174 PHE 0.009 0.001 PHE F 225 TRP 0.006 0.001 TRP E 402 HIS 0.004 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00322 (25980) covalent geometry : angle 0.59546 (35238) hydrogen bonds : bond 0.03593 ( 846) hydrogen bonds : angle 4.69554 ( 2340) Misc. bond : bond 0.00044 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 205 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8443 (m) REVERT: A 58 MET cc_start: 0.8276 (mtt) cc_final: 0.8030 (mtt) REVERT: A 343 GLN cc_start: 0.8270 (mp10) cc_final: 0.7902 (mp10) REVERT: A 416 ASP cc_start: 0.7819 (t0) cc_final: 0.7364 (t0) REVERT: A 461 MET cc_start: 0.3711 (ppp) cc_final: 0.3434 (tmm) REVERT: B 337 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7704 (mp) REVERT: B 343 GLN cc_start: 0.7955 (mp10) cc_final: 0.7709 (mp10) REVERT: B 452 SER cc_start: 0.4094 (OUTLIER) cc_final: 0.3634 (t) REVERT: B 461 MET cc_start: 0.4379 (ppp) cc_final: 0.3953 (tmm) REVERT: B 531 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5857 (mp) REVERT: C 224 MET cc_start: 0.8581 (ttt) cc_final: 0.8178 (ttt) REVERT: C 346 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: C 417 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: C 452 SER cc_start: 0.3634 (OUTLIER) cc_final: 0.3118 (t) REVERT: C 461 MET cc_start: 0.3934 (ppp) cc_final: 0.3599 (tmm) REVERT: D 275 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8087 (mp) REVERT: E 76 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: E 337 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7771 (mp) REVERT: E 340 ASP cc_start: 0.7366 (p0) cc_final: 0.7071 (p0) REVERT: E 343 GLN cc_start: 0.7949 (mt0) cc_final: 0.7595 (mp-120) REVERT: F 43 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8480 (m) REVERT: F 58 MET cc_start: 0.8274 (mtt) cc_final: 0.8042 (mtt) REVERT: F 417 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7391 (m-30) outliers start: 113 outliers final: 46 residues processed: 289 average time/residue: 0.5766 time to fit residues: 194.8780 Evaluate side-chains 250 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 449 GLN Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 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 417 ASP Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 424 THR 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 275 LEU 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 452 SER Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 225 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 13 optimal weight: 0.0040 chunk 268 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 301 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 267 HIS ** 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 226 HIS F 267 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.163991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114652 restraints weight = 30155.135| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.36 r_work: 0.3181 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 25986 Z= 0.270 Angle : 0.717 7.912 35238 Z= 0.365 Chirality : 0.053 0.274 3984 Planarity : 0.005 0.046 4470 Dihedral : 5.955 47.986 3516 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.13 % Favored : 90.68 % Rotamer: Outliers : 4.03 % Allowed : 19.32 % Favored : 76.65 % 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 aren not related in a simple way. whole: -1.27 (0.14), residues: 3156 helix: 0.54 (0.17), residues: 1032 sheet: -1.39 (0.19), residues: 660 loop : -1.56 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.018 0.002 TYR D 174 PHE 0.015 0.002 PHE B 315 TRP 0.021 0.002 TRP E 290 HIS 0.006 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00655 (25980) covalent geometry : angle 0.71727 (35238) hydrogen bonds : bond 0.04919 ( 846) hydrogen bonds : angle 5.02100 ( 2340) Misc. bond : bond 0.00052 ( 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 301 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 190 time to evaluate : 1.051 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: 0.8299 (mp10) cc_final: 0.7898 (mp10) REVERT: A 416 ASP cc_start: 0.7985 (t0) cc_final: 0.7593 (t0) REVERT: A 461 MET cc_start: 0.3846 (ppp) cc_final: 0.3531 (tmm) REVERT: A 531 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5888 (mp) REVERT: B 226 HIS cc_start: 0.6499 (OUTLIER) cc_final: 0.6012 (m170) REVERT: B 337 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 343 GLN cc_start: 0.8135 (mp10) cc_final: 0.7892 (mp10) REVERT: B 452 SER cc_start: 0.4103 (OUTLIER) cc_final: 0.3586 (t) REVERT: B 461 MET cc_start: 0.4036 (ppp) cc_final: 0.3618 (tmm) REVERT: B 531 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6096 (mp) REVERT: C 141 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7898 (mtp85) REVERT: C 224 MET cc_start: 0.8557 (ttt) cc_final: 0.8310 (ttt) REVERT: C 226 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.6080 (m170) REVERT: C 346 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: C 461 MET cc_start: 0.3870 (ppp) cc_final: 0.3646 (tmm) REVERT: D 141 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7753 (mtp85) REVERT: D 224 MET cc_start: 0.8597 (ttt) cc_final: 0.8083 (ttt) REVERT: D 275 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8175 (mp) REVERT: D 417 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: D 461 MET cc_start: 0.3830 (ppp) cc_final: 0.3486 (tpp) REVERT: E 226 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.6160 (m170) REVERT: E 337 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7980 (mp) REVERT: E 340 ASP cc_start: 0.7496 (p0) cc_final: 0.7229 (p0) REVERT: E 343 GLN cc_start: 0.8020 (mt0) cc_final: 0.7662 (mp-120) REVERT: E 530 LYS cc_start: 0.6343 (OUTLIER) cc_final: 0.5534 (mttp) REVERT: F 417 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: F 461 MET cc_start: 0.4162 (ppp) cc_final: 0.3737 (tmm) REVERT: F 531 LEU cc_start: 0.5863 (OUTLIER) cc_final: 0.5609 (mp) outliers start: 111 outliers final: 51 residues processed: 284 average time/residue: 0.6109 time to fit residues: 202.6853 Evaluate side-chains 249 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 182 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 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 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 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 141 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain D residue 141 ARG 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 417 ASP Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 505 LEU 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 272 ILE 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 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 531 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 0.0070 chunk 256 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 223 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 30.0000 chunk 183 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 302 optimal weight: 0.0050 overall best weight: 0.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.170852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121811 restraints weight = 29981.093| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.18 r_work: 0.3286 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25986 Z= 0.113 Angle : 0.586 7.351 35238 Z= 0.293 Chirality : 0.047 0.150 3984 Planarity : 0.004 0.042 4470 Dihedral : 5.507 46.070 3516 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.67 % Favored : 92.14 % Rotamer: Outliers : 3.09 % Allowed : 20.33 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3156 helix: 0.65 (0.17), residues: 1044 sheet: -0.65 (0.22), residues: 564 loop : -1.55 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.006 0.001 TYR C 148 PHE 0.010 0.001 PHE F 225 TRP 0.009 0.001 TRP D 290 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00253 (25980) covalent geometry : angle 0.58585 (35238) hydrogen bonds : bond 0.03352 ( 846) hydrogen bonds : angle 4.71066 ( 2340) Misc. bond : bond 0.00034 ( 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 289 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 204 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 43 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8397 (m) REVERT: A 343 GLN cc_start: 0.8205 (mp10) cc_final: 0.7791 (mp10) REVERT: A 416 ASP cc_start: 0.7937 (t0) cc_final: 0.7515 (t0) REVERT: A 531 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5909 (mp) REVERT: B 76 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: B 337 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7885 (mp) REVERT: B 343 GLN cc_start: 0.7971 (mp10) cc_final: 0.7763 (mp10) REVERT: B 452 SER cc_start: 0.4351 (OUTLIER) cc_final: 0.3951 (t) REVERT: B 461 MET cc_start: 0.4250 (ppp) cc_final: 0.3745 (tmm) REVERT: B 531 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6114 (mp) REVERT: C 43 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8454 (m) REVERT: C 172 THR cc_start: 0.8694 (m) cc_final: 0.8433 (p) REVERT: C 346 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: C 452 SER cc_start: 0.3578 (OUTLIER) cc_final: 0.3045 (t) REVERT: C 461 MET cc_start: 0.4028 (ppp) cc_final: 0.3757 (tmm) REVERT: D 172 THR cc_start: 0.8736 (m) cc_final: 0.8474 (p) REVERT: D 275 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8154 (mp) REVERT: D 461 MET cc_start: 0.4009 (ppp) cc_final: 0.3624 (tpp) REVERT: E 76 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: E 337 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7962 (mp) REVERT: E 340 ASP cc_start: 0.7419 (p0) cc_final: 0.7058 (p0) REVERT: E 343 GLN cc_start: 0.7904 (mt0) cc_final: 0.7486 (mp10) REVERT: E 452 SER cc_start: 0.4654 (OUTLIER) cc_final: 0.4100 (t) REVERT: F 461 MET cc_start: 0.4348 (ppp) cc_final: 0.3811 (tmm) outliers start: 85 outliers final: 35 residues processed: 268 average time/residue: 0.6130 time to fit residues: 191.8958 Evaluate side-chains 241 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 76 TYR 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 43 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 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 424 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 505 LEU 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 253 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 176 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 424 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 293 optimal weight: 0.3980 chunk 307 optimal weight: 0.3980 chunk 162 optimal weight: 3.9990 chunk 260 optimal weight: 0.1980 chunk 184 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 289 optimal weight: 0.2980 chunk 195 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121486 restraints weight = 29508.099| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.05 r_work: 0.3202 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.002 0.037 25986 Z= 0.100 Angle : 0.564 7.155 35238 Z= 0.280 Chirality : 0.047 0.262 3984 Planarity : 0.004 0.039 4470 Dihedral : 5.201 43.951 3516 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.54 % Favored : 92.27 % Rotamer: Outliers : 2.18 % Allowed : 21.71 % Favored : 76.11 % 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 aren not related in a simple way. whole: -0.86 (0.15), residues: 3156 helix: 0.65 (0.17), residues: 1080 sheet: -0.63 (0.22), residues: 570 loop : -1.44 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 37 TYR 0.006 0.001 TYR B 148 PHE 0.009 0.001 PHE F 225 TRP 0.010 0.001 TRP D 290 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00215 (25980) covalent geometry : angle 0.56427 (35238) hydrogen bonds : bond 0.02904 ( 846) hydrogen bonds : angle 4.49233 ( 2340) Misc. bond : bond 0.00032 ( 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 275 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 1.070 Fit side-chains REVERT: A 343 GLN cc_start: 0.8211 (mp10) cc_final: 0.7754 (mp10) REVERT: A 416 ASP cc_start: 0.7947 (t0) cc_final: 0.7499 (t0) REVERT: A 429 ASP cc_start: 0.6976 (m-30) cc_final: 0.6366 (m-30) REVERT: A 531 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5945 (mp) REVERT: B 76 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.6747 (m-80) REVERT: B 337 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7796 (mp) REVERT: B 343 GLN cc_start: 0.7975 (mp10) cc_final: 0.7725 (mp10) REVERT: B 461 MET cc_start: 0.4250 (ppp) cc_final: 0.3718 (tmm) REVERT: B 531 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6063 (mp) REVERT: C 172 THR cc_start: 0.8667 (m) cc_final: 0.8421 (p) REVERT: C 452 SER cc_start: 0.3888 (OUTLIER) cc_final: 0.3344 (t) REVERT: C 461 MET cc_start: 0.4070 (ppp) cc_final: 0.3847 (tmm) REVERT: D 172 THR cc_start: 0.8697 (m) cc_final: 0.8438 (p) REVERT: D 275 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8076 (tp) REVERT: D 461 MET cc_start: 0.4036 (ppp) cc_final: 0.3697 (tpp) REVERT: E 76 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: E 337 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7849 (mp) REVERT: E 343 GLN cc_start: 0.7892 (mt0) cc_final: 0.7553 (mp10) REVERT: E 531 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6187 (mp) REVERT: F 461 MET cc_start: 0.4310 (ppp) cc_final: 0.3839 (tmm) outliers start: 60 outliers final: 24 residues processed: 260 average time/residue: 0.6412 time to fit residues: 194.4018 Evaluate side-chains 231 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 293 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 293 VAL 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 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 531 LEU 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 269 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 109 optimal weight: 0.0570 chunk 219 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 287 optimal weight: 7.9990 chunk 278 optimal weight: 4.9990 chunk 275 optimal weight: 0.6980 chunk 103 optimal weight: 0.0980 chunk 85 optimal weight: 0.0070 chunk 117 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.169328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122042 restraints weight = 29581.531| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.95 r_work: 0.3207 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25986 Z= 0.097 Angle : 0.570 9.558 35238 Z= 0.282 Chirality : 0.046 0.151 3984 Planarity : 0.004 0.037 4470 Dihedral : 5.053 42.592 3516 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.16 % Favored : 92.65 % Rotamer: Outliers : 2.00 % Allowed : 22.44 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.15), residues: 3156 helix: 0.81 (0.16), residues: 1110 sheet: -0.88 (0.22), residues: 588 loop : -1.27 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 37 TYR 0.006 0.001 TYR B 148 PHE 0.009 0.001 PHE D 225 TRP 0.009 0.001 TRP D 290 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00208 (25980) covalent geometry : angle 0.56968 (35238) hydrogen bonds : bond 0.02772 ( 846) hydrogen bonds : angle 4.37660 ( 2340) Misc. bond : bond 0.00031 ( 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 280 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.888 Fit side-chains REVERT: A 174 TYR cc_start: 0.7729 (m-80) cc_final: 0.7402 (m-80) REVERT: A 343 GLN cc_start: 0.8202 (mp10) cc_final: 0.7710 (mp10) REVERT: A 461 MET cc_start: 0.3949 (ppp) cc_final: 0.3498 (tmm) REVERT: A 531 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5915 (mp) REVERT: B 76 TYR cc_start: 0.9226 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: B 320 MET cc_start: 0.8748 (ptp) cc_final: 0.8521 (ptp) REVERT: B 337 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7884 (mp) REVERT: B 343 GLN cc_start: 0.8049 (mp10) cc_final: 0.7783 (mp10) REVERT: B 461 MET cc_start: 0.4347 (ppp) cc_final: 0.3722 (tmm) REVERT: B 531 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6049 (mp) REVERT: C 174 TYR cc_start: 0.7627 (m-80) cc_final: 0.7346 (m-80) REVERT: C 461 MET cc_start: 0.4048 (ppp) cc_final: 0.3832 (tmm) REVERT: D 174 TYR cc_start: 0.7700 (m-80) cc_final: 0.7366 (m-80) REVERT: D 275 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8138 (tp) REVERT: D 461 MET cc_start: 0.3953 (ppp) cc_final: 0.3681 (tpp) REVERT: E 76 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: E 337 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7905 (mp) REVERT: E 343 GLN cc_start: 0.7856 (mt0) cc_final: 0.7635 (mp10) REVERT: E 531 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6154 (mp) REVERT: F 281 LYS cc_start: 0.7559 (tttm) cc_final: 0.7330 (tttm) REVERT: F 452 SER cc_start: 0.3424 (OUTLIER) cc_final: 0.3208 (t) REVERT: F 461 MET cc_start: 0.4299 (ppp) cc_final: 0.3831 (tmm) outliers start: 55 outliers final: 27 residues processed: 263 average time/residue: 0.5967 time to fit residues: 181.9950 Evaluate side-chains 232 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 469 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 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 531 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 531 LEU 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 269 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 293 VAL 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: 5.9990 chunk 17 optimal weight: 0.0970 chunk 231 optimal weight: 2.9990 chunk 281 optimal weight: 0.8980 chunk 276 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120031 restraints weight = 29404.777| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.94 r_work: 0.3198 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25986 Z= 0.114 Angle : 0.584 9.049 35238 Z= 0.291 Chirality : 0.047 0.151 3984 Planarity : 0.004 0.037 4470 Dihedral : 5.032 42.483 3516 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 2.32 % Allowed : 22.29 % Favored : 75.38 % 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 aren not related in a simple way. whole: -0.72 (0.15), residues: 3156 helix: 0.83 (0.17), residues: 1080 sheet: -0.80 (0.22), residues: 600 loop : -1.31 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.016 0.001 TYR F 174 PHE 0.009 0.001 PHE A 225 TRP 0.007 0.001 TRP E 402 HIS 0.006 0.001 HIS F 267 Details of bonding type rmsd covalent geometry : bond 0.00258 (25980) covalent geometry : angle 0.58430 (35238) hydrogen bonds : bond 0.03065 ( 846) hydrogen bonds : angle 4.40116 ( 2340) Misc. bond : bond 0.00032 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 1.023 Fit side-chains REVERT: A 343 GLN cc_start: 0.8253 (mp10) cc_final: 0.7729 (mp10) REVERT: A 452 SER cc_start: 0.3844 (OUTLIER) cc_final: 0.3461 (t) REVERT: A 461 MET cc_start: 0.4080 (ppp) cc_final: 0.3444 (tmm) REVERT: A 531 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5903 (mp) REVERT: B 76 TYR cc_start: 0.9251 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: B 320 MET cc_start: 0.8698 (ptp) cc_final: 0.8470 (ptp) REVERT: B 337 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7818 (mp) REVERT: B 343 GLN cc_start: 0.8025 (mp10) cc_final: 0.7734 (mp10) REVERT: B 461 MET cc_start: 0.4337 (ppp) cc_final: 0.3708 (tmm) REVERT: B 531 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5997 (mp) REVERT: C 452 SER cc_start: 0.4061 (OUTLIER) cc_final: 0.3698 (t) REVERT: C 461 MET cc_start: 0.4067 (ppp) cc_final: 0.3850 (tmm) REVERT: D 275 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8110 (tp) REVERT: D 461 MET cc_start: 0.3971 (ppp) cc_final: 0.3724 (tpp) REVERT: E 76 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: E 337 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7899 (mp) REVERT: E 343 GLN cc_start: 0.7867 (mt0) cc_final: 0.7584 (mp10) REVERT: E 452 SER cc_start: 0.4559 (OUTLIER) cc_final: 0.4075 (t) REVERT: E 531 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6129 (mp) REVERT: F 281 LYS cc_start: 0.7557 (tttm) cc_final: 0.7335 (tttm) REVERT: F 343 GLN cc_start: 0.7885 (mt0) cc_final: 0.7548 (mp10) REVERT: F 452 SER cc_start: 0.3486 (OUTLIER) cc_final: 0.3257 (t) REVERT: F 461 MET cc_start: 0.4161 (ppp) cc_final: 0.3938 (tmm) outliers start: 64 outliers final: 34 residues processed: 243 average time/residue: 0.5916 time to fit residues: 167.8217 Evaluate side-chains 238 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain 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 176 THR 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 531 LEU Chi-restraints excluded: chain C residue 70 ASP 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 70 ASP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 221 ILE 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 293 VAL 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: 0.7980 chunk 138 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 267 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 267 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119998 restraints weight = 29393.297| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.22 r_work: 0.3194 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2347 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 : 0.586 8.697 35238 Z= 0.292 Chirality : 0.047 0.158 3984 Planarity : 0.004 0.041 4470 Dihedral : 5.013 42.388 3516 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 2.14 % Allowed : 22.40 % Favored : 75.45 % 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 aren not related in a simple way. whole: -0.70 (0.15), residues: 3156 helix: 0.86 (0.17), residues: 1080 sheet: -0.82 (0.22), residues: 600 loop : -1.28 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.006 0.001 TYR C 148 PHE 0.008 0.001 PHE F 225 TRP 0.006 0.001 TRP E 402 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00254 (25980) covalent geometry : angle 0.58569 (35238) hydrogen bonds : bond 0.03035 ( 846) hydrogen bonds : angle 4.39453 ( 2340) Misc. bond : bond 0.00030 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.736 Fit side-chains REVERT: A 343 GLN cc_start: 0.8238 (mp10) cc_final: 0.7972 (mp10) REVERT: A 452 SER cc_start: 0.4022 (OUTLIER) cc_final: 0.3691 (t) REVERT: A 461 MET cc_start: 0.4111 (ppp) cc_final: 0.3516 (tmm) REVERT: A 531 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5889 (mp) REVERT: B 76 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: B 320 MET cc_start: 0.8700 (ptp) cc_final: 0.8473 (ptp) REVERT: B 337 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7812 (mp) REVERT: B 343 GLN cc_start: 0.8023 (mp10) cc_final: 0.7806 (mp10) REVERT: B 461 MET cc_start: 0.4357 (ppp) cc_final: 0.3724 (tmm) REVERT: B 531 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.5988 (mp) REVERT: C 275 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8028 (tp) REVERT: C 452 SER cc_start: 0.3995 (OUTLIER) cc_final: 0.3657 (t) REVERT: C 461 MET cc_start: 0.4057 (ppp) cc_final: 0.3832 (tmm) REVERT: D 275 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8104 (tp) REVERT: D 461 MET cc_start: 0.4042 (ppp) cc_final: 0.3786 (tpp) REVERT: E 76 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: E 337 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7879 (mp) REVERT: E 343 GLN cc_start: 0.7859 (mt0) cc_final: 0.7576 (mp10) REVERT: E 452 SER cc_start: 0.4495 (OUTLIER) cc_final: 0.4028 (t) REVERT: E 530 LYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5240 (mttp) REVERT: E 531 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6097 (mp) REVERT: F 281 LYS cc_start: 0.7536 (tttm) cc_final: 0.7305 (tttm) REVERT: F 452 SER cc_start: 0.3901 (OUTLIER) cc_final: 0.3673 (t) REVERT: F 461 MET cc_start: 0.4142 (ppp) cc_final: 0.3917 (tmm) outliers start: 59 outliers final: 32 residues processed: 234 average time/residue: 0.6066 time to fit residues: 164.8337 Evaluate side-chains 231 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 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 176 THR 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 531 LEU 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 452 SER 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 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 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 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 E residue 531 LEU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 221 ILE 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 293 VAL 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: 0.8980 chunk 88 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 74 optimal weight: 0.4980 chunk 138 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 237 optimal weight: 0.3980 chunk 49 optimal weight: 9.9990 chunk 246 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3977 r_free = 0.3977 target = 0.169017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121486 restraints weight = 29394.740| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.05 r_work: 0.3222 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25986 Z= 0.102 Angle : 0.572 8.467 35238 Z= 0.285 Chirality : 0.046 0.144 3984 Planarity : 0.004 0.043 4470 Dihedral : 4.917 42.176 3516 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.26 % Favored : 92.55 % Rotamer: Outliers : 1.96 % Allowed : 22.59 % Favored : 75.45 % 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 aren not related in a simple way. whole: -0.62 (0.15), residues: 3156 helix: 0.93 (0.17), residues: 1080 sheet: -0.80 (0.22), residues: 600 loop : -1.23 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.006 0.001 TYR E 148 PHE 0.009 0.001 PHE D 120 TRP 0.007 0.001 TRP D 290 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00224 (25980) covalent geometry : angle 0.57178 (35238) hydrogen bonds : bond 0.02812 ( 846) hydrogen bonds : angle 4.32535 ( 2340) Misc. bond : bond 0.00025 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8763.19 seconds wall clock time: 150 minutes 2.59 seconds (9002.59 seconds total)