Starting phenix.real_space_refine on Sun Jun 22 04:55:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6m_35200/06_2025/8i6m_35200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6m_35200/06_2025/8i6m_35200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i6m_35200/06_2025/8i6m_35200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6m_35200/06_2025/8i6m_35200.map" model { file = "/net/cci-nas-00/data/ceres_data/8i6m_35200/06_2025/8i6m_35200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6m_35200/06_2025/8i6m_35200.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.198 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 16326 2.51 5 N 4254 2.21 5 O 4764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25464 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: "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: "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: "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: "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: "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: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'OLA': 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 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'OLA': 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 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'OLA': 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 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'OLA': 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 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'OLA': 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 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'OLA': 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 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 17.20, per 1000 atoms: 0.68 Number of scatterers: 25464 At special positions: 0 Unit cell: (169.338, 161.226, 98.358, 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 4764 8.00 N 4254 7.00 C 16326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.52 Conformation dependent library (CDL) restraints added in 3.3 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 36 sheets defined 37.5% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.929A pdb=" N THR A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 278 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.680A pdb=" N LEU A 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 483 through 494 removed outlier: 4.254A pdb=" N PHE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'F' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.582A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 204 removed outlier: 3.928A pdb=" N THR F 202 " --> pdb=" O GLY F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 278 Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.680A pdb=" N LEU F 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 Processing helix chain 'F' and resid 440 through 449 Processing helix chain 'F' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE F 494 " --> pdb=" O PHE F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.671A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 removed outlier: 3.929A pdb=" N THR D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 278 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.680A pdb=" N LEU D 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE D 494 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'C' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 removed outlier: 3.928A pdb=" N THR C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 278 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.679A pdb=" N LEU C 339 " --> pdb=" O GLN C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE C 494 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.928A pdb=" N THR B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 278 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.680A pdb=" N LEU B 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 126 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.929A pdb=" N THR E 202 " --> pdb=" O GLY E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 239 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 278 Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.679A pdb=" N LEU E 339 " --> pdb=" O GLN E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 Processing helix chain 'E' and resid 440 through 449 Processing helix chain 'E' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE E 494 " --> pdb=" O PHE E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.800A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 266 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.547A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER A 328 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.502A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA6, first strand: chain 'A' and resid 453 through 462 removed outlier: 3.518A pdb=" N GLU A 455 " --> pdb=" O THR A 475 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.799A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER F 266 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.548A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL F 66 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER F 328 " --> pdb=" O TYR F 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 361 through 363 removed outlier: 5.502A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 430 through 431 Processing sheet with id=AB3, first strand: chain 'F' and resid 453 through 462 removed outlier: 3.517A pdb=" N GLU F 455 " --> pdb=" O THR F 475 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.799A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER D 266 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.547A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 66 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER D 328 " --> pdb=" O TYR D 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.501A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 430 through 431 Processing sheet with id=AB9, first strand: chain 'D' and resid 453 through 462 removed outlier: 3.517A pdb=" N GLU D 455 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.800A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER C 266 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.547A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 66 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER C 328 " --> pdb=" O TYR C 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.502A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AC6, first strand: chain 'C' and resid 453 through 462 removed outlier: 3.518A pdb=" N GLU C 455 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.799A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 266 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.547A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER B 328 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.502A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 430 through 431 Processing sheet with id=AD3, first strand: chain 'B' and resid 453 through 462 removed outlier: 3.518A pdb=" N GLU B 455 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.800A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER E 266 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.546A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL E 66 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER E 328 " --> pdb=" O TYR E 318 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 361 through 363 removed outlier: 5.501A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 430 through 431 Processing sheet with id=AD9, first strand: chain 'E' and resid 453 through 462 removed outlier: 3.517A pdb=" N GLU E 455 " --> pdb=" O THR E 475 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2430 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: 13.04 Time building geometry restraints manager: 7.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4266 1.28 - 1.41: 6288 1.41 - 1.54: 15155 1.54 - 1.68: 127 1.68 - 1.81: 192 Bond restraints: 26028 Sorted by residual: bond pdb=" CA THR F 202 " pdb=" C THR F 202 " ideal model delta sigma weight residual 1.521 1.413 0.107 9.90e-03 1.02e+04 1.17e+02 bond pdb=" CA THR B 202 " pdb=" C THR B 202 " ideal model delta sigma weight residual 1.521 1.414 0.107 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR E 202 " pdb=" C THR E 202 " ideal model delta sigma weight residual 1.521 1.414 0.107 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR A 202 " pdb=" C THR A 202 " ideal model delta sigma weight residual 1.521 1.414 0.106 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR C 202 " pdb=" C THR C 202 " ideal model delta sigma weight residual 1.521 1.414 0.106 9.90e-03 1.02e+04 1.15e+02 ... (remaining 26023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 34312 2.36 - 4.72: 788 4.72 - 7.08: 120 7.08 - 9.44: 42 9.44 - 11.80: 18 Bond angle restraints: 35280 Sorted by residual: angle pdb=" C THR D 202 " pdb=" CA THR D 202 " pdb=" CB THR D 202 " ideal model delta sigma weight residual 110.08 98.28 11.80 1.57e+00 4.06e-01 5.65e+01 angle pdb=" C THR B 202 " pdb=" CA THR B 202 " pdb=" CB THR B 202 " ideal model delta sigma weight residual 110.08 98.30 11.78 1.57e+00 4.06e-01 5.63e+01 angle pdb=" C THR A 202 " pdb=" CA THR A 202 " pdb=" CB THR A 202 " ideal model delta sigma weight residual 110.08 98.30 11.78 1.57e+00 4.06e-01 5.63e+01 angle pdb=" C THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 110.08 98.32 11.76 1.57e+00 4.06e-01 5.61e+01 angle pdb=" C THR E 202 " pdb=" CA THR E 202 " pdb=" CB THR E 202 " ideal model delta sigma weight residual 110.08 98.32 11.76 1.57e+00 4.06e-01 5.61e+01 ... (remaining 35275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.81: 14725 26.81 - 53.62: 770 53.62 - 80.43: 78 80.43 - 107.24: 30 107.24 - 134.05: 3 Dihedral angle restraints: 15606 sinusoidal: 6378 harmonic: 9228 Sorted by residual: dihedral pdb=" C5' AMP E1002 " pdb=" O5' AMP E1002 " pdb=" P AMP E1002 " pdb=" O3P AMP E1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.06 -134.05 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' AMP A1002 " pdb=" O5' AMP A1002 " pdb=" P AMP A1002 " pdb=" O3P AMP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.05 -134.05 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' AMP C1002 " pdb=" O5' AMP C1002 " pdb=" P AMP C1002 " pdb=" O3P AMP C1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.03 -134.03 1 2.00e+01 2.50e-03 4.07e+01 ... (remaining 15603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3812 0.121 - 0.243: 112 0.243 - 0.364: 42 0.364 - 0.486: 12 0.486 - 0.607: 6 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA MET B 320 " pdb=" N MET B 320 " pdb=" C MET B 320 " pdb=" CB MET B 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA MET F 320 " pdb=" N MET F 320 " pdb=" C MET F 320 " pdb=" CB MET F 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" CA MET A 320 " pdb=" N MET A 320 " pdb=" C MET A 320 " pdb=" CB MET A 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 ... (remaining 3981 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA C1001 " -0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA C1001 " 0.101 2.00e-02 2.50e+03 pdb=" C8 OLA C1001 " -0.101 2.00e-02 2.50e+03 pdb=" C9 OLA C1001 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA D1001 " 0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA D1001 " -0.101 2.00e-02 2.50e+03 pdb=" C8 OLA D1001 " 0.101 2.00e-02 2.50e+03 pdb=" C9 OLA D1001 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA F1001 " 0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA F1001 " -0.100 2.00e-02 2.50e+03 pdb=" C8 OLA F1001 " 0.101 2.00e-02 2.50e+03 pdb=" C9 OLA F1001 " -0.233 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 865 2.71 - 3.26: 24714 3.26 - 3.81: 41241 3.81 - 4.35: 55634 4.35 - 4.90: 90516 Nonbonded interactions: 212970 Sorted by model distance: nonbonded pdb=" O1P AMP E1002 " pdb="MG MG E1003 " model vdw 2.165 2.170 nonbonded pdb=" O3P AMP B1002 " pdb="MG MG B1003 " model vdw 2.166 2.170 nonbonded pdb=" O1P AMP C1002 " pdb="MG MG C1003 " model vdw 2.166 2.170 nonbonded pdb=" O1P AMP A1002 " pdb="MG MG A1003 " model vdw 2.166 2.170 nonbonded pdb=" O3P AMP D1002 " pdb="MG MG D1003 " model vdw 2.167 2.170 ... (remaining 212965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 64.220 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.007 0.137 26034 Z= 0.493 Angle : 0.863 11.799 35280 Z= 0.495 Chirality : 0.067 0.607 3984 Planarity : 0.008 0.179 4470 Dihedral : 16.142 134.054 9666 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.17 % Favored : 91.63 % Rotamer: Outliers : 0.80 % Allowed : 18.81 % Favored : 80.39 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 3156 helix: 0.06 (0.16), residues: 1074 sheet: -1.22 (0.21), residues: 582 loop : -1.31 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 466 HIS 0.005 0.001 HIS E 228 PHE 0.023 0.002 PHE E 186 TYR 0.013 0.001 TYR E 318 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.21392 ( 876) hydrogen bonds : angle 6.79100 ( 2430) covalent geometry : bond 0.00697 (26028) covalent geometry : angle 0.86264 (35280) Misc. bond : bond 0.00116 ( 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 287 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.8442 (mtt) cc_final: 0.8103 (mtt) REVERT: D 158 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7951 (mp0) REVERT: D 176 THR cc_start: 0.8097 (t) cc_final: 0.7629 (m) REVERT: D 395 ASN cc_start: 0.8412 (m-40) cc_final: 0.8167 (m110) REVERT: C 58 MET cc_start: 0.8460 (mtt) cc_final: 0.8124 (mtt) REVERT: E 176 THR cc_start: 0.8144 (t) cc_final: 0.7661 (m) REVERT: E 395 ASN cc_start: 0.8389 (m-40) cc_final: 0.8140 (m110) outliers start: 22 outliers final: 4 residues processed: 278 average time/residue: 1.5290 time to fit residues: 484.9635 Evaluate side-chains 214 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 210 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain B residue 163 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 244 optimal weight: 0.0980 chunk 94 optimal weight: 8.9990 chunk 148 optimal weight: 40.0000 chunk 182 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 209 GLN A 213 HIS A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS F 12 GLN F 29 GLN F 117 HIS F 154 GLN F 209 GLN F 213 HIS F 226 HIS F 228 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS F 450 HIS D 12 GLN D 29 GLN D 117 HIS D 209 GLN D 213 HIS D 226 HIS D 228 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS C 6 ASN C 12 GLN C 29 GLN C 117 HIS C 154 GLN C 209 GLN C 213 HIS C 226 HIS C 228 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 HIS B 6 ASN B 12 GLN B 29 GLN B 117 HIS B 209 GLN B 213 HIS B 226 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS B 450 HIS E 12 GLN E 29 GLN E 117 HIS E 209 GLN E 213 HIS E 226 HIS E 228 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.165064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120142 restraints weight = 28216.791| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.82 r_work: 0.3164 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26034 Z= 0.187 Angle : 0.669 7.300 35280 Z= 0.344 Chirality : 0.050 0.203 3984 Planarity : 0.004 0.041 4470 Dihedral : 8.595 95.546 3560 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.84 % Favored : 90.97 % Rotamer: Outliers : 2.87 % Allowed : 16.49 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3156 helix: 0.51 (0.16), residues: 1080 sheet: -1.00 (0.19), residues: 660 loop : -1.65 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 466 HIS 0.009 0.001 HIS A 228 PHE 0.016 0.002 PHE D 225 TYR 0.012 0.002 TYR A 174 ARG 0.002 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 876) hydrogen bonds : angle 5.08417 ( 2430) covalent geometry : bond 0.00452 (26028) covalent geometry : angle 0.66883 (35280) Misc. bond : bond 0.00078 ( 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 310 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 231 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.8493 (mtt) cc_final: 0.8129 (mtm) REVERT: F 107 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7528 (t70) REVERT: F 281 LYS cc_start: 0.7549 (ttpp) cc_final: 0.7203 (ttmm) REVERT: F 399 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8246 (mptm) REVERT: F 425 ASP cc_start: 0.8002 (t0) cc_final: 0.7797 (t70) REVERT: F 461 MET cc_start: 0.4976 (ppp) cc_final: 0.4378 (tmt) REVERT: D 100 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: D 150 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7572 (mpt-90) REVERT: D 203 ILE cc_start: 0.8811 (mm) cc_final: 0.8611 (tt) REVERT: D 395 ASN cc_start: 0.8310 (m-40) cc_final: 0.8074 (m110) REVERT: C 58 MET cc_start: 0.8500 (mtt) cc_final: 0.8114 (mtt) REVERT: C 107 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7574 (t70) REVERT: C 343 GLN cc_start: 0.7111 (mp10) cc_final: 0.6454 (mt0) REVERT: C 347 TYR cc_start: 0.8650 (m-80) cc_final: 0.8408 (m-80) REVERT: C 418 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6526 (pm20) REVERT: C 461 MET cc_start: 0.5079 (ppp) cc_final: 0.4439 (tmt) REVERT: B 461 MET cc_start: 0.4804 (ppp) cc_final: 0.4404 (tmt) REVERT: E 100 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: E 150 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7593 (mpt-90) REVERT: E 203 ILE cc_start: 0.8824 (mm) cc_final: 0.8608 (tt) REVERT: E 395 ASN cc_start: 0.8241 (m-40) cc_final: 0.7995 (m110) outliers start: 79 outliers final: 27 residues processed: 295 average time/residue: 1.5207 time to fit residues: 520.6895 Evaluate side-chains 234 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 399 LYS Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 212 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** F 267 HIS D 267 HIS ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 HIS ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.161666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116197 restraints weight = 28368.729| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.85 r_work: 0.3104 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 26034 Z= 0.255 Angle : 0.717 7.904 35280 Z= 0.373 Chirality : 0.053 0.251 3984 Planarity : 0.005 0.048 4470 Dihedral : 8.563 71.185 3556 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.33 % Favored : 91.48 % Rotamer: Outliers : 4.18 % Allowed : 15.90 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3156 helix: 0.45 (0.16), residues: 1086 sheet: -1.02 (0.19), residues: 660 loop : -1.74 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 402 HIS 0.011 0.002 HIS A 228 PHE 0.018 0.002 PHE D 225 TYR 0.017 0.002 TYR B 174 ARG 0.003 0.001 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.05528 ( 876) hydrogen bonds : angle 5.02599 ( 2430) covalent geometry : bond 0.00635 (26028) covalent geometry : angle 0.71717 (35280) Misc. bond : bond 0.00119 ( 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 324 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 209 time to evaluate : 3.023 Fit side-chains revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: F 107 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7624 (t70) REVERT: F 203 ILE cc_start: 0.8899 (mm) cc_final: 0.8661 (tt) REVERT: F 343 GLN cc_start: 0.7088 (mp10) cc_final: 0.6331 (mt0) REVERT: F 347 TYR cc_start: 0.8601 (m-80) cc_final: 0.8391 (m-80) REVERT: D 100 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: D 107 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7833 (t70) REVERT: D 150 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7648 (mpt-90) REVERT: D 203 ILE cc_start: 0.8861 (mm) cc_final: 0.8634 (tt) REVERT: D 367 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7758 (mmm) REVERT: D 428 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7605 (mmtp) REVERT: D 466 TRP cc_start: 0.5469 (OUTLIER) cc_final: 0.5211 (m-10) REVERT: C 107 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7642 (t70) REVERT: C 158 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8172 (mm-30) REVERT: C 203 ILE cc_start: 0.8885 (mm) cc_final: 0.8682 (tt) REVERT: C 260 GLN cc_start: 0.8327 (mm110) cc_final: 0.7607 (tt0) REVERT: C 343 GLN cc_start: 0.7132 (mp10) cc_final: 0.6507 (mt0) REVERT: C 347 TYR cc_start: 0.8652 (m-80) cc_final: 0.8441 (m-80) REVERT: C 461 MET cc_start: 0.4877 (ppp) cc_final: 0.4503 (tmt) REVERT: B 158 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: B 466 TRP cc_start: 0.5412 (OUTLIER) cc_final: 0.4809 (m100) REVERT: E 100 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: E 107 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7824 (t70) REVERT: E 150 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7676 (mpt-90) REVERT: E 203 ILE cc_start: 0.8906 (mm) cc_final: 0.8652 (tt) REVERT: E 224 MET cc_start: 0.8768 (ttt) cc_final: 0.8503 (ttt) REVERT: E 367 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7772 (mmm) REVERT: E 428 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7632 (mmtp) outliers start: 115 outliers final: 35 residues processed: 302 average time/residue: 1.4165 time to fit residues: 494.9125 Evaluate side-chains 251 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 367 MET Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 192 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 267 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN D 6 ASN ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110261 restraints weight = 28445.201| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.71 r_work: 0.3180 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26034 Z= 0.143 Angle : 0.622 7.382 35280 Z= 0.317 Chirality : 0.048 0.190 3984 Planarity : 0.004 0.042 4470 Dihedral : 8.020 59.894 3556 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.89 % Favored : 91.92 % Rotamer: Outliers : 2.65 % Allowed : 18.12 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3156 helix: 0.75 (0.16), residues: 1080 sheet: -0.94 (0.20), residues: 648 loop : -1.64 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 402 HIS 0.006 0.001 HIS A 228 PHE 0.013 0.002 PHE B 173 TYR 0.008 0.001 TYR C 234 ARG 0.002 0.000 ARG B 426 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 876) hydrogen bonds : angle 4.71590 ( 2430) covalent geometry : bond 0.00337 (26028) covalent geometry : angle 0.62207 (35280) Misc. bond : bond 0.00052 ( 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 298 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 225 time to evaluate : 5.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8160 (t0) cc_final: 0.7933 (t70) REVERT: F 107 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7553 (t70) REVERT: F 343 GLN cc_start: 0.7028 (mp10) cc_final: 0.6404 (mt0) REVERT: F 347 TYR cc_start: 0.8582 (m-80) cc_final: 0.8343 (m-80) REVERT: F 399 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8403 (mptm) REVERT: D 150 ARG cc_start: 0.8150 (mtm110) cc_final: 0.7679 (mpt-90) REVERT: C 107 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7573 (t70) REVERT: C 343 GLN cc_start: 0.7102 (mp10) cc_final: 0.6579 (mt0) REVERT: C 461 MET cc_start: 0.4930 (ppp) cc_final: 0.4563 (tmt) REVERT: E 150 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7711 (mpt-90) REVERT: E 224 MET cc_start: 0.8709 (ttt) cc_final: 0.8491 (ttt) outliers start: 73 outliers final: 31 residues processed: 281 average time/residue: 1.6921 time to fit residues: 558.2904 Evaluate side-chains 242 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 399 LYS Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 466 TRP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 481 GLN Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 172 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 59 optimal weight: 0.0870 chunk 282 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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** F 6 ASN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.162738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107291 restraints weight = 28292.039| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.72 r_work: 0.3098 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 26034 Z= 0.225 Angle : 0.689 7.684 35280 Z= 0.356 Chirality : 0.051 0.227 3984 Planarity : 0.005 0.044 4470 Dihedral : 8.136 59.399 3556 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.56 % Favored : 91.25 % Rotamer: Outliers : 3.30 % Allowed : 18.16 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3156 helix: 0.68 (0.16), residues: 1080 sheet: -0.96 (0.19), residues: 660 loop : -1.73 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 402 HIS 0.009 0.001 HIS B 228 PHE 0.018 0.002 PHE E 225 TYR 0.014 0.002 TYR A 174 ARG 0.003 0.000 ARG E 190 Details of bonding type rmsd hydrogen bonds : bond 0.05042 ( 876) hydrogen bonds : angle 4.85291 ( 2430) covalent geometry : bond 0.00559 (26028) covalent geometry : angle 0.68896 (35280) Misc. bond : bond 0.00092 ( 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 303 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 212 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8172 (mm-30) REVERT: A 533 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4780 (pt) REVERT: F 107 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7611 (t70) REVERT: F 343 GLN cc_start: 0.7072 (mp10) cc_final: 0.6460 (mt0) REVERT: F 347 TYR cc_start: 0.8601 (m-80) cc_final: 0.8355 (m-80) REVERT: D 100 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: D 150 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7720 (mpt-90) REVERT: D 367 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7749 (mmm) REVERT: C 107 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7666 (t70) REVERT: C 260 GLN cc_start: 0.8349 (mm110) cc_final: 0.7614 (tt0) REVERT: C 343 GLN cc_start: 0.7084 (mp10) cc_final: 0.6502 (mt0) REVERT: C 347 TYR cc_start: 0.8663 (m-80) cc_final: 0.8423 (m-80) REVERT: C 461 MET cc_start: 0.4841 (ppp) cc_final: 0.4444 (tmt) REVERT: B 418 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6638 (pm20) REVERT: B 466 TRP cc_start: 0.5340 (OUTLIER) cc_final: 0.4924 (m-10) REVERT: E 100 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: E 150 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7731 (mpt-90) REVERT: E 367 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7709 (mmm) outliers start: 91 outliers final: 43 residues processed: 280 average time/residue: 1.3684 time to fit residues: 444.2237 Evaluate side-chains 256 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 466 TRP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 481 GLN Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 367 MET Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 301 optimal weight: 0.6980 chunk 303 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 280 optimal weight: 0.0370 chunk 71 optimal weight: 0.0980 chunk 262 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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** C 408 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.166625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112521 restraints weight = 28535.183| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.70 r_work: 0.3195 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26034 Z= 0.121 Angle : 0.600 7.891 35280 Z= 0.301 Chirality : 0.046 0.175 3984 Planarity : 0.004 0.039 4470 Dihedral : 7.441 59.882 3556 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.26 % Favored : 92.55 % Rotamer: Outliers : 2.61 % Allowed : 19.32 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3156 helix: 0.89 (0.16), residues: 1086 sheet: -0.83 (0.20), residues: 648 loop : -1.56 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 466 HIS 0.005 0.001 HIS A 228 PHE 0.012 0.001 PHE C 173 TYR 0.008 0.001 TYR F 234 ARG 0.002 0.000 ARG F 529 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 876) hydrogen bonds : angle 4.58434 ( 2430) covalent geometry : bond 0.00280 (26028) covalent geometry : angle 0.60034 (35280) Misc. bond : bond 0.00031 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 216 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8184 (t0) cc_final: 0.7980 (t70) REVERT: A 533 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4829 (pt) REVERT: F 107 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7598 (t70) REVERT: F 343 GLN cc_start: 0.6971 (mp10) cc_final: 0.6405 (mt0) REVERT: F 347 TYR cc_start: 0.8587 (m-80) cc_final: 0.8376 (m-80) REVERT: D 395 ASN cc_start: 0.8347 (m-40) cc_final: 0.8125 (m110) REVERT: C 107 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7549 (t70) REVERT: C 196 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8930 (m) REVERT: C 203 ILE cc_start: 0.8764 (mm) cc_final: 0.8505 (tt) REVERT: C 343 GLN cc_start: 0.7058 (mp10) cc_final: 0.6502 (mt0) REVERT: C 347 TYR cc_start: 0.8636 (m-80) cc_final: 0.8421 (m-80) REVERT: C 461 MET cc_start: 0.4860 (ppp) cc_final: 0.4529 (tmt) REVERT: B 418 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: E 150 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7730 (mpt-90) REVERT: E 395 ASN cc_start: 0.8284 (m-40) cc_final: 0.8052 (m110) outliers start: 72 outliers final: 34 residues processed: 268 average time/residue: 1.3271 time to fit residues: 414.3870 Evaluate side-chains 242 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 466 TRP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 152 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 75 optimal weight: 0.0370 chunk 125 optimal weight: 3.9990 chunk 254 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.164973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110419 restraints weight = 28591.609| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.71 r_work: 0.3166 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26034 Z= 0.145 Angle : 0.626 8.033 35280 Z= 0.316 Chirality : 0.047 0.182 3984 Planarity : 0.004 0.040 4470 Dihedral : 7.483 58.673 3556 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.83 % Favored : 91.98 % Rotamer: Outliers : 2.11 % Allowed : 19.68 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3156 helix: 0.91 (0.16), residues: 1086 sheet: -0.83 (0.20), residues: 660 loop : -1.55 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 466 HIS 0.007 0.001 HIS B 228 PHE 0.014 0.002 PHE D 225 TYR 0.010 0.001 TYR C 318 ARG 0.002 0.000 ARG B 426 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 876) hydrogen bonds : angle 4.61881 ( 2430) covalent geometry : bond 0.00347 (26028) covalent geometry : angle 0.62611 (35280) Misc. bond : bond 0.00044 ( 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 270 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8198 (t0) cc_final: 0.7991 (t70) REVERT: F 107 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7542 (t70) REVERT: F 343 GLN cc_start: 0.6993 (mp10) cc_final: 0.6422 (mt0) REVERT: F 347 TYR cc_start: 0.8605 (m-80) cc_final: 0.8382 (m-80) REVERT: D 150 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7710 (mpt-90) REVERT: D 395 ASN cc_start: 0.8405 (m-40) cc_final: 0.8186 (m110) REVERT: D 428 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7735 (mmtt) REVERT: C 107 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7594 (t70) REVERT: C 343 GLN cc_start: 0.7063 (mp10) cc_final: 0.6528 (mt0) REVERT: C 347 TYR cc_start: 0.8648 (m-80) cc_final: 0.8418 (m-80) REVERT: C 461 MET cc_start: 0.4717 (ppp) cc_final: 0.4380 (tmt) REVERT: B 418 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6733 (pm20) REVERT: E 150 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7722 (mpt-90) REVERT: E 395 ASN cc_start: 0.8341 (m-40) cc_final: 0.8105 (m110) outliers start: 58 outliers final: 35 residues processed: 255 average time/residue: 1.3312 time to fit residues: 395.8739 Evaluate side-chains 243 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 466 TRP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 256 optimal weight: 20.0000 chunk 237 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 120 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS F 154 GLN ** B 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 = 0.3917 r_free = 0.3917 target = 0.163529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104230 restraints weight = 27109.979| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.85 r_work: 0.3070 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26034 Z= 0.152 Angle : 0.632 8.893 35280 Z= 0.319 Chirality : 0.048 0.191 3984 Planarity : 0.004 0.040 4470 Dihedral : 7.426 59.117 3556 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.76 % Favored : 92.05 % Rotamer: Outliers : 2.18 % Allowed : 19.86 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3156 helix: 0.90 (0.16), residues: 1086 sheet: -0.87 (0.19), residues: 660 loop : -1.55 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 466 HIS 0.011 0.001 HIS D 267 PHE 0.014 0.002 PHE B 173 TYR 0.009 0.001 TYR C 318 ARG 0.002 0.000 ARG B 426 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 876) hydrogen bonds : angle 4.66393 ( 2430) covalent geometry : bond 0.00367 (26028) covalent geometry : angle 0.63245 (35280) Misc. bond : bond 0.00043 ( 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 269 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 209 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: A 320 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.6441 (ttt) REVERT: A 425 ASP cc_start: 0.8158 (t0) cc_final: 0.7943 (t70) REVERT: A 533 LEU cc_start: 0.4945 (OUTLIER) cc_final: 0.4584 (pt) REVERT: F 107 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7518 (t70) REVERT: F 343 GLN cc_start: 0.6904 (mp10) cc_final: 0.6307 (mt0) REVERT: F 347 TYR cc_start: 0.8597 (m-80) cc_final: 0.8348 (m-80) REVERT: D 150 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7572 (mpt-90) REVERT: D 428 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7667 (mmtt) REVERT: C 107 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7548 (t70) REVERT: C 343 GLN cc_start: 0.6976 (mp10) cc_final: 0.6397 (mt0) REVERT: C 347 TYR cc_start: 0.8605 (m-80) cc_final: 0.8350 (m-80) REVERT: C 461 MET cc_start: 0.4726 (ppp) cc_final: 0.4410 (tmt) REVERT: B 418 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6686 (pm20) REVERT: E 150 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7571 (mpt-90) REVERT: E 154 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6988 (pp30) REVERT: E 428 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7736 (mmtt) outliers start: 60 outliers final: 41 residues processed: 255 average time/residue: 1.3717 time to fit residues: 405.2616 Evaluate side-chains 253 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 466 TRP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 237 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 242 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 258 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS D 395 ASN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.160553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100689 restraints weight = 27311.870| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.85 r_work: 0.3018 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 26034 Z= 0.234 Angle : 0.712 9.206 35280 Z= 0.365 Chirality : 0.052 0.224 3984 Planarity : 0.005 0.043 4470 Dihedral : 7.905 59.972 3556 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.17 % Favored : 91.63 % Rotamer: Outliers : 2.43 % Allowed : 19.75 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3156 helix: 0.76 (0.16), residues: 1080 sheet: -0.97 (0.19), residues: 660 loop : -1.63 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 290 HIS 0.011 0.002 HIS A 228 PHE 0.018 0.002 PHE D 225 TYR 0.014 0.002 TYR A 174 ARG 0.004 0.000 ARG E 190 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 876) hydrogen bonds : angle 4.88767 ( 2430) covalent geometry : bond 0.00581 (26028) covalent geometry : angle 0.71250 (35280) Misc. bond : bond 0.00074 ( 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 270 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8164 (mm-30) REVERT: A 533 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4860 (pt) REVERT: F 107 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7566 (t70) REVERT: F 196 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8885 (m) REVERT: F 203 ILE cc_start: 0.8822 (mm) cc_final: 0.8496 (tt) REVERT: F 343 GLN cc_start: 0.6989 (mp10) cc_final: 0.6373 (mt0) REVERT: F 347 TYR cc_start: 0.8608 (m-80) cc_final: 0.8344 (m-80) REVERT: D 150 ARG cc_start: 0.8127 (mtm110) cc_final: 0.7592 (mpt-90) REVERT: C 107 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7621 (t70) REVERT: C 203 ILE cc_start: 0.8837 (mm) cc_final: 0.8522 (tt) REVERT: C 260 GLN cc_start: 0.8311 (mm110) cc_final: 0.7432 (tt0) REVERT: C 343 GLN cc_start: 0.7003 (mp10) cc_final: 0.6481 (mt0) REVERT: C 347 TYR cc_start: 0.8640 (m-80) cc_final: 0.8423 (m-80) REVERT: C 461 MET cc_start: 0.4690 (ppp) cc_final: 0.4448 (tmt) REVERT: B 418 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6617 (pm20) REVERT: E 150 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7584 (mpt-90) REVERT: E 428 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7792 (mmtp) outliers start: 67 outliers final: 48 residues processed: 256 average time/residue: 1.3729 time to fit residues: 412.6159 Evaluate side-chains 253 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 466 TRP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 170 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 182 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 165 optimal weight: 0.0570 chunk 166 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.165448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106860 restraints weight = 27366.922| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.85 r_work: 0.3107 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26034 Z= 0.120 Angle : 0.608 7.791 35280 Z= 0.304 Chirality : 0.046 0.175 3984 Planarity : 0.004 0.039 4470 Dihedral : 7.243 59.384 3556 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.97 % Favored : 92.84 % Rotamer: Outliers : 1.45 % Allowed : 21.02 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 3156 helix: 0.94 (0.16), residues: 1086 sheet: -0.84 (0.20), residues: 648 loop : -1.49 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 HIS 0.008 0.001 HIS D 267 PHE 0.012 0.001 PHE E 225 TYR 0.009 0.001 TYR C 318 ARG 0.002 0.000 ARG B 426 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 876) hydrogen bonds : angle 4.60804 ( 2430) covalent geometry : bond 0.00278 (26028) covalent geometry : angle 0.60800 (35280) Misc. bond : bond 0.00024 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LYS cc_start: 0.8385 (mttt) cc_final: 0.8105 (mmtm) REVERT: A 533 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4854 (pt) REVERT: F 107 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7579 (t70) REVERT: F 343 GLN cc_start: 0.6871 (mp10) cc_final: 0.6296 (mt0) REVERT: F 347 TYR cc_start: 0.8576 (m-80) cc_final: 0.8335 (m-80) REVERT: D 150 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7550 (mpt-90) REVERT: C 107 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7502 (t70) REVERT: C 343 GLN cc_start: 0.6928 (mp10) cc_final: 0.6334 (mt0) REVERT: C 347 TYR cc_start: 0.8583 (m-80) cc_final: 0.8337 (m-80) REVERT: C 461 MET cc_start: 0.4778 (ppp) cc_final: 0.4446 (tmt) REVERT: B 274 HIS cc_start: 0.8601 (t-90) cc_final: 0.8257 (t70) REVERT: B 418 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: E 150 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7550 (mpt-90) REVERT: E 154 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6989 (pp30) REVERT: E 428 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7744 (mmtt) outliers start: 40 outliers final: 32 residues processed: 245 average time/residue: 1.3493 time to fit residues: 384.8399 Evaluate side-chains 243 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 481 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 253 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 268 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101514 restraints weight = 27128.275| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.84 r_work: 0.3030 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 26034 Z= 0.210 Angle : 0.692 8.779 35280 Z= 0.353 Chirality : 0.050 0.210 3984 Planarity : 0.004 0.042 4470 Dihedral : 7.652 59.281 3556 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.11 % Favored : 91.70 % Rotamer: Outliers : 1.89 % Allowed : 20.92 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3156 helix: 0.79 (0.16), residues: 1086 sheet: -0.95 (0.19), residues: 660 loop : -1.58 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 230 HIS 0.010 0.001 HIS B 228 PHE 0.017 0.002 PHE E 225 TYR 0.013 0.002 TYR B 174 ARG 0.003 0.000 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 876) hydrogen bonds : angle 4.80334 ( 2430) covalent geometry : bond 0.00520 (26028) covalent geometry : angle 0.69249 (35280) Misc. bond : bond 0.00064 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21826.27 seconds wall clock time: 380 minutes 36.82 seconds (22836.82 seconds total)