Starting phenix.real_space_refine on Sat Aug 8 03:08:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i6m_35200/08_2026/8i6m_35200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6m_35200/08_2026/8i6m_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2026/8i6m_35200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2026/8i6m_35200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2026/8i6m_35200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2026/8i6m_35200.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2026/8i6m_35200.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2026/8i6m_35200.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.12, per 1000 atoms: 0.20 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: 1.84 Conformation dependent library (CDL) restraints added in 976.3 milliseconds 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: 0.79 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: 4.83 Time building geometry restraints manager: 2.54 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: 34354 2.36 - 4.72: 770 4.72 - 7.08: 108 7.08 - 9.44: 30 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: 3818 0.121 - 0.243: 106 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'D' selection = chain 'C' selection = chain 'B' selection = chain 'E' } 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.970 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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= 0.492 Angle : 0.837 11.799 35280 Z= 0.490 Chirality : 0.066 0.607 3984 Planarity : 0.008 0.179 4470 Dihedral : 16.136 134.054 9666 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.71 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (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 ARG 0.001 0.000 ARG A 502 TYR 0.013 0.001 TYR E 318 PHE 0.023 0.002 PHE E 186 TRP 0.020 0.002 TRP E 466 HIS 0.005 0.001 HIS E 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.49 (26028) covalent geometry : angle 0.83683 / 0.49 (35280) hydrogen bonds : bond 0.21392 / 14.44 ( 876) hydrogen bonds : angle 6.79100 / 4.83 ( 2430) Misc. bond : bond 0.00116 / 0.05 ( 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 : 0.977 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: 0.6961 time to fit residues: 221.0163 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 : 0.879 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 6 ASN F 12 GLN F 29 GLN F 117 HIS F 154 GLN F 209 GLN F 213 HIS F 226 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 267 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 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 6 ASN E 12 GLN E 29 GLN E 117 HIS E 209 GLN E 213 HIS E 226 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119691 restraints weight = 27180.777| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.77 r_work: 0.3140 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26034 Z= 0.127 Angle : 0.593 6.462 35280 Z= 0.303 Chirality : 0.046 0.188 3984 Planarity : 0.004 0.037 4470 Dihedral : 8.531 99.397 3560 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.21 % Favored : 91.60 % Rotamer: Outliers : 2.11 % Allowed : 17.32 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 3156 helix: 0.66 (0.16), residues: 1080 sheet: -0.93 (0.20), residues: 648 loop : -1.52 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 502 TYR 0.008 0.001 TYR C 234 PHE 0.011 0.001 PHE D 225 TRP 0.014 0.001 TRP C 466 HIS 0.006 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (26028) covalent geometry : angle 0.59286 / 0.30 (35280) hydrogen bonds : bond 0.04276 / 2.89 ( 876) hydrogen bonds : angle 4.98623 / 3.57 ( 2430) Misc. bond : bond 0.00048 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6768 (pt0) REVERT: F 58 MET cc_start: 0.8335 (mtt) cc_final: 0.7928 (mtt) REVERT: F 107 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7837 (t70) REVERT: F 418 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: F 461 MET cc_start: 0.4885 (ppp) cc_final: 0.4230 (tmt) REVERT: D 395 ASN cc_start: 0.8231 (m-40) cc_final: 0.7995 (m110) REVERT: C 58 MET cc_start: 0.8352 (mtt) cc_final: 0.7956 (mtt) REVERT: C 107 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7872 (t70) REVERT: C 343 GLN cc_start: 0.7162 (mp10) cc_final: 0.6527 (mt0) REVERT: C 347 TYR cc_start: 0.8703 (m-80) cc_final: 0.8471 (m-80) REVERT: C 418 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6580 (pm20) REVERT: C 461 MET cc_start: 0.5124 (ppp) cc_final: 0.4280 (tmt) REVERT: B 461 MET cc_start: 0.4766 (ppp) cc_final: 0.4268 (tmt) REVERT: E 150 ARG cc_start: 0.8178 (mtm110) cc_final: 0.7741 (mpt-90) REVERT: E 395 ASN cc_start: 0.8208 (m-40) cc_final: 0.7956 (m110) outliers start: 58 outliers final: 17 residues processed: 283 average time/residue: 0.6421 time to fit residues: 210.9359 Evaluate side-chains 222 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 418 GLU 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 394 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain D residue 61 LYS 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 163 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 418 GLU 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 61 LYS Chi-restraints excluded: chain E residue 227 VAL 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 97 optimal weight: 0.0070 chunk 90 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 206 optimal weight: 30.0000 chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 93 optimal weight: 0.0010 chunk 184 optimal weight: 0.9990 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.168232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120582 restraints weight = 27310.276| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.80 r_work: 0.3130 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26034 Z= 0.112 Angle : 0.562 6.448 35280 Z= 0.285 Chirality : 0.045 0.160 3984 Planarity : 0.004 0.037 4470 Dihedral : 8.128 60.844 3556 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 2.47 % Allowed : 17.86 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 3156 helix: 0.89 (0.16), residues: 1080 sheet: -0.76 (0.20), residues: 648 loop : -1.45 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 190 TYR 0.007 0.001 TYR A 148 PHE 0.010 0.001 PHE E 225 TRP 0.010 0.001 TRP D 466 HIS 0.007 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (26028) covalent geometry : angle 0.56197 / 0.29 (35280) hydrogen bonds : bond 0.03708 / 2.50 ( 876) hydrogen bonds : angle 4.65231 / 3.32 ( 2430) Misc. bond : bond 0.00041 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.8304 (mtt) cc_final: 0.8004 (mtm) REVERT: F 107 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7973 (t70) REVERT: F 418 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: D 395 ASN cc_start: 0.8262 (m-40) cc_final: 0.8047 (m110) REVERT: C 58 MET cc_start: 0.8325 (mtt) cc_final: 0.7926 (mtt) REVERT: C 347 TYR cc_start: 0.8753 (m-80) cc_final: 0.8525 (m-80) REVERT: C 418 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6702 (pm20) REVERT: C 461 MET cc_start: 0.4849 (ppp) cc_final: 0.4418 (tmt) REVERT: B 461 MET cc_start: 0.4940 (ppp) cc_final: 0.4482 (tmt) REVERT: E 150 ARG cc_start: 0.8278 (mtm110) cc_final: 0.7894 (mpt-90) REVERT: E 154 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7078 (pp30) REVERT: E 395 ASN cc_start: 0.8175 (m-40) cc_final: 0.7938 (m110) outliers start: 68 outliers final: 20 residues processed: 291 average time/residue: 0.6669 time to fit residues: 223.4662 Evaluate side-chains 227 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 320 MET Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE 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 76 TYR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 394 ASP 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 106 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 218 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113621 restraints weight = 28453.588| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.71 r_work: 0.3213 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26034 Z= 0.132 Angle : 0.593 7.623 35280 Z= 0.302 Chirality : 0.046 0.167 3984 Planarity : 0.004 0.037 4470 Dihedral : 7.846 58.297 3556 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 2.72 % Allowed : 18.08 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.15), residues: 3156 helix: 0.96 (0.16), residues: 1080 sheet: -0.76 (0.20), residues: 648 loop : -1.45 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 190 TYR 0.009 0.001 TYR C 234 PHE 0.012 0.002 PHE E 225 TRP 0.007 0.001 TRP F 402 HIS 0.007 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (26028) covalent geometry : angle 0.59259 / 0.30 (35280) hydrogen bonds : bond 0.03964 / 2.66 ( 876) hydrogen bonds : angle 4.62332 / 3.29 ( 2430) Misc. bond : bond 0.00044 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 206 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: F 58 MET cc_start: 0.8387 (mtt) cc_final: 0.8042 (mtm) REVERT: F 107 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7530 (t70) REVERT: F 347 TYR cc_start: 0.8596 (m-80) cc_final: 0.8363 (m-80) REVERT: F 418 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6646 (pm20) REVERT: D 395 ASN cc_start: 0.8263 (m-40) cc_final: 0.8040 (m110) REVERT: C 58 MET cc_start: 0.8393 (mtt) cc_final: 0.8035 (mtm) REVERT: C 343 GLN cc_start: 0.7079 (mp10) cc_final: 0.6380 (mt0) REVERT: C 347 TYR cc_start: 0.8649 (m-80) cc_final: 0.8428 (m-80) REVERT: C 418 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6622 (pm20) REVERT: C 461 MET cc_start: 0.4941 (ppp) cc_final: 0.4528 (tmt) REVERT: B 418 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6647 (pm20) REVERT: E 150 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7668 (mpt-90) REVERT: E 154 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6961 (pp30) REVERT: E 395 ASN cc_start: 0.8166 (m-40) cc_final: 0.7917 (m110) outliers start: 75 outliers final: 24 residues processed: 262 average time/residue: 0.6582 time to fit residues: 198.8446 Evaluate side-chains 217 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 271 THR 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 418 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 394 ASP 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 86 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 418 GLU 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 394 ASP 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 32 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 HIS ** E 267 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 = 0.3918 r_free = 0.3918 target = 0.162732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117324 restraints weight = 28297.688| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.86 r_work: 0.3110 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2078 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 : 0.699 10.330 35280 Z= 0.362 Chirality : 0.051 0.232 3984 Planarity : 0.005 0.042 4470 Dihedral : 8.303 58.246 3556 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.33 % Favored : 91.48 % Rotamer: Outliers : 3.12 % Allowed : 17.79 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 3156 helix: 0.80 (0.16), residues: 1080 sheet: -0.88 (0.19), residues: 660 loop : -1.62 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 190 TYR 0.014 0.002 TYR A 174 PHE 0.018 0.002 PHE E 225 TRP 0.016 0.002 TRP F 290 HIS 0.010 0.002 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.23 (26028) covalent geometry : angle 0.69922 / 0.36 (35280) hydrogen bonds : bond 0.05212 / 3.44 ( 876) hydrogen bonds : angle 4.97219 / 3.56 ( 2430) Misc. bond : bond 0.00104 / 0.05 ( 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 293 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 207 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8183 (mm-30) REVERT: A 418 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: A 425 ASP cc_start: 0.8123 (t0) cc_final: 0.7892 (t70) REVERT: A 533 LEU cc_start: 0.5180 (OUTLIER) cc_final: 0.4863 (pt) REVERT: F 58 MET cc_start: 0.8590 (mtt) cc_final: 0.8247 (mtm) REVERT: F 107 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7590 (t70) REVERT: F 347 TYR cc_start: 0.8583 (m-80) cc_final: 0.8362 (m-80) REVERT: D 100 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: C 58 MET cc_start: 0.8568 (mtt) cc_final: 0.8219 (mtm) REVERT: C 107 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7638 (t70) REVERT: C 343 GLN cc_start: 0.6992 (mp10) cc_final: 0.6381 (mt0) REVERT: C 461 MET cc_start: 0.4732 (ppp) cc_final: 0.4370 (tmt) REVERT: B 418 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6549 (pm20) REVERT: E 150 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7597 (mpt-90) REVERT: E 367 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7683 (mmm) outliers start: 86 outliers final: 37 residues processed: 275 average time/residue: 0.6742 time to fit residues: 214.0989 Evaluate side-chains 238 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 418 GLU 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 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 438 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 176 THR 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 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 C residue 42 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 107 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 C residue 481 GLN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 418 GLU 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 271 THR Chi-restraints excluded: chain E residue 367 MET Chi-restraints excluded: chain E residue 394 ASP 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 103 optimal weight: 20.0000 chunk 277 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 270 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.165593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120685 restraints weight = 28505.241| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.89 r_work: 0.3173 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26034 Z= 0.146 Angle : 0.616 7.490 35280 Z= 0.315 Chirality : 0.047 0.194 3984 Planarity : 0.004 0.039 4470 Dihedral : 8.027 58.707 3556 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.89 % Rotamer: Outliers : 2.54 % Allowed : 18.99 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3156 helix: 0.93 (0.16), residues: 1080 sheet: -0.84 (0.19), residues: 660 loop : -1.58 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 190 TYR 0.008 0.001 TYR C 318 PHE 0.014 0.002 PHE B 173 TRP 0.008 0.001 TRP C 402 HIS 0.008 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (26028) covalent geometry : angle 0.61593 / 0.32 (35280) hydrogen bonds : bond 0.04172 / 2.78 ( 876) hydrogen bonds : angle 4.80709 / 3.44 ( 2430) Misc. bond : bond 0.00058 / 0.03 ( 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 278 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 208 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6775 (pm20) REVERT: A 533 LEU cc_start: 0.5108 (OUTLIER) cc_final: 0.4739 (pt) REVERT: F 58 MET cc_start: 0.8444 (mtt) cc_final: 0.8058 (mtm) REVERT: F 107 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7536 (t70) REVERT: F 347 TYR cc_start: 0.8549 (m-80) cc_final: 0.8292 (m-80) REVERT: D 395 ASN cc_start: 0.8382 (m-40) cc_final: 0.8159 (m110) REVERT: C 58 MET cc_start: 0.8417 (mtt) cc_final: 0.8072 (mtm) REVERT: C 107 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7578 (t70) REVERT: C 343 GLN cc_start: 0.7003 (mp10) cc_final: 0.6439 (mt0) REVERT: C 461 MET cc_start: 0.4742 (ppp) cc_final: 0.4421 (tmt) REVERT: B 418 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: B 533 LEU cc_start: 0.5321 (OUTLIER) cc_final: 0.4997 (pt) REVERT: E 150 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7600 (mpt-90) REVERT: E 395 ASN cc_start: 0.8307 (m-40) cc_final: 0.8080 (m110) outliers start: 70 outliers final: 32 residues processed: 259 average time/residue: 0.6744 time to fit residues: 202.4615 Evaluate side-chains 231 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 418 GLU 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 227 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 481 GLN Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 481 GLN Chi-restraints excluded: chain B residue 86 ILE 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 533 LEU 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 394 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 235 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 219 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 279 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.166131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121593 restraints weight = 28354.240| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.85 r_work: 0.3171 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2138 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= 0.143 Angle : 0.611 7.696 35280 Z= 0.313 Chirality : 0.047 0.186 3984 Planarity : 0.004 0.039 4470 Dihedral : 7.764 59.973 3556 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.21 % Favored : 91.60 % Rotamer: Outliers : 2.36 % Allowed : 19.43 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 3156 helix: 0.97 (0.16), residues: 1080 sheet: -0.83 (0.19), residues: 660 loop : -1.54 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 190 TYR 0.008 0.001 TYR C 318 PHE 0.014 0.002 PHE E 225 TRP 0.008 0.001 TRP C 402 HIS 0.008 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (26028) covalent geometry : angle 0.61102 / 0.31 (35280) hydrogen bonds : bond 0.04145 / 2.77 ( 876) hydrogen bonds : angle 4.74242 / 3.39 ( 2430) Misc. bond : bond 0.00049 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: A 533 LEU cc_start: 0.4900 (OUTLIER) cc_final: 0.4512 (pt) REVERT: F 58 MET cc_start: 0.8426 (mtt) cc_final: 0.8054 (mtm) REVERT: F 107 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7528 (t70) REVERT: F 347 TYR cc_start: 0.8537 (m-80) cc_final: 0.8284 (m-80) REVERT: F 365 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: D 395 ASN cc_start: 0.8402 (m-40) cc_final: 0.8182 (m110) REVERT: C 58 MET cc_start: 0.8413 (mtt) cc_final: 0.8053 (mtm) REVERT: C 107 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7742 (t70) REVERT: C 343 GLN cc_start: 0.6953 (mp10) cc_final: 0.6414 (mt0) REVERT: C 461 MET cc_start: 0.4694 (ppp) cc_final: 0.4352 (tmt) REVERT: B 274 HIS cc_start: 0.8663 (t-90) cc_final: 0.8374 (t70) REVERT: B 418 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6622 (pm20) REVERT: B 425 ASP cc_start: 0.8122 (t0) cc_final: 0.7829 (t70) REVERT: E 150 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7624 (mpt-90) REVERT: E 154 GLN cc_start: 0.7360 (mm-40) cc_final: 0.6984 (pp30) REVERT: E 224 MET cc_start: 0.8622 (ttt) cc_final: 0.8379 (ttt) REVERT: E 395 ASN cc_start: 0.8312 (m-40) cc_final: 0.8086 (m110) outliers start: 65 outliers final: 39 residues processed: 259 average time/residue: 0.6840 time to fit residues: 205.5651 Evaluate side-chains 244 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 418 GLU 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 365 GLU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 481 GLN Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE 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 C residue 481 GLN Chi-restraints excluded: chain B residue 76 TYR 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 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 394 ASP Chi-restraints excluded: chain E residue 466 TRP 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 223 optimal weight: 0.5980 chunk 243 optimal weight: 0.7980 chunk 198 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 265 optimal weight: 0.0050 chunk 100 optimal weight: 20.0000 chunk 301 optimal weight: 0.1980 chunk 281 optimal weight: 3.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.169337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115761 restraints weight = 28465.806| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.71 r_work: 0.3244 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26034 Z= 0.111 Angle : 0.575 7.028 35280 Z= 0.291 Chirality : 0.045 0.159 3984 Planarity : 0.004 0.038 4470 Dihedral : 7.305 59.416 3556 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.29 % Favored : 92.52 % Rotamer: Outliers : 2.07 % Allowed : 20.26 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3156 helix: 1.09 (0.16), residues: 1080 sheet: -0.78 (0.20), residues: 648 loop : -1.42 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 190 TYR 0.009 0.001 TYR C 234 PHE 0.011 0.001 PHE C 173 TRP 0.009 0.001 TRP A 290 HIS 0.006 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (26028) covalent geometry : angle 0.57481 / 0.29 (35280) hydrogen bonds : bond 0.03468 / 2.32 ( 876) hydrogen bonds : angle 4.60229 / 3.28 ( 2430) Misc. bond : bond 0.00025 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 1.121 Fit side-chains REVERT: A 533 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4583 (pt) REVERT: F 58 MET cc_start: 0.8321 (mtt) cc_final: 0.7981 (mtm) REVERT: F 107 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7746 (t70) REVERT: F 347 TYR cc_start: 0.8550 (m-80) cc_final: 0.8343 (m-80) REVERT: F 365 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: D 154 GLN cc_start: 0.7361 (mm-40) cc_final: 0.6977 (pp30) REVERT: D 395 ASN cc_start: 0.8349 (m-40) cc_final: 0.8121 (m110) REVERT: C 58 MET cc_start: 0.8348 (mtt) cc_final: 0.7998 (mtm) REVERT: C 107 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7808 (t70) REVERT: C 343 GLN cc_start: 0.6986 (mp10) cc_final: 0.6522 (mt0) REVERT: B 418 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6740 (pm20) REVERT: E 150 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7770 (mpt-90) REVERT: E 154 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7102 (pp30) REVERT: E 395 ASN cc_start: 0.8246 (m-40) cc_final: 0.8005 (m110) outliers start: 57 outliers final: 22 residues processed: 259 average time/residue: 0.6847 time to fit residues: 205.3682 Evaluate side-chains 223 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE 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 320 MET 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 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 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 178 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 117 optimal weight: 0.0980 chunk 86 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 268 optimal weight: 0.1980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.164744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120057 restraints weight = 28449.696| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.87 r_work: 0.3162 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26034 Z= 0.168 Angle : 0.641 9.388 35280 Z= 0.328 Chirality : 0.048 0.245 3984 Planarity : 0.004 0.041 4470 Dihedral : 7.614 59.910 3556 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.89 % Favored : 91.92 % Rotamer: Outliers : 1.89 % Allowed : 20.66 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3156 helix: 0.99 (0.16), residues: 1080 sheet: -0.83 (0.19), residues: 660 loop : -1.47 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 190 TYR 0.010 0.001 TYR A 174 PHE 0.015 0.002 PHE E 225 TRP 0.008 0.001 TRP C 402 HIS 0.009 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (26028) covalent geometry : angle 0.64122 / 0.33 (35280) hydrogen bonds : bond 0.04454 / 2.96 ( 876) hydrogen bonds : angle 4.73298 / 3.38 ( 2430) Misc. bond : bond 0.00062 / 0.03 ( 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 252 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 533 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4745 (pt) REVERT: F 58 MET cc_start: 0.8446 (mtt) cc_final: 0.8059 (mtm) REVERT: F 107 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7558 (t70) REVERT: F 347 TYR cc_start: 0.8544 (m-80) cc_final: 0.8281 (m-80) REVERT: D 395 ASN cc_start: 0.8433 (m-40) cc_final: 0.8214 (m110) REVERT: C 58 MET cc_start: 0.8422 (mtt) cc_final: 0.8055 (mtm) REVERT: C 107 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7564 (t70) REVERT: C 343 GLN cc_start: 0.6974 (mp10) cc_final: 0.6462 (mt0) REVERT: B 320 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6420 (ttt) REVERT: B 418 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: B 425 ASP cc_start: 0.8117 (t0) cc_final: 0.7894 (t70) REVERT: E 150 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7634 (mpt-90) REVERT: E 154 GLN cc_start: 0.7360 (mm-40) cc_final: 0.7004 (pp30) REVERT: E 395 ASN cc_start: 0.8342 (m-40) cc_final: 0.8109 (m110) outliers start: 52 outliers final: 33 residues processed: 239 average time/residue: 0.6790 time to fit residues: 188.1451 Evaluate side-chains 232 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE 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 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 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 469 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE 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 314 VAL Chi-restraints excluded: chain C residue 320 MET 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 320 MET 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 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 466 TRP 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 239 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 247 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3955 r_free = 0.3955 target = 0.165837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121297 restraints weight = 28483.968| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.85 r_work: 0.3178 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26034 Z= 0.145 Angle : 0.622 8.695 35280 Z= 0.318 Chirality : 0.047 0.228 3984 Planarity : 0.004 0.043 4470 Dihedral : 7.487 59.326 3556 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.89 % Rotamer: Outliers : 1.56 % Allowed : 21.02 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3156 helix: 0.97 (0.16), residues: 1080 sheet: -0.87 (0.20), residues: 648 loop : -1.45 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 190 TYR 0.008 0.001 TYR F 234 PHE 0.013 0.002 PHE D 225 TRP 0.007 0.001 TRP C 402 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (26028) covalent geometry : angle 0.62159 / 0.32 (35280) hydrogen bonds : bond 0.04103 / 2.73 ( 876) hydrogen bonds : angle 4.72333 / 3.36 ( 2430) Misc. bond : bond 0.00047 / 0.02 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.996 Fit side-chains REVERT: A 533 LEU cc_start: 0.5108 (OUTLIER) cc_final: 0.4735 (pt) REVERT: F 58 MET cc_start: 0.8422 (mtt) cc_final: 0.8055 (mtm) REVERT: F 107 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7558 (t70) REVERT: F 347 TYR cc_start: 0.8541 (m-80) cc_final: 0.8277 (m-80) REVERT: D 395 ASN cc_start: 0.8411 (m-40) cc_final: 0.8189 (m110) REVERT: C 58 MET cc_start: 0.8400 (mtt) cc_final: 0.8042 (mtm) REVERT: C 107 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7757 (t70) REVERT: C 343 GLN cc_start: 0.6959 (mp10) cc_final: 0.6436 (mt0) REVERT: B 418 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: B 425 ASP cc_start: 0.8134 (t0) cc_final: 0.7861 (t70) REVERT: E 150 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7718 (mpt-90) REVERT: E 154 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7077 (pp30) REVERT: E 395 ASN cc_start: 0.8323 (m-40) cc_final: 0.8091 (m110) outliers start: 43 outliers final: 31 residues processed: 227 average time/residue: 0.6747 time to fit residues: 178.0595 Evaluate side-chains 232 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE 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 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 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 469 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE 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 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 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 314 VAL Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 394 ASP 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 181 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 289 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.166439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.111609 restraints weight = 28442.658| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.78 r_work: 0.3191 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26034 Z= 0.129 Angle : 0.602 8.196 35280 Z= 0.307 Chirality : 0.046 0.220 3984 Planarity : 0.004 0.042 4470 Dihedral : 7.354 59.085 3556 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.73 % Favored : 92.08 % Rotamer: Outliers : 1.60 % Allowed : 21.10 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 3156 helix: 1.02 (0.16), residues: 1080 sheet: -0.82 (0.20), residues: 648 loop : -1.39 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 190 TYR 0.008 0.001 TYR C 234 PHE 0.012 0.001 PHE E 225 TRP 0.008 0.001 TRP C 402 HIS 0.006 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (26028) covalent geometry : angle 0.60206 / 0.31 (35280) hydrogen bonds : bond 0.03841 / 2.56 ( 876) hydrogen bonds : angle 4.64819 / 3.30 ( 2430) Misc. bond : bond 0.00036 / 0.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9622.66 seconds wall clock time: 164 minutes 42.47 seconds (9882.47 seconds total)