Starting phenix.real_space_refine on Mon Aug 25 05:27:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6m_35200/08_2025/8i6m_35200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6m_35200/08_2025/8i6m_35200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2025/8i6m_35200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2025/8i6m_35200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2025/8i6m_35200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6m_35200/08_2025/8i6m_35200.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.95, per 1000 atoms: 0.23 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: 2.04 Conformation dependent library (CDL) restraints added in 967.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 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: 0.88 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: 3.63 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4266 1.28 - 1.41: 6288 1.41 - 1.54: 15155 1.54 - 1.68: 127 1.68 - 1.81: 192 Bond restraints: 26028 Sorted by residual: bond pdb=" CA THR F 202 " pdb=" C THR F 202 " ideal model delta sigma weight residual 1.521 1.413 0.107 9.90e-03 1.02e+04 1.17e+02 bond pdb=" CA THR B 202 " pdb=" C THR B 202 " ideal model delta sigma weight residual 1.521 1.414 0.107 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR E 202 " pdb=" C THR E 202 " ideal model delta sigma weight residual 1.521 1.414 0.107 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR A 202 " pdb=" C THR A 202 " ideal model delta sigma weight residual 1.521 1.414 0.106 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR C 202 " pdb=" C THR C 202 " ideal model delta sigma weight residual 1.521 1.414 0.106 9.90e-03 1.02e+04 1.15e+02 ... (remaining 26023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 34312 2.36 - 4.72: 788 4.72 - 7.08: 120 7.08 - 9.44: 42 9.44 - 11.80: 18 Bond angle restraints: 35280 Sorted by residual: angle pdb=" C THR D 202 " pdb=" CA THR D 202 " pdb=" CB THR D 202 " ideal model delta sigma weight residual 110.08 98.28 11.80 1.57e+00 4.06e-01 5.65e+01 angle pdb=" C THR B 202 " pdb=" CA THR B 202 " pdb=" CB THR B 202 " ideal model delta sigma weight residual 110.08 98.30 11.78 1.57e+00 4.06e-01 5.63e+01 angle pdb=" C THR A 202 " pdb=" CA THR A 202 " pdb=" CB THR A 202 " ideal model delta sigma weight residual 110.08 98.30 11.78 1.57e+00 4.06e-01 5.63e+01 angle pdb=" C THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 110.08 98.32 11.76 1.57e+00 4.06e-01 5.61e+01 angle pdb=" C THR E 202 " pdb=" CA THR E 202 " pdb=" CB THR E 202 " ideal model delta sigma weight residual 110.08 98.32 11.76 1.57e+00 4.06e-01 5.61e+01 ... (remaining 35275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.81: 14725 26.81 - 53.62: 770 53.62 - 80.43: 78 80.43 - 107.24: 30 107.24 - 134.05: 3 Dihedral angle restraints: 15606 sinusoidal: 6378 harmonic: 9228 Sorted by residual: dihedral pdb=" C5' AMP E1002 " pdb=" O5' AMP E1002 " pdb=" P AMP E1002 " pdb=" O3P AMP E1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.06 -134.05 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' AMP A1002 " pdb=" O5' AMP A1002 " pdb=" P AMP A1002 " pdb=" O3P AMP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.05 -134.05 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' AMP C1002 " pdb=" O5' AMP C1002 " pdb=" P AMP C1002 " pdb=" O3P AMP C1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.03 -134.03 1 2.00e+01 2.50e-03 4.07e+01 ... (remaining 15603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3812 0.121 - 0.243: 112 0.243 - 0.364: 42 0.364 - 0.486: 12 0.486 - 0.607: 6 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA MET B 320 " pdb=" N MET B 320 " pdb=" C MET B 320 " pdb=" CB MET B 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA MET F 320 " pdb=" N MET F 320 " pdb=" C MET F 320 " pdb=" CB MET F 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" CA MET A 320 " pdb=" N MET A 320 " pdb=" C MET A 320 " pdb=" CB MET A 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 ... (remaining 3981 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA C1001 " -0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA C1001 " 0.101 2.00e-02 2.50e+03 pdb=" C8 OLA C1001 " -0.101 2.00e-02 2.50e+03 pdb=" C9 OLA C1001 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA D1001 " 0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA D1001 " -0.101 2.00e-02 2.50e+03 pdb=" C8 OLA D1001 " 0.101 2.00e-02 2.50e+03 pdb=" C9 OLA D1001 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA F1001 " 0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA F1001 " -0.100 2.00e-02 2.50e+03 pdb=" C8 OLA F1001 " 0.101 2.00e-02 2.50e+03 pdb=" C9 OLA F1001 " -0.233 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 865 2.71 - 3.26: 24714 3.26 - 3.81: 41241 3.81 - 4.35: 55634 4.35 - 4.90: 90516 Nonbonded interactions: 212970 Sorted by model distance: nonbonded pdb=" O1P AMP E1002 " pdb="MG MG E1003 " model vdw 2.165 2.170 nonbonded pdb=" O3P AMP B1002 " pdb="MG MG B1003 " model vdw 2.166 2.170 nonbonded pdb=" O1P AMP C1002 " pdb="MG MG C1003 " model vdw 2.166 2.170 nonbonded pdb=" O1P AMP A1002 " pdb="MG MG A1003 " model vdw 2.166 2.170 nonbonded pdb=" O3P AMP D1002 " pdb="MG MG D1003 " model vdw 2.167 2.170 ... (remaining 212965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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: 0.010 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.370 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 26034 Z= 0.493 Angle : 0.863 11.799 35280 Z= 0.495 Chirality : 0.067 0.607 3984 Planarity : 0.008 0.179 4470 Dihedral : 16.142 134.054 9666 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.71 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 aren 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 covalent geometry : bond 0.00697 (26028) covalent geometry : angle 0.86264 (35280) hydrogen bonds : bond 0.21392 ( 876) hydrogen bonds : angle 6.79100 ( 2430) Misc. bond : bond 0.00116 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 0.806 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: 0.8134 time to fit residues: 256.3243 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 : 1.087 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 29 GLN A 117 HIS A 209 GLN A 213 HIS A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS F 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 = 0.167234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119626 restraints weight = 27178.703| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.77 r_work: 0.3133 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 : 0.607 6.522 35280 Z= 0.306 Chirality : 0.047 0.190 3984 Planarity : 0.004 0.037 4470 Dihedral : 8.218 84.291 3560 Min Nonbonded Distance : 2.048 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 aren not related in a simple way. whole: -0.99 (0.15), residues: 3156 helix: 0.66 (0.16), residues: 1080 sheet: -0.95 (0.19), residues: 648 loop : -1.52 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 529 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 covalent geometry : bond 0.00287 (26028) covalent geometry : angle 0.60717 (35280) hydrogen bonds : bond 0.04266 ( 876) hydrogen bonds : angle 4.99136 ( 2430) Misc. bond : bond 0.00055 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 234 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6795 (pt0) REVERT: F 58 MET cc_start: 0.8344 (mtt) cc_final: 0.7936 (mtt) REVERT: F 107 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7911 (t70) REVERT: F 418 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: F 461 MET cc_start: 0.4933 (ppp) cc_final: 0.4248 (tmt) REVERT: D 395 ASN cc_start: 0.8275 (m-40) cc_final: 0.8036 (m110) REVERT: C 58 MET cc_start: 0.8363 (mtt) cc_final: 0.7968 (mtt) REVERT: C 107 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7943 (t70) REVERT: C 343 GLN cc_start: 0.7202 (mp10) cc_final: 0.6577 (mt0) REVERT: C 347 TYR cc_start: 0.8757 (m-80) cc_final: 0.8537 (m-80) REVERT: C 418 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6610 (pm20) REVERT: C 461 MET cc_start: 0.5180 (ppp) cc_final: 0.4316 (tmt) REVERT: B 461 MET cc_start: 0.4849 (ppp) cc_final: 0.4356 (tmt) REVERT: E 150 ARG cc_start: 0.8259 (mtm110) cc_final: 0.7857 (mpt-90) REVERT: E 395 ASN cc_start: 0.8234 (m-40) cc_final: 0.7982 (m110) REVERT: E 418 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6782 (pt0) outliers start: 58 outliers final: 18 residues processed: 283 average time/residue: 0.6780 time to fit residues: 221.8105 Evaluate side-chains 223 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 320 MET Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 418 GLU 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: 8.9990 chunk 90 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS F 6 ASN ** 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** 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 = 0.3977 r_free = 0.3977 target = 0.167670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122969 restraints weight = 28630.248| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.93 r_work: 0.3186 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26034 Z= 0.134 Angle : 0.602 7.296 35280 Z= 0.303 Chirality : 0.047 0.173 3984 Planarity : 0.004 0.039 4470 Dihedral : 7.904 59.915 3556 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.32 % Favored : 92.49 % Rotamer: Outliers : 2.72 % Allowed : 17.65 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 3156 helix: 0.82 (0.16), residues: 1080 sheet: -0.82 (0.20), residues: 648 loop : -1.51 (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 B 234 PHE 0.012 0.002 PHE E 225 TRP 0.008 0.001 TRP C 466 HIS 0.007 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00314 (26028) covalent geometry : angle 0.60167 (35280) hydrogen bonds : bond 0.04150 ( 876) hydrogen bonds : angle 4.75721 ( 2430) Misc. bond : bond 0.00036 ( 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 291 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 216 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.8391 (mtt) cc_final: 0.8013 (mtm) REVERT: F 107 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7679 (t70) REVERT: F 418 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: D 395 ASN cc_start: 0.8235 (m-40) cc_final: 0.8009 (m110) REVERT: C 58 MET cc_start: 0.8383 (mtt) cc_final: 0.7987 (mtt) REVERT: C 107 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7842 (t70) REVERT: C 343 GLN cc_start: 0.6988 (mp10) cc_final: 0.6388 (mt0) REVERT: C 347 TYR cc_start: 0.8618 (m-80) cc_final: 0.8340 (m-80) REVERT: C 418 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: C 461 MET cc_start: 0.4893 (ppp) cc_final: 0.4426 (tmt) REVERT: B 35 ASN cc_start: 0.8010 (m-40) cc_final: 0.7745 (m-40) REVERT: B 461 MET cc_start: 0.4964 (ppp) cc_final: 0.4459 (tmt) REVERT: E 150 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7510 (mpt-90) REVERT: E 395 ASN cc_start: 0.8153 (m-40) cc_final: 0.7909 (m110) REVERT: E 418 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6862 (pm20) outliers start: 75 outliers final: 22 residues processed: 280 average time/residue: 0.7229 time to fit residues: 232.9263 Evaluate side-chains 228 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 418 GLU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 409 THR 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 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain B residue 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 394 ASP Chi-restraints excluded: chain E residue 418 GLU 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: 8.9990 chunk 218 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** 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 228 HIS ** 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 = 0.3937 r_free = 0.3937 target = 0.164444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118737 restraints weight = 28212.347| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.89 r_work: 0.3138 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 26034 Z= 0.197 Angle : 0.673 7.865 35280 Z= 0.344 Chirality : 0.050 0.212 3984 Planarity : 0.004 0.042 4470 Dihedral : 7.975 58.866 3556 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.24 % Favored : 91.57 % Rotamer: Outliers : 3.30 % Allowed : 17.14 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3156 helix: 0.76 (0.16), residues: 1080 sheet: -0.87 (0.19), residues: 660 loop : -1.61 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 190 TYR 0.013 0.002 TYR A 174 PHE 0.016 0.002 PHE E 225 TRP 0.010 0.002 TRP F 290 HIS 0.009 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00482 (26028) covalent geometry : angle 0.67267 (35280) hydrogen bonds : bond 0.04868 ( 876) hydrogen bonds : angle 4.87343 ( 2430) Misc. bond : bond 0.00079 ( 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 295 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 204 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: A 320 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6607 (tmm) REVERT: A 425 ASP cc_start: 0.8186 (t0) cc_final: 0.7954 (t70) REVERT: F 58 MET cc_start: 0.8521 (mtt) cc_final: 0.8137 (mtm) REVERT: F 107 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7601 (t70) REVERT: F 347 TYR cc_start: 0.8601 (m-80) cc_final: 0.8347 (m-80) REVERT: D 100 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: D 395 ASN cc_start: 0.8365 (m-40) cc_final: 0.8142 (m110) REVERT: C 58 MET cc_start: 0.8524 (mtt) cc_final: 0.8122 (mtt) REVERT: C 107 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7628 (t70) REVERT: C 343 GLN cc_start: 0.7096 (mp10) cc_final: 0.6538 (mt0) REVERT: C 347 TYR cc_start: 0.8660 (m-80) cc_final: 0.8416 (m-80) REVERT: C 461 MET cc_start: 0.4901 (ppp) cc_final: 0.4500 (tmt) REVERT: B 320 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6688 (tmm) REVERT: B 418 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6679 (pm20) REVERT: E 150 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7674 (mpt-90) REVERT: E 395 ASN cc_start: 0.8298 (m-40) cc_final: 0.8057 (m110) outliers start: 91 outliers final: 35 residues processed: 273 average time/residue: 0.7417 time to fit residues: 232.2300 Evaluate side-chains 242 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 481 GLN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 481 GLN Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 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 343 GLN 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 271 THR Chi-restraints excluded: chain E residue 394 ASP 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: 7.9990 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110587 restraints weight = 28090.181| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.71 r_work: 0.3145 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26034 Z= 0.158 Angle : 0.634 7.906 35280 Z= 0.322 Chirality : 0.048 0.199 3984 Planarity : 0.004 0.042 4470 Dihedral : 7.739 59.727 3556 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.83 % Favored : 91.98 % Rotamer: Outliers : 2.76 % Allowed : 18.08 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.15), residues: 3156 helix: 0.86 (0.16), residues: 1080 sheet: -0.88 (0.19), residues: 660 loop : -1.60 (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 A 174 PHE 0.014 0.002 PHE B 173 TRP 0.009 0.001 TRP F 402 HIS 0.008 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00381 (26028) covalent geometry : angle 0.63355 (35280) hydrogen bonds : bond 0.04297 ( 876) hydrogen bonds : angle 4.77327 ( 2430) Misc. bond : bond 0.00058 ( 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 287 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 211 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: A 533 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4866 (pt) REVERT: F 58 MET cc_start: 0.8477 (mtt) cc_final: 0.8077 (mtm) REVERT: F 107 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7582 (t70) REVERT: F 347 TYR cc_start: 0.8577 (m-80) cc_final: 0.8332 (m-80) REVERT: D 395 ASN cc_start: 0.8359 (m-40) cc_final: 0.8137 (m110) REVERT: C 58 MET cc_start: 0.8464 (mtt) cc_final: 0.8113 (mtm) REVERT: C 107 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7608 (t70) REVERT: C 203 ILE cc_start: 0.8801 (mm) cc_final: 0.8576 (tt) REVERT: C 343 GLN cc_start: 0.7052 (mp10) cc_final: 0.6559 (mt0) REVERT: C 461 MET cc_start: 0.4857 (ppp) cc_final: 0.4483 (tmt) REVERT: B 320 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6585 (tmm) REVERT: B 418 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6715 (pm20) REVERT: B 466 TRP cc_start: 0.5568 (OUTLIER) cc_final: 0.5323 (m100) REVERT: E 150 ARG cc_start: 0.8092 (mtm110) cc_final: 0.7652 (mpt-90) REVERT: E 395 ASN cc_start: 0.8317 (m-40) cc_final: 0.8080 (m110) outliers start: 76 outliers final: 32 residues processed: 267 average time/residue: 0.7088 time to fit residues: 218.3698 Evaluate side-chains 237 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 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 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 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 103 optimal weight: 0.7980 chunk 277 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115034 restraints weight = 28503.482| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.71 r_work: 0.3237 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2027 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= 0.113 Angle : 0.588 6.638 35280 Z= 0.294 Chirality : 0.046 0.162 3984 Planarity : 0.004 0.037 4470 Dihedral : 7.262 59.346 3556 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.41 % Favored : 92.40 % Rotamer: Outliers : 2.36 % Allowed : 18.92 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.15), residues: 3156 helix: 1.01 (0.16), residues: 1080 sheet: -0.77 (0.20), residues: 648 loop : -1.49 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 529 TYR 0.007 0.001 TYR A 148 PHE 0.011 0.001 PHE D 225 TRP 0.008 0.001 TRP D 290 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00256 (26028) covalent geometry : angle 0.58802 (35280) hydrogen bonds : bond 0.03543 ( 876) hydrogen bonds : angle 4.57484 ( 2430) Misc. bond : bond 0.00027 ( 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 283 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 LEU cc_start: 0.5090 (OUTLIER) cc_final: 0.4721 (pt) REVERT: F 58 MET cc_start: 0.8353 (mtt) cc_final: 0.8001 (mtm) REVERT: F 107 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7739 (t70) REVERT: F 347 TYR cc_start: 0.8550 (m-80) cc_final: 0.8330 (m-80) REVERT: D 100 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: D 395 ASN cc_start: 0.8294 (m-40) cc_final: 0.8066 (m110) REVERT: C 58 MET cc_start: 0.8334 (mtt) cc_final: 0.7963 (mtm) REVERT: C 107 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7767 (t70) REVERT: C 461 MET cc_start: 0.4707 (ppp) cc_final: 0.4263 (tmt) REVERT: B 35 ASN cc_start: 0.8040 (m-40) cc_final: 0.7812 (m-40) REVERT: B 418 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: E 150 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7770 (mpt-90) REVERT: E 154 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7072 (pp30) REVERT: E 395 ASN cc_start: 0.8187 (m-40) cc_final: 0.7935 (m110) outliers start: 65 outliers final: 28 residues processed: 268 average time/residue: 0.7147 time to fit residues: 221.6007 Evaluate side-chains 232 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 320 MET 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 314 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 394 ASP Chi-restraints excluded: chain C residue 481 GLN 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 314 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 235 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 219 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 279 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** 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** ** 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 = 0.3980 r_free = 0.3980 target = 0.167862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122716 restraints weight = 28369.196| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.91 r_work: 0.3200 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2104 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= 0.125 Angle : 0.602 7.186 35280 Z= 0.301 Chirality : 0.046 0.165 3984 Planarity : 0.004 0.039 4470 Dihedral : 7.073 59.630 3556 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.89 % Favored : 91.92 % Rotamer: Outliers : 1.82 % Allowed : 19.83 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.15), residues: 3156 helix: 1.05 (0.16), residues: 1080 sheet: -0.78 (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 B 529 TYR 0.008 0.001 TYR D 218 PHE 0.012 0.001 PHE D 225 TRP 0.007 0.001 TRP F 402 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00290 (26028) covalent geometry : angle 0.60204 (35280) hydrogen bonds : bond 0.03792 ( 876) hydrogen bonds : angle 4.55721 ( 2430) Misc. bond : bond 0.00035 ( 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 264 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6882 (pm20) REVERT: A 533 LEU cc_start: 0.4878 (OUTLIER) cc_final: 0.4480 (pt) REVERT: F 58 MET cc_start: 0.8411 (mtt) cc_final: 0.8047 (mtm) REVERT: F 107 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7482 (t70) REVERT: F 347 TYR cc_start: 0.8496 (m-80) cc_final: 0.8267 (m-80) REVERT: D 100 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: D 154 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6900 (pp30) REVERT: D 395 ASN cc_start: 0.8312 (m-40) cc_final: 0.8087 (m110) REVERT: C 58 MET cc_start: 0.8417 (mtt) cc_final: 0.8044 (mtm) REVERT: C 107 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7521 (t70) REVERT: C 347 TYR cc_start: 0.8563 (m-80) cc_final: 0.8324 (m-80) REVERT: C 461 MET cc_start: 0.4720 (ppp) cc_final: 0.4288 (tmt) REVERT: B 35 ASN cc_start: 0.8058 (m-40) cc_final: 0.7803 (m-40) REVERT: B 196 THR cc_start: 0.9194 (t) cc_final: 0.8925 (m) REVERT: B 274 HIS cc_start: 0.8594 (t-90) cc_final: 0.8341 (t70) REVERT: B 418 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6692 (pm20) REVERT: E 150 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7595 (mpt-90) REVERT: E 154 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6989 (pp30) REVERT: E 395 ASN cc_start: 0.8205 (m-40) cc_final: 0.7952 (m110) outliers start: 50 outliers final: 24 residues processed: 246 average time/residue: 0.6586 time to fit residues: 187.3441 Evaluate side-chains 230 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 320 MET 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 314 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 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 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 394 ASP 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: 0.6980 chunk 243 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 301 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** 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 = 0.3948 r_free = 0.3948 target = 0.165264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120413 restraints weight = 28418.824| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.86 r_work: 0.3170 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26034 Z= 0.157 Angle : 0.635 7.130 35280 Z= 0.321 Chirality : 0.048 0.190 3984 Planarity : 0.004 0.040 4470 Dihedral : 7.191 58.240 3556 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.33 % Favored : 91.48 % Rotamer: Outliers : 1.89 % Allowed : 20.19 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.15), residues: 3156 helix: 0.96 (0.16), residues: 1086 sheet: -0.83 (0.19), residues: 660 loop : -1.50 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 190 TYR 0.008 0.001 TYR C 318 PHE 0.014 0.002 PHE E 225 TRP 0.007 0.001 TRP C 402 HIS 0.008 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00378 (26028) covalent geometry : angle 0.63478 (35280) hydrogen bonds : bond 0.04280 ( 876) hydrogen bonds : angle 4.66826 ( 2430) Misc. bond : bond 0.00047 ( 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 258 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6506 (ttt) REVERT: A 418 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6806 (pm20) REVERT: A 533 LEU cc_start: 0.4955 (OUTLIER) cc_final: 0.4582 (pt) REVERT: F 58 MET cc_start: 0.8442 (mtt) cc_final: 0.8065 (mtm) REVERT: F 107 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7546 (t70) REVERT: F 163 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8050 (t70) REVERT: F 347 TYR cc_start: 0.8534 (m-80) cc_final: 0.8279 (m-80) REVERT: D 100 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: D 395 ASN cc_start: 0.8419 (m-40) cc_final: 0.8200 (m110) REVERT: C 58 MET cc_start: 0.8416 (mtt) cc_final: 0.8048 (mtm) REVERT: C 107 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7576 (t70) REVERT: C 343 GLN cc_start: 0.7169 (mp10) cc_final: 0.6340 (mt0) REVERT: B 274 HIS cc_start: 0.8660 (t-90) cc_final: 0.8379 (t70) REVERT: B 418 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: B 425 ASP cc_start: 0.8108 (t0) cc_final: 0.7886 (t70) REVERT: E 150 ARG cc_start: 0.8082 (mtm110) cc_final: 0.7672 (mpt-90) REVERT: E 154 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7053 (pp30) REVERT: E 395 ASN cc_start: 0.8337 (m-40) cc_final: 0.8104 (m110) outliers start: 52 outliers final: 31 residues processed: 243 average time/residue: 0.6195 time to fit residues: 174.0017 Evaluate side-chains 238 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 MET 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 320 MET 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 314 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 466 TRP 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 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 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 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 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 178 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 280 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 268 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** 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 = 0.3936 r_free = 0.3936 target = 0.164402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119238 restraints weight = 28240.595| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.87 r_work: 0.3142 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26034 Z= 0.187 Angle : 0.671 7.570 35280 Z= 0.342 Chirality : 0.049 0.208 3984 Planarity : 0.004 0.041 4470 Dihedral : 7.420 59.397 3556 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.95 % Favored : 91.86 % Rotamer: Outliers : 2.03 % Allowed : 20.12 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.15), residues: 3156 helix: 0.83 (0.16), residues: 1086 sheet: -0.90 (0.19), residues: 660 loop : -1.54 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 190 TYR 0.011 0.002 TYR A 174 PHE 0.016 0.002 PHE E 225 TRP 0.010 0.001 TRP F 290 HIS 0.009 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00459 (26028) covalent geometry : angle 0.67076 (35280) hydrogen bonds : bond 0.04683 ( 876) hydrogen bonds : angle 4.79375 ( 2430) Misc. bond : bond 0.00057 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6665 (ttt) REVERT: A 418 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: A 533 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4731 (pt) REVERT: F 58 MET cc_start: 0.8514 (mtt) cc_final: 0.8233 (mtm) REVERT: F 107 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7636 (t70) REVERT: F 163 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8141 (t70) REVERT: F 347 TYR cc_start: 0.8589 (m-80) cc_final: 0.8330 (m-80) REVERT: C 58 MET cc_start: 0.8509 (mtt) cc_final: 0.8177 (mtm) REVERT: C 107 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7662 (t70) REVERT: C 343 GLN cc_start: 0.7172 (mp10) cc_final: 0.6428 (mt0) REVERT: B 418 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: B 425 ASP cc_start: 0.8145 (t0) cc_final: 0.7850 (t70) REVERT: E 150 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7707 (mpt-90) outliers start: 56 outliers final: 34 residues processed: 248 average time/residue: 0.6455 time to fit residues: 186.4278 Evaluate side-chains 242 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 321 SER 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 320 MET Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 466 TRP 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 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 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: 0.7980 chunk 211 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** 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 = 0.3914 r_free = 0.3914 target = 0.163240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104037 restraints weight = 27124.551| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.85 r_work: 0.3066 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26034 Z= 0.163 Angle : 0.650 7.884 35280 Z= 0.328 Chirality : 0.048 0.195 3984 Planarity : 0.004 0.042 4470 Dihedral : 7.167 58.508 3556 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.05 % Favored : 91.76 % Rotamer: Outliers : 1.74 % Allowed : 20.48 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.15), residues: 3156 helix: 0.87 (0.16), residues: 1086 sheet: -0.89 (0.19), residues: 660 loop : -1.51 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 190 TYR 0.011 0.001 TYR C 234 PHE 0.014 0.002 PHE E 225 TRP 0.007 0.001 TRP C 402 HIS 0.009 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00397 (26028) covalent geometry : angle 0.64983 (35280) hydrogen bonds : bond 0.04315 ( 876) hydrogen bonds : angle 4.74092 ( 2430) Misc. bond : bond 0.00045 ( 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 252 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6494 (ttt) REVERT: A 418 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6867 (pm20) REVERT: A 533 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4796 (pt) REVERT: F 58 MET cc_start: 0.8459 (mtt) cc_final: 0.8080 (mtm) REVERT: F 107 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7544 (t70) REVERT: F 347 TYR cc_start: 0.8573 (m-80) cc_final: 0.8304 (m-80) REVERT: D 367 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7436 (mmm) REVERT: C 58 MET cc_start: 0.8433 (mtt) cc_final: 0.8062 (mtm) REVERT: C 107 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7560 (t70) REVERT: C 343 GLN cc_start: 0.7059 (mp10) cc_final: 0.6318 (mt0) REVERT: B 274 HIS cc_start: 0.8637 (t-90) cc_final: 0.8339 (t70) REVERT: B 418 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6690 (pm20) REVERT: B 425 ASP cc_start: 0.8091 (t0) cc_final: 0.7829 (t70) REVERT: E 150 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7550 (mpt-90) outliers start: 48 outliers final: 33 residues processed: 239 average time/residue: 0.6376 time to fit residues: 176.1543 Evaluate side-chains 240 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 320 MET 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 320 MET Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 466 TRP 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 394 ASP 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 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 181 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 149 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 chunk 289 optimal weight: 0.0050 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN C 331 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109215 restraints weight = 27191.557| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.84 r_work: 0.3140 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26034 Z= 0.114 Angle : 0.596 8.165 35280 Z= 0.297 Chirality : 0.046 0.189 3984 Planarity : 0.004 0.040 4470 Dihedral : 6.849 59.917 3556 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.48 % Favored : 92.33 % Rotamer: Outliers : 1.38 % Allowed : 20.84 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.15), residues: 3156 helix: 1.03 (0.16), residues: 1086 sheet: -0.78 (0.20), residues: 648 loop : -1.36 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 211 TYR 0.012 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 A 274 Details of bonding type rmsd covalent geometry : bond 0.00263 (26028) covalent geometry : angle 0.59628 (35280) hydrogen bonds : bond 0.03477 ( 876) hydrogen bonds : angle 4.58644 ( 2430) Misc. bond : bond 0.00018 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10007.75 seconds wall clock time: 171 minutes 25.24 seconds (10285.24 seconds total)