Starting phenix.real_space_refine on Fri Jun 27 11:15:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4n_17420/06_2025/8p4n_17420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4n_17420/06_2025/8p4n_17420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4n_17420/06_2025/8p4n_17420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4n_17420/06_2025/8p4n_17420.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4n_17420/06_2025/8p4n_17420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4n_17420/06_2025/8p4n_17420.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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: 9 Type Number sf(0) Gaussians K 7 8.98 5 P 14 5.49 5 Mg 7 5.21 5 S 147 5.16 5 Be 7 3.05 5 C 19845 2.51 5 N 5565 2.21 5 O 6517 1.98 5 F 21 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.44s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32130 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 687 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "P" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 687 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "Q" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 687 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 687 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "S" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 687 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "T" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 687 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "U" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 687 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 20.91, per 1000 atoms: 0.65 Number of scatterers: 32130 At special positions: 0 Unit cell: (155.87, 155.87, 142.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 7 19.00 S 147 16.00 P 14 15.00 Mg 7 11.99 F 21 9.00 O 6517 8.00 N 5565 7.00 C 19845 6.00 Be 7 4.00 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: 8.54 Conformation dependent library (CDL) restraints added in 4.8 seconds 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7826 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 60 sheets defined 51.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 4.062A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 64 through 86 removed outlier: 4.099A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 108 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.779A pdb=" N GLU A 232 " --> pdb=" O ASN A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.831A pdb=" N MET A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 297 removed outlier: 3.693A pdb=" N LYS A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 338 through 354 removed outlier: 3.794A pdb=" N ILE A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.533A pdb=" N CYS A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.633A pdb=" N GLY A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.711A pdb=" N LEU A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 86 removed outlier: 4.031A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 108 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.523A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.596A pdb=" N GLU B 232 " --> pdb=" O ASN B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.622A pdb=" N ARG B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.684A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 358 through 373 removed outlier: 3.522A pdb=" N ARG B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 426 removed outlier: 3.756A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.519A pdb=" N ARG B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 472 removed outlier: 3.539A pdb=" N GLY B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.817A pdb=" N LEU B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 28 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 64 through 86 removed outlier: 4.014A pdb=" N GLU C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 108 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.571A pdb=" N GLU C 232 " --> pdb=" O ASN C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 255 through 268 removed outlier: 3.676A pdb=" N MET C 267 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.577A pdb=" N LEU C 317 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 355 removed outlier: 3.655A pdb=" N ILE C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 373 Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 removed outlier: 3.715A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 447 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 461 through 472 removed outlier: 3.618A pdb=" N VAL C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.917A pdb=" N LEU C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 28 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 52 through 59 removed outlier: 4.023A pdb=" N GLU D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 4.084A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 108 removed outlier: 3.510A pdb=" N ALA D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.703A pdb=" N MET D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.734A pdb=" N ILE D 305 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 338 through 355 removed outlier: 3.594A pdb=" N ILE D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 355 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 373 removed outlier: 3.534A pdb=" N ARG D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 426 removed outlier: 3.618A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.503A pdb=" N ARG D 452 " --> pdb=" O GLU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 472 removed outlier: 3.679A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.793A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 29 removed outlier: 4.050A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 58 Processing helix chain 'E' and resid 64 through 86 removed outlier: 4.093A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 108 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 229 through 232 removed outlier: 3.701A pdb=" N GLU E 232 " --> pdb=" O ASN E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 229 through 232' Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 255 through 268 removed outlier: 3.524A pdb=" N ARG E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 338 through 355 removed outlier: 3.549A pdb=" N ILE E 342 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 373 Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 426 removed outlier: 3.559A pdb=" N ILE E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.544A pdb=" N ARG E 452 " --> pdb=" O GLU E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.766A pdb=" N LEU E 513 " --> pdb=" O SER E 509 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 52 through 58 Processing helix chain 'F' and resid 64 through 86 removed outlier: 4.110A pdb=" N GLU F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 108 removed outlier: 3.541A pdb=" N ALA F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 229 through 232 removed outlier: 3.538A pdb=" N GLU F 232 " --> pdb=" O ASN F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 229 through 232' Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.923A pdb=" N MET F 267 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG F 268 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 297 removed outlier: 3.691A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 338 through 354 removed outlier: 3.657A pdb=" N ILE F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 373 Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 426 removed outlier: 3.770A pdb=" N ILE F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 461 through 472 removed outlier: 3.589A pdb=" N VAL F 465 " --> pdb=" O GLU F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.658A pdb=" N LEU F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 28 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 52 through 58 Processing helix chain 'G' and resid 64 through 86 removed outlier: 4.170A pdb=" N GLU G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 108 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 255 through 268 removed outlier: 3.574A pdb=" N MET G 267 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG G 268 " --> pdb=" O VAL G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 338 through 355 Processing helix chain 'G' and resid 358 through 373 Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 426 removed outlier: 3.664A pdb=" N ILE G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 447 Processing helix chain 'G' and resid 448 through 458 removed outlier: 3.502A pdb=" N ARG G 452 " --> pdb=" O GLU G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 472 removed outlier: 3.596A pdb=" N VAL G 465 " --> pdb=" O GLU G 461 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY G 472 " --> pdb=" O THR G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.762A pdb=" N LEU G 513 " --> pdb=" O SER G 509 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 4.789A pdb=" N THR A 517 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL B 39 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS A 519 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.802A pdb=" N ASN A 37 " --> pdb=" O CYS G 519 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N VAL G 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 39 " --> pdb=" O VAL G 521 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ASP G 523 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.530A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.868A pdb=" N MET A 193 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 322 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.102A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLU A 252 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N ALA A 223 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N VAL A 254 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 12.050A pdb=" N LYS A 225 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 8 removed outlier: 5.910A pdb=" N ASN C 37 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 519 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.403A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 195 removed outlier: 3.828A pdb=" N MET B 193 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.408A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.408A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 8 removed outlier: 7.436A pdb=" N VAL D 39 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET C 520 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.187A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 195 removed outlier: 3.878A pdb=" N MET C 193 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.297A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.297A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC3, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AC4, first strand: chain 'D' and resid 4 through 8 removed outlier: 4.930A pdb=" N THR D 517 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL E 39 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS D 519 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.341A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.785A pdb=" N MET D 193 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.406A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.406A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD1, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AD2, first strand: chain 'E' and resid 4 through 8 removed outlier: 4.656A pdb=" N THR E 517 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL F 39 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS E 519 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 174 through 179 removed outlier: 6.433A pdb=" N VAL E 174 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE E 379 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR E 176 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL E 381 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU E 178 " --> pdb=" O VAL E 381 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.802A pdb=" N MET E 193 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 273 through 277 removed outlier: 7.432A pdb=" N LYS E 225 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 254 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE E 227 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 273 through 277 removed outlier: 7.432A pdb=" N LYS E 225 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 254 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE E 227 " --> pdb=" O VAL E 254 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD8, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AD9, first strand: chain 'F' and resid 4 through 8 removed outlier: 4.755A pdb=" N THR F 517 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL G 39 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS F 519 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.340A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.601A pdb=" N MET F 193 " --> pdb=" O ILE F 332 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 273 through 277 removed outlier: 6.518A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU F 252 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LYS F 225 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL F 254 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE F 227 " --> pdb=" O VAL F 254 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE5, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AE6, first strand: chain 'G' and resid 174 through 179 Processing sheet with id=AE7, first strand: chain 'G' and resid 193 through 195 removed outlier: 3.946A pdb=" N MET G 193 " --> pdb=" O ILE G 332 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 273 through 277 removed outlier: 3.687A pdb=" N GLU G 252 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LYS G 225 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL G 254 " --> pdb=" O LYS G 225 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE G 227 " --> pdb=" O VAL G 254 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AF1, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AF2, first strand: chain 'O' and resid 3 through 5 removed outlier: 3.658A pdb=" N ARG O 4 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE U 66 " --> pdb=" O LEU U 92 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE U 94 " --> pdb=" O ILE U 64 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE U 64 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE U 11 " --> pdb=" O LEU U 41 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL U 43 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG U 9 " --> pdb=" O VAL U 43 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARG U 14 " --> pdb=" O GLU U 82 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLU U 82 " --> pdb=" O ARG U 14 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 74 through 78 removed outlier: 8.405A pdb=" N GLU O 82 " --> pdb=" O ARG O 14 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG O 14 " --> pdb=" O GLU O 82 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG O 9 " --> pdb=" O VAL O 43 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL O 43 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE O 11 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE O 64 " --> pdb=" O VAL O 95 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 47 through 48 removed outlier: 3.518A pdb=" N ARG O 47 " --> pdb=" O LYS O 55 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS O 55 " --> pdb=" O ARG O 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'P' and resid 74 through 78 removed outlier: 8.549A pdb=" N GLU P 82 " --> pdb=" O ARG P 14 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARG P 14 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG P 9 " --> pdb=" O VAL P 43 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL P 43 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE P 11 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE P 64 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE P 94 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE P 66 " --> pdb=" O LEU P 92 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 47 through 48 Processing sheet with id=AF7, first strand: chain 'Q' and resid 74 through 78 removed outlier: 8.052A pdb=" N GLU Q 82 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG Q 14 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG Q 9 " --> pdb=" O VAL Q 43 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL Q 43 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE Q 11 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE Q 64 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE Q 94 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE Q 66 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 47 through 48 Processing sheet with id=AF9, first strand: chain 'R' and resid 74 through 78 removed outlier: 8.399A pdb=" N GLU R 82 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG R 14 " --> pdb=" O GLU R 82 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ARG R 9 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL R 43 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE R 11 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE R 64 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE R 94 " --> pdb=" O ILE R 64 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE R 66 " --> pdb=" O LEU R 92 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 47 through 48 Processing sheet with id=AG2, first strand: chain 'S' and resid 74 through 78 removed outlier: 8.129A pdb=" N GLU S 82 " --> pdb=" O ARG S 14 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG S 14 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE S 11 " --> pdb=" O LEU S 41 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE S 64 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE S 94 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE S 66 " --> pdb=" O LEU S 92 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 47 through 48 removed outlier: 3.630A pdb=" N ARG S 47 " --> pdb=" O LYS S 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS S 55 " --> pdb=" O ARG S 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'T' and resid 74 through 78 removed outlier: 8.870A pdb=" N GLU T 82 " --> pdb=" O ARG T 14 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG T 14 " --> pdb=" O GLU T 82 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ARG T 9 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL T 43 " --> pdb=" O ARG T 9 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE T 11 " --> pdb=" O LEU T 41 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE T 64 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE T 94 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE T 66 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 47 through 48 removed outlier: 3.562A pdb=" N ARG T 47 " --> pdb=" O LYS T 55 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 47 through 48 removed outlier: 3.687A pdb=" N ARG U 47 " --> pdb=" O LYS U 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS U 55 " --> pdb=" O ARG U 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 1932 hydrogen bonds defined for protein. 5487 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.63 Time building geometry restraints manager: 9.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6584 1.33 - 1.45: 5834 1.45 - 1.57: 19495 1.57 - 1.69: 21 1.69 - 1.81: 273 Bond restraints: 32207 Sorted by residual: bond pdb=" F1 BEF E1602 " pdb="BE BEF E1602 " ideal model delta sigma weight residual 1.476 1.536 -0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" F1 BEF C1602 " pdb="BE BEF C1602 " ideal model delta sigma weight residual 1.476 1.535 -0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" F2 BEF E1602 " pdb="BE BEF E1602 " ideal model delta sigma weight residual 1.476 1.535 -0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" F1 BEF D1602 " pdb="BE BEF D1602 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.54e+00 bond pdb=" F2 BEF D1602 " pdb="BE BEF D1602 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.39e+00 ... (remaining 32202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 43052 2.46 - 4.93: 377 4.93 - 7.39: 58 7.39 - 9.85: 4 9.85 - 12.31: 21 Bond angle restraints: 43512 Sorted by residual: angle pdb=" C HIS S 7 " pdb=" CA HIS S 7 " pdb=" CB HIS S 7 " ideal model delta sigma weight residual 117.23 110.91 6.32 1.36e+00 5.41e-01 2.16e+01 angle pdb=" F2 BEF D1602 " pdb="BE BEF D1602 " pdb=" F3 BEF D1602 " ideal model delta sigma weight residual 119.96 107.65 12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" F1 BEF G1602 " pdb="BE BEF G1602 " pdb=" F2 BEF G1602 " ideal model delta sigma weight residual 119.91 107.75 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" F2 BEF E1602 " pdb="BE BEF E1602 " pdb=" F3 BEF E1602 " ideal model delta sigma weight residual 119.96 108.02 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" F1 BEF F1602 " pdb="BE BEF F1602 " pdb=" F2 BEF F1602 " ideal model delta sigma weight residual 119.91 108.06 11.85 3.00e+00 1.11e-01 1.56e+01 ... (remaining 43507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 19636 35.95 - 71.90: 262 71.90 - 107.85: 24 107.85 - 143.80: 0 143.80 - 179.75: 7 Dihedral angle restraints: 19929 sinusoidal: 7735 harmonic: 12194 Sorted by residual: dihedral pdb=" O1B ADP F1600 " pdb=" O3A ADP F1600 " pdb=" PB ADP F1600 " pdb=" PA ADP F1600 " ideal model delta sinusoidal sigma weight residual 300.00 120.25 179.75 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP A1600 " pdb=" O3A ADP A1600 " pdb=" PB ADP A1600 " pdb=" PA ADP A1600 " ideal model delta sinusoidal sigma weight residual 300.00 120.88 179.11 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP E1600 " pdb=" O3A ADP E1600 " pdb=" PB ADP E1600 " pdb=" PA ADP E1600 " ideal model delta sinusoidal sigma weight residual 300.00 121.01 178.99 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 19926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3499 0.037 - 0.074: 1215 0.074 - 0.111: 447 0.111 - 0.147: 155 0.147 - 0.184: 4 Chirality restraints: 5320 Sorted by residual: chirality pdb=" CA GLU B 408 " pdb=" N GLU B 408 " pdb=" C GLU B 408 " pdb=" CB GLU B 408 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA GLU F 129 " pdb=" N GLU F 129 " pdb=" C GLU F 129 " pdb=" CB GLU F 129 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CG LEU E 222 " pdb=" CB LEU E 222 " pdb=" CD1 LEU E 222 " pdb=" CD2 LEU E 222 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 5317 not shown) Planarity restraints: 5642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 201 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO G 202 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 202 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 202 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 207 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO D 208 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 208 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 208 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 391 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" CD GLU C 391 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU C 391 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 391 " 0.013 2.00e-02 2.50e+03 ... (remaining 5639 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.07: 26 2.07 - 2.84: 10122 2.84 - 3.61: 50384 3.61 - 4.37: 86945 4.37 - 5.14: 160164 Nonbonded interactions: 307641 Sorted by model distance: nonbonded pdb=" O3B ADP E1600 " pdb=" F3 BEF E1602 " model vdw 1.307 2.990 nonbonded pdb=" O3B ADP E1600 " pdb="BE BEF E1602 " model vdw 1.400 2.420 nonbonded pdb="MG MG A1601 " pdb=" O HOH A2001 " model vdw 1.832 2.170 nonbonded pdb="MG MG C1601 " pdb=" O HOH C2001 " model vdw 1.832 2.170 nonbonded pdb="MG MG D1601 " pdb=" O HOH D2001 " model vdw 1.852 2.170 ... (remaining 307636 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 76.470 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.170 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.900 32213 Z= 1.243 Angle : 0.668 12.313 43512 Z= 0.344 Chirality : 0.045 0.184 5320 Planarity : 0.004 0.075 5642 Dihedral : 13.693 179.750 12103 Min Nonbonded Distance : 1.307 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.06 % Allowed : 0.06 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.12), residues: 4305 helix: 2.01 (0.11), residues: 2030 sheet: 1.03 (0.21), residues: 511 loop : -0.46 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 401 PHE 0.013 0.001 PHE F 195 TYR 0.025 0.002 TYR E 199 ARG 0.007 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.16865 ( 1919) hydrogen bonds : angle 5.81966 ( 5487) covalent geometry : bond 0.00439 (32207) covalent geometry : angle 0.66845 (43512) Misc. bond : bond 0.89963 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 606 time to evaluate : 3.519 Fit side-chains revert: symmetry clash REVERT: B 362 ARG cc_start: 0.6545 (mtm-85) cc_final: 0.6330 (ttp-110) REVERT: C 25 ASP cc_start: 0.7914 (m-30) cc_final: 0.7696 (m-30) REVERT: C 114 MET cc_start: 0.7108 (mmt) cc_final: 0.6906 (tpp) REVERT: D 288 MET cc_start: 0.7124 (mpp) cc_final: 0.6802 (mpt) REVERT: F 254 VAL cc_start: 0.7945 (t) cc_final: 0.7744 (t) REVERT: F 322 ARG cc_start: 0.7495 (ttt90) cc_final: 0.7137 (ttp80) REVERT: R 64 ILE cc_start: 0.8574 (mp) cc_final: 0.8252 (mp) REVERT: S 87 SER cc_start: 0.8405 (t) cc_final: 0.8159 (m) REVERT: T 15 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7617 (mmtm) outliers start: 2 outliers final: 0 residues processed: 606 average time/residue: 1.6946 time to fit residues: 1182.8908 Evaluate side-chains 457 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 360 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 334 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 203 optimal weight: 0.3980 chunk 249 optimal weight: 2.9990 chunk 387 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 343 GLN B 433 ASN C 352 GLN D 265 ASN D 319 GLN D 366 GLN F 366 GLN F 436 GLN G 184 GLN G 348 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.170369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133329 restraints weight = 35531.686| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.73 r_work: 0.3233 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32213 Z= 0.137 Angle : 0.570 7.525 43512 Z= 0.295 Chirality : 0.044 0.154 5320 Planarity : 0.003 0.048 5642 Dihedral : 8.590 177.397 4634 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.61 % Allowed : 9.60 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.13), residues: 4305 helix: 2.22 (0.11), residues: 2079 sheet: 1.10 (0.21), residues: 511 loop : -0.30 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS T 7 PHE 0.013 0.001 PHE G 195 TYR 0.021 0.002 TYR D 360 ARG 0.006 0.000 ARG G 197 Details of bonding type rmsd hydrogen bonds : bond 0.05699 ( 1919) hydrogen bonds : angle 4.39944 ( 5487) covalent geometry : bond 0.00294 (32207) covalent geometry : angle 0.57012 (43512) Misc. bond : bond 0.00248 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 477 time to evaluate : 3.205 Fit side-chains REVERT: A 334 ASP cc_start: 0.7750 (m-30) cc_final: 0.7532 (m-30) REVERT: A 366 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7096 (mt0) REVERT: A 398 ASP cc_start: 0.8083 (m-30) cc_final: 0.7796 (OUTLIER) REVERT: B 197 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7211 (mpt-90) REVERT: B 233 MET cc_start: 0.7153 (mmm) cc_final: 0.6863 (tpp) REVERT: C 25 ASP cc_start: 0.8390 (m-30) cc_final: 0.8165 (m-30) REVERT: C 483 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: D 225 LYS cc_start: 0.7294 (ptmm) cc_final: 0.6761 (pptt) REVERT: D 288 MET cc_start: 0.7546 (mpp) cc_final: 0.6876 (mpt) REVERT: D 364 LYS cc_start: 0.7580 (mttm) cc_final: 0.7232 (mmtt) REVERT: F 59 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7642 (mm-30) REVERT: F 111 MET cc_start: 0.8904 (mmt) cc_final: 0.8393 (mmt) REVERT: F 315 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7488 (mp0) REVERT: G 196 ASP cc_start: 0.7719 (p0) cc_final: 0.7471 (p0) REVERT: G 391 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7034 (tt0) REVERT: P 34 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6230 (mttm) REVERT: R 39 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: R 64 ILE cc_start: 0.8524 (mp) cc_final: 0.8308 (mm) REVERT: R 86 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8297 (ptt) REVERT: T 15 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7246 (mmtm) REVERT: T 64 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7926 (mm) outliers start: 87 outliers final: 27 residues processed: 514 average time/residue: 1.5827 time to fit residues: 947.4720 Evaluate side-chains 470 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 435 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 272 LYS Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 34 LYS Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain R residue 39 GLU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain T residue 64 ILE Chi-restraints excluded: chain U residue 82 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 61 optimal weight: 2.9990 chunk 390 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 375 optimal weight: 0.0050 chunk 200 optimal weight: 6.9990 chunk 376 optimal weight: 10.0000 chunk 364 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 330 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN C 352 GLN D 265 ASN D 366 GLN E 343 GLN F 366 GLN G 348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.168704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128608 restraints weight = 35801.898| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.67 r_work: 0.3189 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32213 Z= 0.163 Angle : 0.573 7.652 43512 Z= 0.295 Chirality : 0.045 0.158 5320 Planarity : 0.003 0.039 5642 Dihedral : 8.234 172.292 4634 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.88 % Allowed : 12.36 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.13), residues: 4305 helix: 2.16 (0.11), residues: 2072 sheet: 1.09 (0.21), residues: 511 loop : -0.34 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS T 7 PHE 0.016 0.001 PHE E 195 TYR 0.018 0.002 TYR B 506 ARG 0.010 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.05947 ( 1919) hydrogen bonds : angle 4.19919 ( 5487) covalent geometry : bond 0.00385 (32207) covalent geometry : angle 0.57301 (43512) Misc. bond : bond 0.00124 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 465 time to evaluate : 3.490 Fit side-chains REVERT: A 321 LYS cc_start: 0.8333 (mttt) cc_final: 0.8004 (mptp) REVERT: A 334 ASP cc_start: 0.7827 (m-30) cc_final: 0.7627 (m-30) REVERT: A 366 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: A 398 ASP cc_start: 0.8105 (m-30) cc_final: 0.7833 (OUTLIER) REVERT: B 160 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7744 (ptmt) REVERT: B 233 MET cc_start: 0.7254 (mmm) cc_final: 0.7027 (tpp) REVERT: B 343 GLN cc_start: 0.7410 (mm-40) cc_final: 0.7089 (mm110) REVERT: C 25 ASP cc_start: 0.8485 (m-30) cc_final: 0.8269 (m-30) REVERT: C 483 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: D 59 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: D 61 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: D 225 LYS cc_start: 0.7248 (ptmm) cc_final: 0.6711 (pptt) REVERT: D 232 GLU cc_start: 0.7223 (pm20) cc_final: 0.6947 (pm20) REVERT: D 233 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7939 (mmm) REVERT: D 255 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: D 288 MET cc_start: 0.7530 (mpp) cc_final: 0.7300 (mpp) REVERT: D 304 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7488 (pt0) REVERT: D 488 MET cc_start: 0.9253 (mmm) cc_final: 0.8817 (mmp) REVERT: E 366 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: F 111 MET cc_start: 0.8950 (mmt) cc_final: 0.8421 (mmt) REVERT: F 315 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7500 (mp0) REVERT: F 366 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7591 (tp-100) REVERT: G 193 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7589 (ttt) REVERT: G 196 ASP cc_start: 0.7754 (p0) cc_final: 0.7528 (p0) REVERT: G 391 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: P 34 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6426 (mttm) REVERT: P 48 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.6950 (pp) REVERT: P 86 MET cc_start: 0.7827 (ptt) cc_final: 0.7602 (ptp) REVERT: R 86 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8229 (ptt) REVERT: T 64 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8148 (mm) REVERT: U 9 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7935 (mtt180) REVERT: U 37 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7503 (mtt-85) outliers start: 96 outliers final: 42 residues processed: 502 average time/residue: 1.5781 time to fit residues: 921.3353 Evaluate side-chains 495 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 438 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 272 LYS Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 366 GLN Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain O residue 4 ARG Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain P residue 34 LYS Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain T residue 64 ILE Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 82 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 257 optimal weight: 0.0980 chunk 290 optimal weight: 0.0980 chunk 286 optimal weight: 0.9990 chunk 227 optimal weight: 0.0040 chunk 391 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 386 optimal weight: 20.0000 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 GLN D 265 ASN D 366 GLN G 348 GLN O 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.172854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135965 restraints weight = 35810.797| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.88 r_work: 0.3246 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32213 Z= 0.104 Angle : 0.507 7.835 43512 Z= 0.261 Chirality : 0.043 0.150 5320 Planarity : 0.003 0.037 5642 Dihedral : 7.822 171.372 4634 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.52 % Allowed : 14.14 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.13), residues: 4305 helix: 2.49 (0.11), residues: 2079 sheet: 1.38 (0.24), residues: 406 loop : -0.38 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS T 7 PHE 0.011 0.001 PHE E 195 TYR 0.020 0.001 TYR B 506 ARG 0.005 0.000 ARG R 9 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1919) hydrogen bonds : angle 3.94442 ( 5487) covalent geometry : bond 0.00209 (32207) covalent geometry : angle 0.50710 (43512) Misc. bond : bond 0.00061 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 480 time to evaluate : 8.013 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8318 (mttt) cc_final: 0.7960 (mptp) REVERT: A 334 ASP cc_start: 0.7771 (m-30) cc_final: 0.7567 (m-30) REVERT: A 366 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7029 (mt0) REVERT: A 398 ASP cc_start: 0.8058 (m-30) cc_final: 0.7742 (m-30) REVERT: B 160 LYS cc_start: 0.7981 (ttpp) cc_final: 0.7517 (ptmt) REVERT: B 193 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7313 (tpp) REVERT: B 197 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6886 (mpt-90) REVERT: B 233 MET cc_start: 0.7257 (mmm) cc_final: 0.7041 (tpp) REVERT: B 268 ARG cc_start: 0.7286 (mmt90) cc_final: 0.6844 (mmm-85) REVERT: B 315 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: B 339 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6566 (tp30) REVERT: C 14 VAL cc_start: 0.8553 (t) cc_final: 0.8165 (m) REVERT: C 25 ASP cc_start: 0.8413 (m-30) cc_final: 0.8195 (m-30) REVERT: D 129 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: D 225 LYS cc_start: 0.7072 (ptmm) cc_final: 0.6499 (pptt) REVERT: D 232 GLU cc_start: 0.7054 (pm20) cc_final: 0.6756 (pm20) REVERT: D 233 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7573 (mmm) REVERT: D 255 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: D 288 MET cc_start: 0.7575 (mpp) cc_final: 0.6858 (mpp) REVERT: D 351 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6450 (mp10) REVERT: D 364 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7192 (mmtt) REVERT: D 460 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: D 488 MET cc_start: 0.9182 (mmm) cc_final: 0.8705 (mmp) REVERT: E 288 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7923 (mpp) REVERT: E 366 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6813 (mp10) REVERT: F 59 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7623 (mm-30) REVERT: F 111 MET cc_start: 0.8978 (mmt) cc_final: 0.8485 (mmt) REVERT: F 315 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7564 (mp0) REVERT: F 366 GLN cc_start: 0.7690 (tp-100) cc_final: 0.6793 (mt0) REVERT: G 193 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7369 (ttt) REVERT: G 196 ASP cc_start: 0.7651 (p0) cc_final: 0.7394 (p0) REVERT: G 305 ILE cc_start: 0.7652 (tp) cc_final: 0.7292 (tt) REVERT: G 391 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6404 (pp20) REVERT: P 34 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6320 (mttm) REVERT: P 45 ASN cc_start: 0.8208 (t0) cc_final: 0.7692 (m-40) REVERT: P 48 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6800 (pp) REVERT: Q 73 VAL cc_start: 0.8282 (t) cc_final: 0.7999 (p) REVERT: Q 88 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: R 60 LYS cc_start: 0.8143 (ptpp) cc_final: 0.7804 (ptpp) REVERT: R 86 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7901 (ptt) REVERT: S 19 THR cc_start: 0.7855 (p) cc_final: 0.7580 (p) REVERT: T 64 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8074 (mm) REVERT: U 37 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7346 (mtt-85) REVERT: U 74 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7162 (mmmt) REVERT: U 86 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7721 (ptm) outliers start: 84 outliers final: 20 residues processed: 511 average time/residue: 1.8869 time to fit residues: 1123.3107 Evaluate side-chains 477 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 433 time to evaluate : 4.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 364 LYS Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain P residue 34 LYS Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain T residue 64 ILE Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 82 GLU Chi-restraints excluded: chain U residue 86 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 346 optimal weight: 1.9990 chunk 278 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 311 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 GLN C 352 GLN D 265 ASN D 319 GLN E 343 GLN G 348 GLN O 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.169511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131562 restraints weight = 35589.091| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.75 r_work: 0.3200 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32213 Z= 0.150 Angle : 0.547 7.446 43512 Z= 0.280 Chirality : 0.044 0.178 5320 Planarity : 0.003 0.033 5642 Dihedral : 7.709 158.022 4634 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.27 % Allowed : 14.65 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.13), residues: 4305 helix: 2.33 (0.11), residues: 2079 sheet: 1.28 (0.24), residues: 406 loop : -0.46 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS T 7 PHE 0.014 0.001 PHE E 195 TYR 0.019 0.002 TYR B 506 ARG 0.006 0.000 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.05419 ( 1919) hydrogen bonds : angle 3.96906 ( 5487) covalent geometry : bond 0.00353 (32207) covalent geometry : angle 0.54750 (43512) Misc. bond : bond 0.00126 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 445 time to evaluate : 3.606 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8160 (tp30) cc_final: 0.7927 (tp30) REVERT: A 111 MET cc_start: 0.8799 (mmp) cc_final: 0.8527 (mmt) REVERT: A 309 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7589 (tp) REVERT: A 321 LYS cc_start: 0.8373 (mttt) cc_final: 0.8030 (mptp) REVERT: A 366 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7172 (mt0) REVERT: A 398 ASP cc_start: 0.8093 (m-30) cc_final: 0.7816 (OUTLIER) REVERT: B 25 ASP cc_start: 0.8297 (m-30) cc_final: 0.7916 (m-30) REVERT: B 160 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7749 (ptmm) REVERT: B 193 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7343 (tpp) REVERT: B 197 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6937 (mpt180) REVERT: B 268 ARG cc_start: 0.7328 (mmt90) cc_final: 0.6890 (mmm-85) REVERT: B 343 GLN cc_start: 0.7189 (mm-40) cc_final: 0.6873 (mm110) REVERT: B 467 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7975 (m110) REVERT: C 25 ASP cc_start: 0.8467 (m-30) cc_final: 0.8249 (m-30) REVERT: C 178 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8177 (pp20) REVERT: C 420 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8647 (mt) REVERT: D 61 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: D 129 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: D 172 GLU cc_start: 0.7055 (tp30) cc_final: 0.6809 (tp30) REVERT: D 225 LYS cc_start: 0.7265 (ptmm) cc_final: 0.6733 (pptt) REVERT: D 232 GLU cc_start: 0.7177 (pm20) cc_final: 0.6793 (pm20) REVERT: D 233 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7726 (mmm) REVERT: D 255 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: D 288 MET cc_start: 0.7575 (mpp) cc_final: 0.6807 (mpt) REVERT: D 304 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: D 351 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6349 (mp10) REVERT: D 364 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7259 (mmtt) REVERT: D 366 GLN cc_start: 0.7465 (mm-40) cc_final: 0.6842 (mt0) REVERT: D 488 MET cc_start: 0.9222 (mmm) cc_final: 0.8863 (mmp) REVERT: E 266 THR cc_start: 0.7528 (m) cc_final: 0.7244 (m) REVERT: E 366 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6989 (mp10) REVERT: F 59 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7697 (mm-30) REVERT: F 111 MET cc_start: 0.8980 (mmt) cc_final: 0.8499 (mmt) REVERT: F 366 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7272 (tp-100) REVERT: G 193 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7507 (ttt) REVERT: G 196 ASP cc_start: 0.7670 (p0) cc_final: 0.7419 (p0) REVERT: G 272 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7432 (mtpm) REVERT: G 362 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6522 (ttp-170) REVERT: G 391 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: P 34 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6453 (mttm) REVERT: P 45 ASN cc_start: 0.8244 (t0) cc_final: 0.7777 (m-40) REVERT: P 48 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6841 (pp) REVERT: Q 73 VAL cc_start: 0.8387 (t) cc_final: 0.8096 (p) REVERT: R 39 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7023 (tt0) REVERT: R 60 LYS cc_start: 0.8203 (ptpp) cc_final: 0.7888 (ptpp) REVERT: R 86 MET cc_start: 0.8518 (ptt) cc_final: 0.8077 (ptt) REVERT: S 19 THR cc_start: 0.7915 (p) cc_final: 0.7643 (p) REVERT: T 64 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8191 (mm) REVERT: U 37 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7460 (mtt-85) REVERT: U 74 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7275 (mmmt) outliers start: 109 outliers final: 38 residues processed: 493 average time/residue: 1.6297 time to fit residues: 936.1000 Evaluate side-chains 494 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 432 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 364 LYS Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain P residue 34 LYS Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 39 GLU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain T residue 64 ILE Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 82 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 330 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 408 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 291 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN C 351 GLN C 352 GLN D 265 ASN D 319 GLN D 366 GLN E 343 GLN F 348 GLN G 348 GLN O 45 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.165777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128228 restraints weight = 35884.633| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.98 r_work: 0.3109 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 32213 Z= 0.245 Angle : 0.650 8.225 43512 Z= 0.331 Chirality : 0.048 0.192 5320 Planarity : 0.004 0.038 5642 Dihedral : 7.992 174.255 4634 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.51 % Allowed : 15.73 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.12), residues: 4305 helix: 1.81 (0.11), residues: 2072 sheet: 0.87 (0.21), residues: 511 loop : -0.43 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS U 7 PHE 0.019 0.002 PHE G 195 TYR 0.020 0.002 TYR B 506 ARG 0.007 0.001 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.07230 ( 1919) hydrogen bonds : angle 4.21667 ( 5487) covalent geometry : bond 0.00606 (32207) covalent geometry : angle 0.65007 (43512) Misc. bond : bond 0.00245 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 457 time to evaluate : 3.262 Fit side-chains REVERT: A 59 GLU cc_start: 0.8230 (tp30) cc_final: 0.7965 (tp30) REVERT: A 111 MET cc_start: 0.8967 (mmp) cc_final: 0.8713 (mmt) REVERT: A 229 ASN cc_start: 0.7739 (t0) cc_final: 0.7184 (t0) REVERT: A 309 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7578 (tp) REVERT: A 321 LYS cc_start: 0.8363 (mttt) cc_final: 0.8080 (mptp) REVERT: A 366 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: A 483 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: B 25 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: B 160 LYS cc_start: 0.8089 (ttpp) cc_final: 0.7689 (ptmm) REVERT: B 193 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7629 (tpt) REVERT: B 197 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6876 (mpt-90) REVERT: B 268 ARG cc_start: 0.7310 (mmt90) cc_final: 0.6661 (tpp80) REVERT: B 343 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6906 (mm110) REVERT: C 172 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7269 (mm-30) REVERT: C 178 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8146 (pp20) REVERT: C 420 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8635 (mt) REVERT: D 61 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: D 232 GLU cc_start: 0.7393 (pm20) cc_final: 0.6742 (pm20) REVERT: D 255 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: D 288 MET cc_start: 0.7525 (mpp) cc_final: 0.6810 (mpp) REVERT: D 304 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: D 351 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6456 (mp10) REVERT: D 488 MET cc_start: 0.9272 (mmm) cc_final: 0.8806 (mmp) REVERT: E 266 THR cc_start: 0.7661 (m) cc_final: 0.7396 (m) REVERT: E 288 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7967 (mpp) REVERT: E 366 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: F 59 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7889 (mm-30) REVERT: F 111 MET cc_start: 0.9011 (mmt) cc_final: 0.8423 (mmt) REVERT: F 366 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7375 (tp-100) REVERT: P 34 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6496 (mttm) REVERT: P 45 ASN cc_start: 0.8330 (t0) cc_final: 0.7874 (m-40) REVERT: P 48 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.6932 (pp) REVERT: R 39 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: R 60 LYS cc_start: 0.8166 (ptpp) cc_final: 0.7860 (ptpp) REVERT: R 86 MET cc_start: 0.8589 (ptt) cc_final: 0.8154 (ptt) REVERT: U 37 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6914 (mtt180) outliers start: 117 outliers final: 59 residues processed: 509 average time/residue: 1.6037 time to fit residues: 946.3489 Evaluate side-chains 519 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 440 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 467 ASN Chi-restraints excluded: chain F residue 523 ASP Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 425 LYS Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain P residue 34 LYS Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 39 GLU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 82 GLU Chi-restraints excluded: chain U residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 346 optimal weight: 0.9980 chunk 335 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 425 optimal weight: 5.9990 chunk 279 optimal weight: 0.0970 chunk 332 optimal weight: 2.9990 chunk 393 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN D 265 ASN G 348 GLN O 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.168989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129889 restraints weight = 35828.694| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.77 r_work: 0.3188 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32213 Z= 0.137 Angle : 0.547 7.302 43512 Z= 0.281 Chirality : 0.044 0.176 5320 Planarity : 0.003 0.034 5642 Dihedral : 7.844 178.882 4634 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.73 % Allowed : 17.32 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.13), residues: 4305 helix: 2.17 (0.11), residues: 2065 sheet: 1.26 (0.22), residues: 476 loop : -0.49 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 7 PHE 0.013 0.001 PHE E 195 TYR 0.021 0.002 TYR B 506 ARG 0.007 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.05286 ( 1919) hydrogen bonds : angle 4.00883 ( 5487) covalent geometry : bond 0.00310 (32207) covalent geometry : angle 0.54681 (43512) Misc. bond : bond 0.00121 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 453 time to evaluate : 3.761 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8122 (tp30) cc_final: 0.7899 (tp30) REVERT: A 111 MET cc_start: 0.8899 (mmp) cc_final: 0.8601 (mmt) REVERT: A 229 ASN cc_start: 0.7730 (t0) cc_final: 0.7195 (t0) REVERT: A 366 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7033 (mt0) REVERT: B 25 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: B 160 LYS cc_start: 0.8023 (ttpp) cc_final: 0.7631 (ptmm) REVERT: B 197 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.6866 (mpt-90) REVERT: B 268 ARG cc_start: 0.7297 (mmt90) cc_final: 0.6786 (mmm-85) REVERT: B 343 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6882 (mm110) REVERT: C 14 VAL cc_start: 0.8620 (t) cc_final: 0.8219 (m) REVERT: C 25 ASP cc_start: 0.8398 (m-30) cc_final: 0.8171 (m-30) REVERT: C 172 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: C 178 GLU cc_start: 0.8422 (pt0) cc_final: 0.8133 (pp20) REVERT: C 209 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.4679 (mp0) REVERT: C 420 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8629 (mt) REVERT: D 61 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: D 172 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6867 (mm-30) REVERT: D 225 LYS cc_start: 0.7071 (ptmm) cc_final: 0.6494 (pptt) REVERT: D 232 GLU cc_start: 0.7478 (pm20) cc_final: 0.7013 (pm20) REVERT: D 255 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: D 288 MET cc_start: 0.7441 (mpp) cc_final: 0.6698 (mpp) REVERT: D 364 LYS cc_start: 0.7564 (mttm) cc_final: 0.7259 (mmtt) REVERT: D 366 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6657 (mt0) REVERT: D 460 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: D 488 MET cc_start: 0.9231 (mmm) cc_final: 0.8790 (mmp) REVERT: E 266 THR cc_start: 0.7639 (m) cc_final: 0.7343 (m) REVERT: E 288 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7947 (mpp) REVERT: E 366 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6936 (mp10) REVERT: F 59 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7654 (mm-30) REVERT: F 111 MET cc_start: 0.8976 (mmt) cc_final: 0.8451 (mmt) REVERT: F 188 ASP cc_start: 0.7890 (p0) cc_final: 0.7559 (p0) REVERT: F 189 VAL cc_start: 0.8911 (p) cc_final: 0.8614 (t) REVERT: F 315 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7566 (mp0) REVERT: F 322 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7016 (ttt90) REVERT: F 366 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7476 (tp-100) REVERT: G 193 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7582 (ttt) REVERT: G 362 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6548 (ttp-170) REVERT: G 391 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: P 34 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6370 (mttm) REVERT: P 45 ASN cc_start: 0.8262 (t0) cc_final: 0.7810 (m110) REVERT: P 48 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.6909 (pp) REVERT: P 87 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8520 (m) REVERT: Q 73 VAL cc_start: 0.8402 (t) cc_final: 0.8182 (p) REVERT: Q 86 MET cc_start: 0.8843 (ptt) cc_final: 0.8456 (ptt) REVERT: R 39 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: R 60 LYS cc_start: 0.8203 (ptpp) cc_final: 0.7898 (ptpp) REVERT: R 86 MET cc_start: 0.8507 (ptt) cc_final: 0.8065 (ptt) REVERT: U 37 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7361 (mtt-85) outliers start: 91 outliers final: 39 residues processed: 493 average time/residue: 1.9038 time to fit residues: 1093.0327 Evaluate side-chains 496 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 435 time to evaluate : 5.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 523 ASP Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain P residue 34 LYS Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 39 GLU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 82 GLU Chi-restraints excluded: chain U residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 352 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 425 optimal weight: 20.0000 chunk 229 optimal weight: 0.3980 chunk 349 optimal weight: 9.9990 chunk 340 optimal weight: 0.8980 chunk 323 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 268 optimal weight: 0.4980 chunk 401 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN D 206 ASN D 265 ASN D 366 GLN G 72 GLN G 348 GLN O 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.171567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132244 restraints weight = 35657.678| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.84 r_work: 0.3235 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32213 Z= 0.115 Angle : 0.524 7.782 43512 Z= 0.269 Chirality : 0.043 0.185 5320 Planarity : 0.003 0.033 5642 Dihedral : 7.519 174.429 4634 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.46 % Allowed : 17.71 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.13), residues: 4305 helix: 2.40 (0.11), residues: 2065 sheet: 1.76 (0.30), residues: 287 loop : -0.34 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS T 7 PHE 0.012 0.001 PHE E 195 TYR 0.022 0.001 TYR B 506 ARG 0.007 0.000 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 1919) hydrogen bonds : angle 3.87713 ( 5487) covalent geometry : bond 0.00247 (32207) covalent geometry : angle 0.52354 (43512) Misc. bond : bond 0.00076 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 458 time to evaluate : 3.336 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8170 (tp30) cc_final: 0.7879 (tp30) REVERT: A 111 MET cc_start: 0.8864 (mmp) cc_final: 0.8555 (mmt) REVERT: A 229 ASN cc_start: 0.7704 (t0) cc_final: 0.7147 (t0) REVERT: A 309 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 366 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6840 (mt0) REVERT: A 398 ASP cc_start: 0.7919 (m-30) cc_final: 0.7594 (m-30) REVERT: B 25 ASP cc_start: 0.8152 (m-30) cc_final: 0.7797 (m-30) REVERT: B 160 LYS cc_start: 0.7907 (ttpp) cc_final: 0.7491 (ptmm) REVERT: B 197 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.6680 (mpt180) REVERT: B 268 ARG cc_start: 0.7293 (mmt90) cc_final: 0.6779 (mmm-85) REVERT: B 343 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6937 (mm110) REVERT: C 14 VAL cc_start: 0.8557 (t) cc_final: 0.8156 (m) REVERT: C 25 ASP cc_start: 0.8364 (m-30) cc_final: 0.8118 (m-30) REVERT: C 172 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: C 178 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8130 (pp20) REVERT: C 420 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8511 (mt) REVERT: D 129 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: D 232 GLU cc_start: 0.7466 (pm20) cc_final: 0.6964 (pm20) REVERT: D 288 MET cc_start: 0.7333 (mpp) cc_final: 0.6456 (mpp) REVERT: D 364 LYS cc_start: 0.7484 (mttm) cc_final: 0.7189 (mmtt) REVERT: D 366 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6547 (mt0) REVERT: D 488 MET cc_start: 0.9245 (mmm) cc_final: 0.8916 (mmp) REVERT: E 233 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7319 (mtt) REVERT: E 266 THR cc_start: 0.7406 (m) cc_final: 0.7171 (m) REVERT: E 288 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7937 (mpp) REVERT: E 366 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: F 111 MET cc_start: 0.8970 (mmt) cc_final: 0.8476 (mmt) REVERT: F 188 ASP cc_start: 0.7744 (p0) cc_final: 0.7454 (p0) REVERT: F 189 VAL cc_start: 0.8905 (p) cc_final: 0.8660 (t) REVERT: F 315 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7543 (mp0) REVERT: F 366 GLN cc_start: 0.7882 (tp-100) cc_final: 0.7421 (tp-100) REVERT: G 193 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7533 (ttt) REVERT: G 307 MET cc_start: 0.7223 (ptm) cc_final: 0.6645 (pmm) REVERT: G 362 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6420 (ttp-170) REVERT: G 391 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6324 (pp20) REVERT: P 34 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6353 (mttm) REVERT: P 45 ASN cc_start: 0.8248 (t0) cc_final: 0.7758 (m-40) REVERT: P 48 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6836 (pp) REVERT: P 87 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8438 (m) REVERT: Q 73 VAL cc_start: 0.8354 (t) cc_final: 0.8130 (p) REVERT: R 39 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: R 60 LYS cc_start: 0.8150 (ptpp) cc_final: 0.7817 (ptpp) REVERT: R 86 MET cc_start: 0.8429 (ptt) cc_final: 0.7921 (ptt) REVERT: U 37 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7238 (mtt-85) outliers start: 82 outliers final: 33 residues processed: 496 average time/residue: 1.6004 time to fit residues: 925.0317 Evaluate side-chains 491 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 439 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 366 GLN Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 523 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain P residue 34 LYS Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 39 GLU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 82 GLU Chi-restraints excluded: chain U residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 352 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 365 optimal weight: 0.4980 chunk 408 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN C 352 GLN D 265 ASN E 343 GLN G 348 GLN O 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.170356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131064 restraints weight = 35654.541| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.79 r_work: 0.3201 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32213 Z= 0.139 Angle : 0.544 7.891 43512 Z= 0.279 Chirality : 0.044 0.174 5320 Planarity : 0.003 0.055 5642 Dihedral : 7.456 170.610 4634 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.37 % Allowed : 18.01 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.13), residues: 4305 helix: 2.30 (0.11), residues: 2072 sheet: 0.60 (0.21), residues: 546 loop : -0.38 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 7 PHE 0.013 0.001 PHE E 195 TYR 0.026 0.002 TYR A 506 ARG 0.014 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.05002 ( 1919) hydrogen bonds : angle 3.90039 ( 5487) covalent geometry : bond 0.00323 (32207) covalent geometry : angle 0.54401 (43512) Misc. bond : bond 0.00112 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 442 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8180 (tp30) cc_final: 0.7885 (tp30) REVERT: A 111 MET cc_start: 0.8890 (mmp) cc_final: 0.8572 (mmt) REVERT: A 229 ASN cc_start: 0.7711 (t0) cc_final: 0.7164 (t0) REVERT: A 309 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7431 (tp) REVERT: A 366 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6975 (mt0) REVERT: A 398 ASP cc_start: 0.7914 (m-30) cc_final: 0.7607 (m-30) REVERT: B 25 ASP cc_start: 0.8212 (m-30) cc_final: 0.7855 (m-30) REVERT: B 160 LYS cc_start: 0.7914 (ttpp) cc_final: 0.7489 (ptmm) REVERT: B 197 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6690 (mpt180) REVERT: B 268 ARG cc_start: 0.7295 (mmt90) cc_final: 0.6761 (mmm-85) REVERT: B 514 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8505 (mtp) REVERT: C 14 VAL cc_start: 0.8608 (t) cc_final: 0.8191 (m) REVERT: C 25 ASP cc_start: 0.8394 (m-30) cc_final: 0.8149 (m-30) REVERT: C 172 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: C 178 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8139 (pp20) REVERT: C 209 GLU cc_start: 0.5706 (OUTLIER) cc_final: 0.4740 (mp0) REVERT: C 420 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8556 (mt) REVERT: D 225 LYS cc_start: 0.6672 (ptmm) cc_final: 0.6210 (pptt) REVERT: D 232 GLU cc_start: 0.7600 (pm20) cc_final: 0.7089 (pm20) REVERT: D 288 MET cc_start: 0.7378 (mpp) cc_final: 0.6505 (mpt) REVERT: D 351 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6502 (mp10) REVERT: D 488 MET cc_start: 0.9245 (mmm) cc_final: 0.8927 (mmp) REVERT: E 233 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7373 (mtm) REVERT: E 288 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7948 (mpp) REVERT: E 366 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: F 59 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: F 111 MET cc_start: 0.8976 (mmt) cc_final: 0.8450 (mmt) REVERT: F 188 ASP cc_start: 0.7749 (p0) cc_final: 0.7467 (p0) REVERT: F 189 VAL cc_start: 0.8903 (p) cc_final: 0.8648 (t) REVERT: F 315 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7522 (mp0) REVERT: F 366 GLN cc_start: 0.7868 (tp-100) cc_final: 0.7417 (tp-100) REVERT: G 193 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7557 (ttt) REVERT: G 305 ILE cc_start: 0.7561 (tp) cc_final: 0.7126 (tt) REVERT: G 391 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6390 (pp20) REVERT: P 34 LYS cc_start: 0.6628 (OUTLIER) cc_final: 0.6308 (mttm) REVERT: P 45 ASN cc_start: 0.8173 (t0) cc_final: 0.7726 (m-40) REVERT: P 48 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.6852 (pp) REVERT: P 87 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8444 (m) REVERT: Q 73 VAL cc_start: 0.8366 (t) cc_final: 0.8143 (p) REVERT: R 39 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: R 60 LYS cc_start: 0.8128 (ptpp) cc_final: 0.7803 (ptpp) REVERT: R 86 MET cc_start: 0.8451 (ptt) cc_final: 0.7979 (ptt) REVERT: U 37 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7246 (mtt-85) REVERT: U 86 MET cc_start: 0.8127 (ptt) cc_final: 0.7862 (ptt) outliers start: 79 outliers final: 43 residues processed: 475 average time/residue: 1.6459 time to fit residues: 908.3358 Evaluate side-chains 495 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 432 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 523 ASP Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain P residue 34 LYS Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 39 GLU Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 82 GLU Chi-restraints excluded: chain U residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 240 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 326 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 284 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN C 352 GLN D 265 ASN G 348 GLN O 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133579 restraints weight = 35647.515| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.80 r_work: 0.3247 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32213 Z= 0.108 Angle : 0.513 8.040 43512 Z= 0.264 Chirality : 0.043 0.173 5320 Planarity : 0.003 0.060 5642 Dihedral : 7.149 162.989 4634 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.01 % Allowed : 18.58 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.13), residues: 4305 helix: 2.48 (0.11), residues: 2072 sheet: 0.74 (0.21), residues: 546 loop : -0.30 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS T 7 PHE 0.010 0.001 PHE E 195 TYR 0.026 0.001 TYR B 506 ARG 0.014 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 1919) hydrogen bonds : angle 3.80029 ( 5487) covalent geometry : bond 0.00232 (32207) covalent geometry : angle 0.51298 (43512) Misc. bond : bond 0.00052 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8610 Ramachandran restraints generated. 4305 Oldfield, 0 Emsley, 4305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 450 time to evaluate : 3.507 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8121 (tp30) cc_final: 0.7881 (tp30) REVERT: A 111 MET cc_start: 0.8836 (mmp) cc_final: 0.8549 (mmt) REVERT: A 209 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5944 (pm20) REVERT: A 229 ASN cc_start: 0.7692 (t0) cc_final: 0.7131 (t0) REVERT: A 309 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7466 (tp) REVERT: A 366 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6959 (mt0) REVERT: A 398 ASP cc_start: 0.7961 (m-30) cc_final: 0.7623 (m-30) REVERT: B 160 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7543 (ptmm) REVERT: B 197 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6659 (mpt180) REVERT: B 268 ARG cc_start: 0.7156 (mmt90) cc_final: 0.6854 (mmm-85) REVERT: C 14 VAL cc_start: 0.8537 (t) cc_final: 0.8172 (m) REVERT: C 25 ASP cc_start: 0.8390 (m-30) cc_final: 0.8145 (m-30) REVERT: C 172 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7132 (mm-30) REVERT: C 178 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: C 209 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.4738 (mp0) REVERT: C 322 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.7180 (mtp85) REVERT: C 420 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8524 (mt) REVERT: D 83 ASP cc_start: 0.7070 (m-30) cc_final: 0.6847 (m-30) REVERT: D 129 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: D 232 GLU cc_start: 0.7510 (pm20) cc_final: 0.6991 (pm20) REVERT: D 288 MET cc_start: 0.7409 (mpp) cc_final: 0.6527 (mpp) REVERT: D 351 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.6438 (mp10) REVERT: D 364 LYS cc_start: 0.7516 (mttm) cc_final: 0.7209 (mmtt) REVERT: D 488 MET cc_start: 0.9220 (mmm) cc_final: 0.8915 (mmp) REVERT: E 233 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7475 (mtm) REVERT: E 366 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6875 (mp10) REVERT: E 460 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7636 (mm-30) REVERT: E 488 MET cc_start: 0.8974 (mmp) cc_final: 0.8704 (mmp) REVERT: F 59 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: F 111 MET cc_start: 0.8954 (mmt) cc_final: 0.8489 (mmt) REVERT: F 188 ASP cc_start: 0.7742 (p0) cc_final: 0.7450 (p0) REVERT: F 315 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7540 (mp0) REVERT: F 366 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7436 (tp-100) REVERT: G 193 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7574 (ttt) REVERT: G 231 ARG cc_start: 0.7292 (mmt180) cc_final: 0.7038 (mmm160) REVERT: G 305 ILE cc_start: 0.7503 (tp) cc_final: 0.6757 (tt) REVERT: G 307 MET cc_start: 0.7264 (ptm) cc_final: 0.6938 (pmm) REVERT: G 351 GLN cc_start: 0.6352 (mp10) cc_final: 0.6148 (mp10) REVERT: G 391 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6315 (pp20) REVERT: P 34 LYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6376 (mttm) REVERT: P 45 ASN cc_start: 0.8245 (t0) cc_final: 0.7752 (m110) REVERT: P 48 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.6836 (pp) REVERT: P 87 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8452 (m) REVERT: Q 73 VAL cc_start: 0.8330 (t) cc_final: 0.8096 (p) REVERT: R 60 LYS cc_start: 0.8157 (ptpp) cc_final: 0.7834 (ptpp) REVERT: R 86 MET cc_start: 0.8400 (ptt) cc_final: 0.7889 (ptt) REVERT: U 86 MET cc_start: 0.8096 (ptt) cc_final: 0.7843 (ptt) outliers start: 67 outliers final: 30 residues processed: 478 average time/residue: 1.6124 time to fit residues: 898.2485 Evaluate side-chains 487 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 439 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 523 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain P residue 34 LYS Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 82 GLU Chi-restraints excluded: chain U residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 18 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 377 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 397 optimal weight: 0.9980 chunk 346 optimal weight: 0.9990 chunk 134 optimal weight: 0.0070 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN C 351 GLN C 352 GLN D 265 ASN O 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.173083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133551 restraints weight = 35663.495| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.78 r_work: 0.3263 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32213 Z= 0.109 Angle : 0.517 8.279 43512 Z= 0.265 Chirality : 0.043 0.170 5320 Planarity : 0.003 0.050 5642 Dihedral : 7.039 156.572 4634 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.80 % Allowed : 18.97 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.13), residues: 4305 helix: 2.51 (0.11), residues: 2072 sheet: 0.82 (0.21), residues: 546 loop : -0.29 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS T 7 PHE 0.011 0.001 PHE E 195 TYR 0.031 0.002 TYR A 506 ARG 0.015 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 1919) hydrogen bonds : angle 3.77544 ( 5487) covalent geometry : bond 0.00237 (32207) covalent geometry : angle 0.51737 (43512) Misc. bond : bond 0.00042 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26716.74 seconds wall clock time: 465 minutes 4.34 seconds (27904.34 seconds total)