Starting phenix.real_space_refine on Tue Jul 29 00:34:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pqu_13605/07_2025/7pqu_13605.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pqu_13605/07_2025/7pqu_13605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pqu_13605/07_2025/7pqu_13605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pqu_13605/07_2025/7pqu_13605.map" model { file = "/net/cci-nas-00/data/ceres_data/7pqu_13605/07_2025/7pqu_13605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pqu_13605/07_2025/7pqu_13605.cif" } resolution = 3.03 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= 0.003 sd= 0.053 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 72 5.16 5 C 7100 2.51 5 N 1780 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10798 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "B" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "C" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "D" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Unusual residues: {' K': 4, '805': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'805': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'805': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'805': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALYS A 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 449 " occ=0.50 residue: pdb=" N ALYS B 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 449 " occ=0.50 residue: pdb=" N ALYS C 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 449 " occ=0.50 residue: pdb=" N ALYS D 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 449 " occ=0.50 Time building chain proxies: 11.17, per 1000 atoms: 1.03 Number of scatterers: 10798 At special positions: 0 Unit cell: (100.04, 100.04, 115.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 72 16.00 O 1842 8.00 N 1780 7.00 C 7100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 2.4 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 4 sheets defined 61.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.921A pdb=" N TRP A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 39' Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.662A pdb=" N TYR A 87 " --> pdb=" O CYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.691A pdb=" N GLN A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 211 removed outlier: 4.544A pdb=" N PHE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 260 removed outlier: 3.945A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 removed outlier: 4.033A pdb=" N TYR A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.926A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.582A pdb=" N ARG A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 370 removed outlier: 4.075A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.847A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 removed outlier: 3.906A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 451 removed outlier: 3.828A pdb=" N ASN A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.921A pdb=" N TRP B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 32 through 39' Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.662A pdb=" N TYR B 87 " --> pdb=" O CYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.691A pdb=" N GLN B 111 " --> pdb=" O MET B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 211 removed outlier: 4.544A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 260 removed outlier: 3.946A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 4.033A pdb=" N TYR B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.925A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.582A pdb=" N ARG B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 370 removed outlier: 4.076A pdb=" N LEU B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 399 removed outlier: 3.847A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 removed outlier: 3.905A pdb=" N LEU B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 451 removed outlier: 3.827A pdb=" N ASN B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.920A pdb=" N TRP C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 32 through 39' Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.662A pdb=" N TYR C 87 " --> pdb=" O CYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.690A pdb=" N GLN C 111 " --> pdb=" O MET C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 211 removed outlier: 4.544A pdb=" N PHE C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 260 removed outlier: 3.945A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 4.032A pdb=" N TYR C 290 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.925A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 removed outlier: 3.583A pdb=" N ARG C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 370 removed outlier: 4.076A pdb=" N LEU C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 removed outlier: 3.848A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 removed outlier: 3.906A pdb=" N LEU C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 451 removed outlier: 3.828A pdb=" N ASN C 438 " --> pdb=" O VAL C 434 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.921A pdb=" N TRP D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 32 through 39' Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 83 through 95 removed outlier: 3.662A pdb=" N TYR D 87 " --> pdb=" O CYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 111 removed outlier: 3.691A pdb=" N GLN D 111 " --> pdb=" O MET D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 211 removed outlier: 4.544A pdb=" N PHE D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 260 removed outlier: 3.945A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 removed outlier: 4.033A pdb=" N TYR D 290 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 320 through 325 removed outlier: 3.926A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.582A pdb=" N ARG D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 370 removed outlier: 4.076A pdb=" N LEU D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 399 removed outlier: 3.847A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 removed outlier: 3.906A pdb=" N LEU D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 451 removed outlier: 3.827A pdb=" N ASN D 438 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 439 " --> pdb=" O ILE D 435 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.903A pdb=" N THR A 17 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 14 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 47 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.903A pdb=" N THR B 17 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 14 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP B 47 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.903A pdb=" N THR C 17 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 14 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP C 47 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.904A pdb=" N THR D 17 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 14 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP D 47 " --> pdb=" O PHE D 56 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1412 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: 2.63 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1612 1.27 - 1.41: 3220 1.41 - 1.54: 6140 1.54 - 1.67: 16 1.67 - 1.81: 112 Bond restraints: 11100 Sorted by residual: bond pdb=" C GLY A 402 " pdb=" O GLY A 402 " ideal model delta sigma weight residual 1.235 1.142 0.093 1.35e-02 5.49e+03 4.75e+01 bond pdb=" C GLY B 402 " pdb=" O GLY B 402 " ideal model delta sigma weight residual 1.235 1.142 0.093 1.35e-02 5.49e+03 4.72e+01 bond pdb=" C GLY D 402 " pdb=" O GLY D 402 " ideal model delta sigma weight residual 1.235 1.142 0.093 1.35e-02 5.49e+03 4.70e+01 bond pdb=" C GLY C 402 " pdb=" O GLY C 402 " ideal model delta sigma weight residual 1.235 1.142 0.092 1.35e-02 5.49e+03 4.69e+01 bond pdb=" N11 805 B 601 " pdb=" S08 805 B 601 " ideal model delta sigma weight residual 1.693 1.772 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 11095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 14806 2.61 - 5.22: 214 5.22 - 7.82: 64 7.82 - 10.43: 12 10.43 - 13.04: 8 Bond angle restraints: 15104 Sorted by residual: angle pdb=" N VAL D 264 " pdb=" CA VAL D 264 " pdb=" C VAL D 264 " ideal model delta sigma weight residual 113.71 107.57 6.14 9.50e-01 1.11e+00 4.17e+01 angle pdb=" N VAL A 264 " pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 113.71 107.61 6.10 9.50e-01 1.11e+00 4.13e+01 angle pdb=" N VAL C 264 " pdb=" CA VAL C 264 " pdb=" C VAL C 264 " ideal model delta sigma weight residual 113.71 107.62 6.09 9.50e-01 1.11e+00 4.11e+01 angle pdb=" N VAL B 264 " pdb=" CA VAL B 264 " pdb=" C VAL B 264 " ideal model delta sigma weight residual 113.71 107.63 6.08 9.50e-01 1.11e+00 4.09e+01 angle pdb=" C14 805 B 601 " pdb=" C16 805 B 601 " pdb=" N18 805 B 601 " ideal model delta sigma weight residual 116.11 129.15 -13.04 3.00e+00 1.11e-01 1.89e+01 ... (remaining 15099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 5517 17.36 - 34.72: 637 34.72 - 52.09: 157 52.09 - 69.45: 49 69.45 - 86.81: 20 Dihedral angle restraints: 6380 sinusoidal: 2548 harmonic: 3832 Sorted by residual: dihedral pdb=" CA ARG C 314 " pdb=" C ARG C 314 " pdb=" N PHE C 315 " pdb=" CA PHE C 315 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ARG B 314 " pdb=" C ARG B 314 " pdb=" N PHE B 315 " pdb=" CA PHE B 315 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ARG D 314 " pdb=" C ARG D 314 " pdb=" N PHE D 315 " pdb=" CA PHE D 315 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 6377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1038 0.039 - 0.079: 465 0.079 - 0.118: 136 0.118 - 0.157: 21 0.157 - 0.197: 4 Chirality restraints: 1664 Sorted by residual: chirality pdb=" CB ILE B 286 " pdb=" CA ILE B 286 " pdb=" CG1 ILE B 286 " pdb=" CG2 ILE B 286 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB ILE A 286 " pdb=" CA ILE A 286 " pdb=" CG1 ILE A 286 " pdb=" CG2 ILE A 286 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" CB ILE C 286 " pdb=" CA ILE C 286 " pdb=" CG1 ILE C 286 " pdb=" CG2 ILE C 286 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 1661 not shown) Planarity restraints: 1876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 325 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C THR D 325 " 0.056 2.00e-02 2.50e+03 pdb=" O THR D 325 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG D 326 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 325 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THR A 325 " -0.056 2.00e-02 2.50e+03 pdb=" O THR A 325 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 326 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 325 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THR B 325 " -0.056 2.00e-02 2.50e+03 pdb=" O THR B 325 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG B 326 " 0.019 2.00e-02 2.50e+03 ... (remaining 1873 not shown) Histogram of nonbonded interaction distances: 0.05 - 1.07: 7 1.07 - 2.09: 4 2.09 - 3.10: 8057 3.10 - 4.12: 29577 4.12 - 5.14: 64960 Warning: very small nonbonded interaction distances. Nonbonded interactions: 102605 Sorted by model distance: nonbonded pdb=" O HOH B 703 " pdb=" O HOH B 704 " model vdw 0.051 3.040 nonbonded pdb=" O HOH A 702 " pdb=" O HOH A 703 " model vdw 0.057 3.040 nonbonded pdb=" O HOH A 701 " pdb=" O HOH A 702 " model vdw 0.066 3.040 nonbonded pdb=" O HOH B 701 " pdb=" O HOH B 702 " model vdw 0.076 3.040 nonbonded pdb=" O HOH D 702 " pdb=" O HOH D 703 " model vdw 0.079 3.040 ... (remaining 102600 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) selection = (chain 'B' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) selection = (chain 'C' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) selection = (chain 'D' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.220 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 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 : 0.008 0.093 11100 Z= 0.374 Angle : 0.904 13.038 15104 Z= 0.468 Chirality : 0.047 0.197 1664 Planarity : 0.005 0.046 1876 Dihedral : 17.235 86.809 3908 Min Nonbonded Distance : 0.051 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.91 % Favored : 92.01 % Rotamer: Outliers : 5.14 % Allowed : 21.90 % Favored : 72.96 % 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: -3.95 (0.21), residues: 1272 helix: -2.39 (0.15), residues: 772 sheet: None (None), residues: 0 loop : -2.81 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 94 HIS 0.003 0.001 HIS D 19 PHE 0.010 0.002 PHE C 359 TYR 0.017 0.002 TYR B 22 ARG 0.003 0.001 ARG D 320 Details of bonding type rmsd hydrogen bonds : bond 0.09112 ( 484) hydrogen bonds : angle 5.37041 ( 1412) covalent geometry : bond 0.00790 (11100) covalent geometry : angle 0.90371 (15104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 1.042 Fit side-chains REVERT: A 33 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7329 (ttp-170) REVERT: A 281 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7194 (tp) REVERT: B 33 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7597 (ttp-170) REVERT: C 33 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7595 (ttp-170) REVERT: D 33 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7441 (ttp-170) outliers start: 58 outliers final: 44 residues processed: 254 average time/residue: 0.3082 time to fit residues: 102.8074 Evaluate side-chains 240 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 43 HIS A 60 HIS A 111 GLN A 450 GLN B 19 HIS B 60 HIS B 111 GLN C 19 HIS C 60 HIS C 111 GLN D 19 HIS D 60 HIS D 111 GLN D 409 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096374 restraints weight = 48445.358| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 4.24 r_work: 0.3119 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11100 Z= 0.156 Angle : 0.622 8.153 15104 Z= 0.319 Chirality : 0.043 0.213 1664 Planarity : 0.006 0.063 1876 Dihedral : 9.491 55.611 1611 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.76 % Allowed : 20.48 % Favored : 73.76 % 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: -2.73 (0.22), residues: 1272 helix: -1.24 (0.17), residues: 804 sheet: None (None), residues: 0 loop : -2.70 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 94 HIS 0.003 0.001 HIS B 19 PHE 0.012 0.001 PHE D 289 TYR 0.015 0.002 TYR C 247 ARG 0.006 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 484) hydrogen bonds : angle 4.28719 ( 1412) covalent geometry : bond 0.00376 (11100) covalent geometry : angle 0.62224 (15104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 1.163 Fit side-chains REVERT: A 71 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8241 (m-10) REVERT: A 113 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.8387 (mmm-85) REVERT: A 255 TRP cc_start: 0.7811 (t60) cc_final: 0.7578 (t-100) REVERT: A 281 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7219 (tp) REVERT: A 310 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6411 (tp) REVERT: B 71 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: B 113 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.8442 (mmm-85) REVERT: B 210 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7394 (mp0) REVERT: B 310 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6423 (tp) REVERT: B 325 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8033 (m) REVERT: C 71 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8279 (m-10) REVERT: C 113 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8411 (mmm-85) REVERT: C 255 TRP cc_start: 0.7751 (t60) cc_final: 0.7538 (t-100) REVERT: C 325 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.8012 (m) REVERT: D 71 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: D 113 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8293 (mmm-85) outliers start: 65 outliers final: 35 residues processed: 251 average time/residue: 0.3134 time to fit residues: 106.6080 Evaluate side-chains 234 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 450 GLN C 43 HIS C 111 GLN D 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097578 restraints weight = 52641.875| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.34 r_work: 0.3122 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11100 Z= 0.132 Angle : 0.567 8.443 15104 Z= 0.291 Chirality : 0.042 0.186 1664 Planarity : 0.006 0.068 1876 Dihedral : 6.983 57.723 1544 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.79 % Allowed : 20.12 % Favored : 75.09 % 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: -1.91 (0.23), residues: 1272 helix: -0.62 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -2.34 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.003 0.000 HIS D 19 PHE 0.010 0.001 PHE C 289 TYR 0.015 0.001 TYR D 247 ARG 0.005 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 484) hydrogen bonds : angle 4.10275 ( 1412) covalent geometry : bond 0.00312 (11100) covalent geometry : angle 0.56655 (15104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 1.391 Fit side-chains REVERT: A 71 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8293 (m-10) REVERT: A 86 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7664 (tt) REVERT: A 113 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8459 (mmm-85) REVERT: A 247 TYR cc_start: 0.7946 (m-80) cc_final: 0.7158 (m-80) REVERT: B 71 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8236 (m-10) REVERT: B 86 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7646 (tt) REVERT: B 210 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7366 (mt-10) REVERT: B 247 TYR cc_start: 0.7992 (m-80) cc_final: 0.7149 (m-80) REVERT: B 325 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7802 (p) REVERT: C 71 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8234 (m-10) REVERT: C 325 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7947 (m) REVERT: D 71 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8247 (m-10) REVERT: D 113 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.8353 (mmm-85) REVERT: D 247 TYR cc_start: 0.7909 (m-80) cc_final: 0.7145 (m-80) outliers start: 54 outliers final: 34 residues processed: 235 average time/residue: 0.3281 time to fit residues: 106.2451 Evaluate side-chains 224 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 43 HIS B 111 GLN B 112 HIS C 111 GLN C 112 HIS D 43 HIS D 111 GLN D 327 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096068 restraints weight = 46798.136| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.18 r_work: 0.3108 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11100 Z= 0.173 Angle : 0.586 8.770 15104 Z= 0.300 Chirality : 0.044 0.173 1664 Planarity : 0.006 0.070 1876 Dihedral : 6.576 58.760 1536 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.67 % Allowed : 19.50 % Favored : 74.82 % 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 (0.23), residues: 1272 helix: -0.45 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -2.16 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 94 HIS 0.003 0.001 HIS A 19 PHE 0.009 0.001 PHE D 359 TYR 0.031 0.002 TYR D 70 ARG 0.005 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 484) hydrogen bonds : angle 4.19585 ( 1412) covalent geometry : bond 0.00425 (11100) covalent geometry : angle 0.58601 (15104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 1.735 Fit side-chains REVERT: A 71 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: A 113 ARG cc_start: 0.8711 (mmm-85) cc_final: 0.8466 (mmm-85) REVERT: A 247 TYR cc_start: 0.7979 (m-80) cc_final: 0.7176 (m-80) REVERT: A 281 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7204 (tp) REVERT: B 71 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8355 (m-10) REVERT: B 98 GLU cc_start: 0.8275 (mp0) cc_final: 0.7980 (mp0) REVERT: B 210 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7322 (mt-10) REVERT: B 247 TYR cc_start: 0.7987 (m-80) cc_final: 0.7179 (m-80) REVERT: B 255 TRP cc_start: 0.7655 (t-100) cc_final: 0.7406 (t-100) REVERT: B 325 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7970 (m) REVERT: C 71 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8322 (m-10) REVERT: C 116 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5692 (pp20) REVERT: C 258 PHE cc_start: 0.7965 (t80) cc_final: 0.7754 (t80) REVERT: C 325 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7948 (m) REVERT: D 71 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8423 (m-10) REVERT: D 113 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8342 (mmm-85) REVERT: D 240 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: D 247 TYR cc_start: 0.7946 (m-80) cc_final: 0.7175 (m-80) outliers start: 64 outliers final: 46 residues processed: 234 average time/residue: 0.2843 time to fit residues: 92.9219 Evaluate side-chains 239 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 445 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 112 HIS B 111 GLN C 111 GLN D 111 GLN D 112 HIS D 327 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.095335 restraints weight = 45225.638| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.12 r_work: 0.3097 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11100 Z= 0.196 Angle : 0.599 8.488 15104 Z= 0.308 Chirality : 0.044 0.158 1664 Planarity : 0.006 0.073 1876 Dihedral : 6.682 59.955 1536 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 6.12 % Allowed : 20.04 % Favored : 73.85 % 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: -1.54 (0.23), residues: 1272 helix: -0.36 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.11 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.004 0.001 HIS A 19 PHE 0.011 0.001 PHE B 258 TYR 0.030 0.002 TYR D 70 ARG 0.005 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 484) hydrogen bonds : angle 4.20459 ( 1412) covalent geometry : bond 0.00484 (11100) covalent geometry : angle 0.59879 (15104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 186 time to evaluate : 1.302 Fit side-chains REVERT: A 71 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8359 (m-10) REVERT: A 116 GLU cc_start: 0.5675 (OUTLIER) cc_final: 0.5251 (pp20) REVERT: A 255 TRP cc_start: 0.7686 (t60) cc_final: 0.7436 (t-100) REVERT: A 281 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7231 (tp) REVERT: B 71 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8365 (m-10) REVERT: B 210 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7372 (mt-10) REVERT: B 255 TRP cc_start: 0.7649 (t-100) cc_final: 0.7431 (t-100) REVERT: C 71 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8375 (m-10) REVERT: C 98 GLU cc_start: 0.8265 (mp0) cc_final: 0.7976 (mp0) REVERT: C 116 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5615 (pp20) REVERT: D 71 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8452 (m-10) REVERT: D 240 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6777 (mt-10) outliers start: 69 outliers final: 51 residues processed: 239 average time/residue: 0.3269 time to fit residues: 109.9213 Evaluate side-chains 240 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 26 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098004 restraints weight = 50468.402| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.32 r_work: 0.3150 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11100 Z= 0.117 Angle : 0.547 7.617 15104 Z= 0.279 Chirality : 0.041 0.171 1664 Planarity : 0.005 0.077 1876 Dihedral : 5.982 59.729 1536 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.05 % Allowed : 21.01 % Favored : 73.94 % 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: -1.03 (0.24), residues: 1272 helix: 0.08 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.90 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 392 HIS 0.002 0.000 HIS A 19 PHE 0.010 0.001 PHE C 258 TYR 0.019 0.001 TYR D 70 ARG 0.005 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 484) hydrogen bonds : angle 3.98015 ( 1412) covalent geometry : bond 0.00272 (11100) covalent geometry : angle 0.54708 (15104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 1.192 Fit side-chains REVERT: A 71 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8270 (m-10) REVERT: A 86 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7568 (tt) REVERT: A 113 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8522 (mmm-85) REVERT: A 116 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.5435 (pp20) REVERT: A 247 TYR cc_start: 0.8011 (m-80) cc_final: 0.7237 (m-80) REVERT: A 255 TRP cc_start: 0.7612 (t60) cc_final: 0.7404 (t-100) REVERT: A 281 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7255 (tp) REVERT: B 71 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: B 86 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7603 (tt) REVERT: B 98 GLU cc_start: 0.8296 (mp0) cc_final: 0.8038 (mp0) REVERT: B 210 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7325 (mt-10) REVERT: B 247 TYR cc_start: 0.8022 (m-80) cc_final: 0.7208 (m-80) REVERT: C 71 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8285 (m-10) REVERT: C 86 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7558 (tt) REVERT: C 98 GLU cc_start: 0.8272 (mp0) cc_final: 0.7995 (mp0) REVERT: C 116 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5650 (pp20) REVERT: D 71 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8379 (m-10) REVERT: D 86 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7565 (tt) REVERT: D 113 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.8334 (mmm-85) REVERT: D 247 TYR cc_start: 0.7958 (m-80) cc_final: 0.7200 (m-80) outliers start: 57 outliers final: 38 residues processed: 233 average time/residue: 0.2696 time to fit residues: 86.4055 Evaluate side-chains 235 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 19 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN C 327 HIS D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101633 restraints weight = 42773.252| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 4.06 r_work: 0.3188 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11100 Z= 0.117 Angle : 0.541 7.315 15104 Z= 0.275 Chirality : 0.042 0.175 1664 Planarity : 0.005 0.072 1876 Dihedral : 5.753 59.692 1536 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.52 % Allowed : 20.66 % Favored : 74.82 % 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: -0.80 (0.24), residues: 1272 helix: 0.27 (0.20), residues: 780 sheet: None (None), residues: 0 loop : -1.80 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 255 HIS 0.002 0.000 HIS C 19 PHE 0.012 0.001 PHE B 258 TYR 0.025 0.001 TYR A 70 ARG 0.005 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 484) hydrogen bonds : angle 3.92044 ( 1412) covalent geometry : bond 0.00275 (11100) covalent geometry : angle 0.54087 (15104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 2.670 Fit side-chains REVERT: A 71 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8459 (m-10) REVERT: A 86 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7458 (tt) REVERT: A 116 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.5388 (pp20) REVERT: A 247 TYR cc_start: 0.8050 (m-80) cc_final: 0.7254 (m-80) REVERT: A 281 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7248 (tp) REVERT: B 71 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8366 (m-10) REVERT: B 86 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7513 (tt) REVERT: B 98 GLU cc_start: 0.8283 (mp0) cc_final: 0.8008 (mp0) REVERT: B 210 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7365 (mt-10) REVERT: B 247 TYR cc_start: 0.8018 (m-80) cc_final: 0.7220 (m-80) REVERT: C 71 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8262 (m-10) REVERT: C 86 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7481 (tt) REVERT: C 98 GLU cc_start: 0.8294 (mp0) cc_final: 0.8019 (mp0) REVERT: C 116 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5616 (pp20) REVERT: D 71 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: D 86 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7481 (tt) REVERT: D 113 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8313 (mmm-85) REVERT: D 199 PHE cc_start: 0.8078 (m-80) cc_final: 0.7592 (m-10) REVERT: D 247 TYR cc_start: 0.7957 (m-80) cc_final: 0.7183 (m-80) outliers start: 51 outliers final: 33 residues processed: 226 average time/residue: 0.6743 time to fit residues: 230.2078 Evaluate side-chains 230 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 327 HIS C 111 GLN D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.138246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.100074 restraints weight = 50918.641| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 4.44 r_work: 0.3167 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11100 Z= 0.127 Angle : 0.549 7.204 15104 Z= 0.279 Chirality : 0.042 0.173 1664 Planarity : 0.005 0.069 1876 Dihedral : 5.601 59.530 1533 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.17 % Allowed : 20.83 % Favored : 75.00 % 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: -0.67 (0.24), residues: 1272 helix: 0.31 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.64 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 255 HIS 0.002 0.000 HIS D 19 PHE 0.012 0.001 PHE B 258 TYR 0.022 0.001 TYR A 70 ARG 0.005 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 484) hydrogen bonds : angle 3.93012 ( 1412) covalent geometry : bond 0.00301 (11100) covalent geometry : angle 0.54891 (15104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 1.190 Fit side-chains REVERT: A 71 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8475 (m-10) REVERT: A 86 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7486 (tt) REVERT: A 116 GLU cc_start: 0.5756 (OUTLIER) cc_final: 0.5300 (pp20) REVERT: A 281 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7249 (tp) REVERT: B 71 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8369 (m-10) REVERT: B 86 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7501 (tt) REVERT: B 210 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 247 TYR cc_start: 0.8072 (m-80) cc_final: 0.7298 (m-80) REVERT: C 71 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8341 (m-10) REVERT: C 86 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7483 (tt) REVERT: C 98 GLU cc_start: 0.8313 (mp0) cc_final: 0.8032 (mp0) REVERT: C 116 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5556 (pp20) REVERT: D 71 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: D 86 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7471 (tt) REVERT: D 113 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.8317 (mmm-85) REVERT: D 199 PHE cc_start: 0.8072 (m-80) cc_final: 0.7551 (m-10) REVERT: D 247 TYR cc_start: 0.8034 (m-80) cc_final: 0.7277 (m-80) outliers start: 47 outliers final: 32 residues processed: 223 average time/residue: 0.2443 time to fit residues: 75.3540 Evaluate side-chains 231 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 126 optimal weight: 0.3980 chunk 73 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 81 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101041 restraints weight = 37511.512| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.83 r_work: 0.3207 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11100 Z= 0.135 Angle : 0.555 7.793 15104 Z= 0.282 Chirality : 0.043 0.172 1664 Planarity : 0.005 0.067 1876 Dihedral : 5.498 59.537 1530 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.17 % Allowed : 21.01 % Favored : 74.82 % 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: -0.59 (0.24), residues: 1272 helix: 0.35 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.55 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 255 HIS 0.003 0.000 HIS B 19 PHE 0.011 0.001 PHE B 258 TYR 0.024 0.002 TYR A 247 ARG 0.005 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 484) hydrogen bonds : angle 3.92665 ( 1412) covalent geometry : bond 0.00323 (11100) covalent geometry : angle 0.55523 (15104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 1.171 Fit side-chains REVERT: A 71 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: A 86 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7447 (tt) REVERT: A 113 ARG cc_start: 0.8717 (mmm160) cc_final: 0.8514 (mmm-85) REVERT: A 116 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5192 (pp20) REVERT: A 247 TYR cc_start: 0.8181 (m-80) cc_final: 0.7356 (m-80) REVERT: A 281 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7247 (tp) REVERT: B 71 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8320 (m-10) REVERT: B 86 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7448 (tt) REVERT: B 210 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7284 (mt-10) REVERT: B 247 TYR cc_start: 0.8039 (m-80) cc_final: 0.7248 (m-80) REVERT: C 71 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8332 (m-10) REVERT: C 86 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7451 (tt) REVERT: C 98 GLU cc_start: 0.8279 (mp0) cc_final: 0.7995 (mp0) REVERT: C 116 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5469 (pp20) REVERT: D 71 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: D 86 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7440 (tt) REVERT: D 113 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8309 (mmm-85) REVERT: D 199 PHE cc_start: 0.8040 (m-80) cc_final: 0.7566 (m-10) REVERT: D 247 TYR cc_start: 0.8038 (m-80) cc_final: 0.7267 (m-80) REVERT: D 258 PHE cc_start: 0.7822 (t80) cc_final: 0.7340 (t80) outliers start: 47 outliers final: 34 residues processed: 220 average time/residue: 0.2659 time to fit residues: 81.1519 Evaluate side-chains 231 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099823 restraints weight = 53149.154| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.52 r_work: 0.3152 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11100 Z= 0.134 Angle : 0.554 7.159 15104 Z= 0.282 Chirality : 0.042 0.182 1664 Planarity : 0.005 0.066 1876 Dihedral : 5.496 59.405 1530 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.90 % Allowed : 21.37 % Favored : 74.73 % 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: -0.49 (0.24), residues: 1272 helix: 0.40 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.45 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 255 HIS 0.002 0.000 HIS B 19 PHE 0.013 0.001 PHE D 199 TYR 0.023 0.002 TYR A 247 ARG 0.004 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 484) hydrogen bonds : angle 3.88224 ( 1412) covalent geometry : bond 0.00320 (11100) covalent geometry : angle 0.55447 (15104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 1.210 Fit side-chains REVERT: A 71 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: A 86 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7509 (tt) REVERT: A 113 ARG cc_start: 0.8700 (mmm160) cc_final: 0.8389 (mmm-85) REVERT: A 116 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.5190 (pp20) REVERT: A 281 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7245 (tp) REVERT: B 71 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: B 86 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7476 (tt) REVERT: B 210 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7344 (mt-10) REVERT: B 247 TYR cc_start: 0.8086 (m-80) cc_final: 0.7285 (m-80) REVERT: B 281 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7183 (tp) REVERT: C 71 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8332 (m-10) REVERT: C 86 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7474 (tt) REVERT: C 98 GLU cc_start: 0.8330 (mp0) cc_final: 0.8052 (mp0) REVERT: C 116 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5564 (pp20) REVERT: D 71 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: D 86 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7497 (tt) REVERT: D 113 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8320 (mmm-85) REVERT: D 199 PHE cc_start: 0.8011 (m-80) cc_final: 0.7499 (m-10) REVERT: D 247 TYR cc_start: 0.8066 (m-80) cc_final: 0.7323 (m-80) outliers start: 44 outliers final: 32 residues processed: 213 average time/residue: 0.2577 time to fit residues: 76.3913 Evaluate side-chains 225 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099567 restraints weight = 42103.651| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.09 r_work: 0.3171 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11100 Z= 0.150 Angle : 0.565 7.269 15104 Z= 0.288 Chirality : 0.043 0.183 1664 Planarity : 0.005 0.065 1876 Dihedral : 5.595 59.394 1530 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.08 % Allowed : 21.54 % Favored : 74.38 % 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: -0.49 (0.24), residues: 1272 helix: 0.36 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 255 HIS 0.003 0.000 HIS B 19 PHE 0.012 0.001 PHE B 258 TYR 0.035 0.002 TYR A 247 ARG 0.005 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 484) hydrogen bonds : angle 3.93184 ( 1412) covalent geometry : bond 0.00363 (11100) covalent geometry : angle 0.56477 (15104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7370.40 seconds wall clock time: 137 minutes 18.48 seconds (8238.48 seconds total)