Starting phenix.real_space_refine on Fri Sep 11 18:15:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pqu_13605/09_2026/7pqu_13605.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pqu_13605/09_2026/7pqu_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_13605/09_2026/7pqu_13605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pqu_13605/09_2026/7pqu_13605.map" model { file = "/net/cci-nas-00/data/ceres_data/7pqu_13605/09_2026/7pqu_13605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pqu_13605/09_2026/7pqu_13605.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pqu_13605/09_2026/7pqu_13605.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pqu_13605/09_2026/7pqu_13605.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 4.53, per 1000 atoms: 0.42 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: 0.94 Conformation dependent library (CDL) restraints added in 873.2 milliseconds 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: 0.30 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: 1.70 Time building geometry restraints manager: 1.28 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 601)) selection = (chain 'B' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 601)) selection = (chain 'C' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 601)) selection = (chain 'D' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 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: 4.270 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 14.69 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.003 0.001 ARG D 320 TYR 0.017 0.002 TYR B 22 PHE 0.010 0.002 PHE C 359 TRP 0.009 0.001 TRP C 94 HIS 0.003 0.001 HIS D 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.37 (11100) covalent geometry : angle 0.90371 / 0.47 (15104) hydrogen bonds : bond 0.09112 / 6.47 ( 484) hydrogen bonds : angle 5.37041 / 3.84 ( 1412) *********************** 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 : 0.425 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: 0.1302 time to fit residues: 43.9496 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 : 0.395 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3793 r_free = 0.3793 target = 0.135300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096861 restraints weight = 49081.461| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 4.22 r_work: 0.3119 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1389 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= 0.140 Angle : 0.613 8.076 15104 Z= 0.314 Chirality : 0.043 0.218 1664 Planarity : 0.006 0.064 1876 Dihedral : 9.433 55.486 1611 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.67 % Allowed : 20.21 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.22), residues: 1272 helix: -1.17 (0.17), residues: 804 sheet: None (None), residues: 0 loop : -2.69 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 311 TYR 0.015 0.001 TYR C 247 PHE 0.017 0.001 PHE D 289 TRP 0.012 0.001 TRP C 94 HIS 0.003 0.001 HIS B 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (11100) covalent geometry : angle 0.61325 / 0.31 (15104) hydrogen bonds : bond 0.04477 / 3.05 ( 484) hydrogen bonds : angle 4.23611 / 2.95 ( 1412) *********************** 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 262 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 0.402 Fit side-chains REVERT: A 71 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8230 (m-10) REVERT: A 113 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8392 (mmm-85) REVERT: A 281 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7231 (tp) REVERT: B 71 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: B 113 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8446 (mmm-85) REVERT: B 210 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7391 (mp0) REVERT: B 310 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6435 (tp) REVERT: B 325 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8058 (m) REVERT: C 71 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8270 (m-10) REVERT: C 113 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8415 (mmm-85) REVERT: C 325 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8020 (m) REVERT: D 71 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: D 113 ARG cc_start: 0.8547 (mmm-85) cc_final: 0.8284 (mmm-85) outliers start: 64 outliers final: 34 residues processed: 251 average time/residue: 0.1240 time to fit residues: 42.0933 Evaluate side-chains 236 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 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 74 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 59 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN B 43 HIS B 111 GLN B 112 HIS C 43 HIS C 111 GLN C 112 HIS D 43 HIS D 111 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095616 restraints weight = 46948.073| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.15 r_work: 0.3102 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11100 Z= 0.181 Angle : 0.601 8.985 15104 Z= 0.309 Chirality : 0.044 0.189 1664 Planarity : 0.006 0.067 1876 Dihedral : 7.226 57.788 1542 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.14 % Allowed : 20.30 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.23), residues: 1272 helix: -0.78 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -2.51 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.016 0.002 TYR A 247 PHE 0.009 0.001 PHE D 359 TRP 0.011 0.001 TRP B 94 HIS 0.004 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (11100) covalent geometry : angle 0.60143 / 0.31 (15104) hydrogen bonds : bond 0.04789 / 3.26 ( 484) hydrogen bonds : angle 4.23777 / 2.93 ( 1412) *********************** 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 251 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 0.383 Fit side-chains REVERT: A 71 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8331 (m-10) REVERT: A 113 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8469 (mmm-85) REVERT: A 247 TYR cc_start: 0.7908 (m-80) cc_final: 0.7115 (m-80) REVERT: B 71 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8320 (m-10) REVERT: B 210 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7367 (mt-10) REVERT: B 247 TYR cc_start: 0.7968 (m-80) cc_final: 0.7117 (m-80) REVERT: B 310 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6473 (tp) REVERT: B 325 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7977 (m) REVERT: C 71 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8361 (m-10) REVERT: C 325 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7933 (m) REVERT: D 71 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8352 (m-10) REVERT: D 113 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8340 (mmm-85) REVERT: D 247 TYR cc_start: 0.7895 (m-80) cc_final: 0.7116 (m-80) REVERT: D 325 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.7948 (p) outliers start: 58 outliers final: 44 residues processed: 237 average time/residue: 0.1109 time to fit residues: 36.4805 Evaluate side-chains 235 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 54 GLU 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 287 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 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 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 49 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 LEU 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 287 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 312 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 325 THR 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 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN B 111 GLN B 327 HIS C 111 GLN D 111 GLN D 327 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097757 restraints weight = 49287.159| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.32 r_work: 0.3132 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11100 Z= 0.127 Angle : 0.556 8.230 15104 Z= 0.286 Chirality : 0.042 0.171 1664 Planarity : 0.005 0.070 1876 Dihedral : 6.517 58.837 1538 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.50 % Allowed : 19.95 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.24), residues: 1272 helix: -0.36 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.17 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 18 TYR 0.016 0.001 TYR C 247 PHE 0.007 0.001 PHE D 359 TRP 0.011 0.001 TRP C 392 HIS 0.002 0.000 HIS D 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11100) covalent geometry : angle 0.55603 / 0.29 (15104) hydrogen bonds : bond 0.04282 / 2.91 ( 484) hydrogen bonds : angle 4.06225 / 2.80 ( 1412) *********************** 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 252 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.403 Fit side-chains REVERT: A 71 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: A 86 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7608 (tt) REVERT: A 113 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8482 (mmm-85) REVERT: A 281 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7212 (tp) REVERT: B 71 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8299 (m-10) REVERT: B 98 GLU cc_start: 0.8273 (mp0) cc_final: 0.7977 (mp0) REVERT: B 210 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 325 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8001 (m) REVERT: C 71 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8324 (m-10) REVERT: C 116 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5718 (pp20) REVERT: C 255 TRP cc_start: 0.7500 (t60) cc_final: 0.7244 (t60) REVERT: C 325 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7978 (m) REVERT: D 71 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: D 113 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8361 (mmm-85) REVERT: D 240 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6875 (mt-10) REVERT: D 255 TRP cc_start: 0.7479 (t60) cc_final: 0.7269 (t60) REVERT: D 325 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8313 (m) outliers start: 62 outliers final: 35 residues processed: 239 average time/residue: 0.1105 time to fit residues: 36.5654 Evaluate side-chains 229 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 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 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 116 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL 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 240 GLU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 0.0670 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 58 optimal weight: 0.0980 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN B 111 GLN C 111 GLN D 111 GLN D 327 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099334 restraints weight = 39427.110| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.86 r_work: 0.3179 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2329 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= 0.114 Angle : 0.542 7.974 15104 Z= 0.277 Chirality : 0.041 0.152 1664 Planarity : 0.005 0.063 1876 Dihedral : 5.923 59.329 1536 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.34 % Allowed : 21.19 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.24), residues: 1272 helix: 0.00 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -2.00 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 18 TYR 0.027 0.001 TYR D 70 PHE 0.008 0.001 PHE A 289 TRP 0.011 0.001 TRP B 392 HIS 0.002 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (11100) covalent geometry : angle 0.54179 / 0.28 (15104) hydrogen bonds : bond 0.03982 / 2.71 ( 484) hydrogen bonds : angle 3.96712 / 2.75 ( 1412) *********************** 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 247 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.390 Fit side-chains REVERT: A 71 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8373 (m-10) REVERT: A 86 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7526 (tt) REVERT: A 89 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 113 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.8485 (mmm-85) REVERT: A 116 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5419 (pp20) REVERT: A 247 TYR cc_start: 0.7979 (m-80) cc_final: 0.7185 (m-80) REVERT: A 281 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7281 (tp) REVERT: B 71 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8295 (m-10) REVERT: B 86 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7518 (tt) REVERT: B 98 GLU cc_start: 0.8232 (mp0) cc_final: 0.7954 (mp0) REVERT: B 210 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7275 (mt-10) REVERT: B 247 TYR cc_start: 0.7998 (m-80) cc_final: 0.7184 (m-80) REVERT: C 71 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: C 86 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7543 (tt) REVERT: C 116 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5643 (pp20) REVERT: D 71 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8382 (m-10) REVERT: D 113 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8318 (mmm-85) REVERT: D 240 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: D 247 TYR cc_start: 0.7948 (m-80) cc_final: 0.7187 (m-80) REVERT: D 325 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8305 (m) outliers start: 49 outliers final: 28 residues processed: 233 average time/residue: 0.1098 time to fit residues: 35.6455 Evaluate side-chains 222 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 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 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 246 THR 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 240 GLU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 112 HIS B 111 GLN C 111 GLN C 327 HIS D 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098752 restraints weight = 50136.688| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 4.31 r_work: 0.3150 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11100 Z= 0.127 Angle : 0.555 8.003 15104 Z= 0.281 Chirality : 0.042 0.146 1664 Planarity : 0.005 0.058 1876 Dihedral : 5.681 59.636 1532 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.43 % Allowed : 21.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.24), residues: 1272 helix: 0.11 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.85 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 18 TYR 0.020 0.001 TYR C 70 PHE 0.014 0.001 PHE A 244 TRP 0.018 0.001 TRP D 255 HIS 0.002 0.000 HIS D 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11100) covalent geometry : angle 0.55474 / 0.28 (15104) hydrogen bonds : bond 0.04080 / 2.77 ( 484) hydrogen bonds : angle 4.01771 / 2.78 ( 1412) *********************** 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 237 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.391 Fit side-chains REVERT: A 71 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8396 (m-10) REVERT: A 86 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7583 (tt) REVERT: A 113 ARG cc_start: 0.8722 (mmm-85) cc_final: 0.8488 (mmm-85) REVERT: A 116 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.5343 (pp20) REVERT: A 281 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7297 (tp) REVERT: B 71 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8308 (m-10) REVERT: B 86 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7566 (tt) REVERT: B 98 GLU cc_start: 0.8286 (mp0) cc_final: 0.8054 (mp0) REVERT: B 210 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7380 (mt-10) REVERT: B 255 TRP cc_start: 0.7517 (t60) cc_final: 0.7207 (t60) REVERT: C 71 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8354 (m-10) REVERT: C 86 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7562 (tt) REVERT: C 116 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5621 (pp20) REVERT: D 71 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8409 (m-10) REVERT: D 113 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8338 (mmm-85) REVERT: D 325 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8165 (m) outliers start: 50 outliers final: 34 residues processed: 221 average time/residue: 0.1082 time to fit residues: 33.5078 Evaluate side-chains 229 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 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 21 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 97 ASP 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 325 THR 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 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN B 111 GLN C 111 GLN D 111 GLN D 112 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.099208 restraints weight = 44633.941| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.08 r_work: 0.3177 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2529 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 : 0.546 7.780 15104 Z= 0.278 Chirality : 0.042 0.144 1664 Planarity : 0.005 0.055 1876 Dihedral : 5.653 59.995 1532 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.52 % Allowed : 20.92 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.24), residues: 1272 helix: 0.22 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 18 TYR 0.022 0.001 TYR B 48 PHE 0.012 0.001 PHE B 258 TRP 0.019 0.001 TRP C 255 HIS 0.002 0.000 HIS B 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (11100) covalent geometry : angle 0.54603 / 0.28 (15104) hydrogen bonds : bond 0.04148 / 2.83 ( 484) hydrogen bonds : angle 3.97587 / 2.76 ( 1412) *********************** 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 : 0.366 Fit side-chains REVERT: A 71 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8389 (m-10) REVERT: A 86 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 113 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8487 (mmm-85) REVERT: A 116 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.5252 (pp20) REVERT: A 247 TYR cc_start: 0.8031 (m-80) cc_final: 0.7286 (m-80) REVERT: A 281 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7294 (tp) REVERT: B 71 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8312 (m-10) REVERT: B 86 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7540 (tt) REVERT: B 98 GLU cc_start: 0.8310 (mp0) cc_final: 0.8080 (mp0) REVERT: B 210 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7332 (mt-10) REVERT: B 255 TRP cc_start: 0.7509 (t60) cc_final: 0.7216 (t60) REVERT: C 71 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8306 (m-10) REVERT: C 86 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7499 (tt) REVERT: C 98 GLU cc_start: 0.8293 (mp0) cc_final: 0.8052 (mp0) REVERT: C 116 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5547 (pp20) REVERT: D 71 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8435 (m-10) REVERT: D 86 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7520 (tt) REVERT: D 113 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8330 (mmm-85) REVERT: D 247 TYR cc_start: 0.7972 (m-80) cc_final: 0.7232 (m-80) REVERT: D 325 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8124 (m) outliers start: 51 outliers final: 36 residues processed: 225 average time/residue: 0.1034 time to fit residues: 32.7327 Evaluate side-chains 234 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 108 THR 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 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 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 97 ASP 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 325 THR 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 103 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.8009 > 50:) chunk 105 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN B 111 GLN C 111 GLN C 409 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 = 0.3766 r_free = 0.3766 target = 0.132908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094056 restraints weight = 49623.698| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.29 r_work: 0.3072 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11100 Z= 0.257 Angle : 0.644 8.693 15104 Z= 0.332 Chirality : 0.047 0.173 1664 Planarity : 0.005 0.054 1876 Dihedral : 6.561 59.159 1531 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.88 % Allowed : 20.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.23), residues: 1272 helix: -0.31 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -1.66 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 18 TYR 0.030 0.002 TYR C 70 PHE 0.014 0.002 PHE B 258 TRP 0.019 0.002 TRP D 255 HIS 0.005 0.001 HIS D 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.26 (11100) covalent geometry : angle 0.64446 / 0.33 (15104) hydrogen bonds : bond 0.05264 / 3.60 ( 484) hydrogen bonds : angle 4.32404 / 2.99 ( 1412) *********************** 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 231 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.392 Fit side-chains REVERT: A 71 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8474 (m-10) REVERT: A 116 GLU cc_start: 0.5585 (OUTLIER) cc_final: 0.5158 (pp20) REVERT: A 281 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7325 (tp) REVERT: B 71 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.8385 (m-10) REVERT: B 98 GLU cc_start: 0.8300 (mp0) cc_final: 0.8028 (mp0) REVERT: B 210 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7324 (mt-10) REVERT: B 247 TYR cc_start: 0.7997 (m-80) cc_final: 0.7047 (m-80) REVERT: C 71 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8391 (m-10) REVERT: C 98 GLU cc_start: 0.8286 (mp0) cc_final: 0.7994 (mp0) REVERT: D 71 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8561 (m-10) REVERT: D 113 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8357 (mmm-85) REVERT: D 247 TYR cc_start: 0.7998 (m-80) cc_final: 0.7244 (m-80) REVERT: D 325 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8198 (m) outliers start: 55 outliers final: 42 residues processed: 216 average time/residue: 0.1036 time to fit residues: 31.6382 Evaluate side-chains 219 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 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 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 108 THR 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 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 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 C residue 445 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 97 ASP 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 325 THR Chi-restraints excluded: chain D residue 338 LEU 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 42 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3821 r_free = 0.3821 target = 0.137623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099157 restraints weight = 48554.498| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.32 r_work: 0.3171 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2496 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= 0.137 Angle : 0.566 7.940 15104 Z= 0.288 Chirality : 0.042 0.146 1664 Planarity : 0.005 0.081 1876 Dihedral : 5.966 59.884 1531 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.26 % Allowed : 21.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.24), residues: 1272 helix: 0.17 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.69 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 18 TYR 0.023 0.001 TYR D 70 PHE 0.010 0.001 PHE B 258 TRP 0.021 0.001 TRP A 255 HIS 0.003 0.000 HIS B 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (11100) covalent geometry : angle 0.56569 / 0.29 (15104) hydrogen bonds : bond 0.04328 / 2.95 ( 484) hydrogen bonds : angle 4.05686 / 2.82 ( 1412) *********************** 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 226 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 0.319 Fit side-chains REVERT: A 71 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8419 (m-10) REVERT: A 86 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7469 (tt) REVERT: A 113 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8515 (mmm-85) REVERT: A 116 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.5237 (pp20) REVERT: A 247 TYR cc_start: 0.8041 (m-80) cc_final: 0.7292 (m-80) REVERT: A 281 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7252 (tp) REVERT: B 71 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8327 (m-10) REVERT: B 98 GLU cc_start: 0.8297 (mp0) cc_final: 0.8050 (mp0) REVERT: B 210 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7258 (mt-10) REVERT: B 281 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7101 (tp) REVERT: C 71 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8326 (m-10) REVERT: C 98 GLU cc_start: 0.8329 (mp0) cc_final: 0.8071 (mp0) REVERT: D 71 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8401 (m-10) REVERT: D 113 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8311 (mmm-85) REVERT: D 325 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8094 (m) outliers start: 48 outliers final: 34 residues processed: 212 average time/residue: 0.1002 time to fit residues: 29.9705 Evaluate side-chains 219 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 A residue 419 LEU 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 108 THR 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 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 206 THR Chi-restraints excluded: chain C residue 246 THR 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 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 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU 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 64 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 0.0170 chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3831 r_free = 0.3831 target = 0.138787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100477 restraints weight = 52253.305| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.51 r_work: 0.3182 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2750 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= 0.119 Angle : 0.539 7.635 15104 Z= 0.275 Chirality : 0.042 0.151 1664 Planarity : 0.005 0.078 1876 Dihedral : 5.444 59.814 1531 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.81 % Allowed : 21.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.24), residues: 1272 helix: 0.43 (0.20), residues: 780 sheet: None (None), residues: 0 loop : -1.46 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 18 TYR 0.024 0.001 TYR D 247 PHE 0.010 0.001 PHE B 258 TRP 0.022 0.001 TRP D 255 HIS 0.002 0.000 HIS B 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (11100) covalent geometry : angle 0.53943 / 0.27 (15104) hydrogen bonds : bond 0.03969 / 2.70 ( 484) hydrogen bonds : angle 3.93685 / 2.71 ( 1412) ********************** 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 229 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.266 Fit side-chains REVERT: A 71 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8355 (m-10) REVERT: A 86 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7449 (tt) REVERT: A 116 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5280 (pp20) REVERT: A 281 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7260 (tp) REVERT: B 71 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8339 (m-10) REVERT: B 86 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7481 (tt) REVERT: B 98 GLU cc_start: 0.8319 (mp0) cc_final: 0.8091 (mp0) REVERT: B 210 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7298 (mt-10) REVERT: B 255 TRP cc_start: 0.7458 (t60) cc_final: 0.7139 (t60) REVERT: B 281 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7172 (tp) REVERT: C 71 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8328 (m-10) REVERT: C 98 GLU cc_start: 0.8345 (mp0) cc_final: 0.8110 (mp0) REVERT: D 71 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8456 (m-10) REVERT: D 86 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7411 (tt) REVERT: D 113 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8366 (mmm-85) REVERT: D 325 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8034 (m) outliers start: 43 outliers final: 29 residues processed: 215 average time/residue: 0.1089 time to fit residues: 32.7427 Evaluate side-chains 222 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 108 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 B residue 445 LEU 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 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 254 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU 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 79 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 0.0070 chunk 73 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 74 optimal weight: 0.0020 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3855 r_free = 0.3855 target = 0.140663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103228 restraints weight = 38609.383| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.93 r_work: 0.3219 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2937 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= 0.110 Angle : 0.538 7.414 15104 Z= 0.274 Chirality : 0.041 0.149 1664 Planarity : 0.005 0.077 1876 Dihedral : 5.134 59.635 1529 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.46 % Allowed : 21.90 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.25), residues: 1272 helix: 0.56 (0.20), residues: 796 sheet: None (None), residues: 0 loop : -1.17 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 9 TYR 0.033 0.001 TYR D 247 PHE 0.012 0.001 PHE A 244 TRP 0.021 0.001 TRP D 255 HIS 0.002 0.000 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11100) covalent geometry : angle 0.53751 / 0.27 (15104) hydrogen bonds : bond 0.03787 / 2.58 ( 484) hydrogen bonds : angle 3.77043 / 2.60 ( 1412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.81 seconds wall clock time: 55 minutes 5.82 seconds (3305.82 seconds total)