Starting phenix.real_space_refine on Sat Jul 20 12:20:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/07_2024/7pqu_13605.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/07_2024/7pqu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/07_2024/7pqu_13605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/07_2024/7pqu_13605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/07_2024/7pqu_13605.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/07_2024/7pqu_13605.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 72 5.16 5 C 7100 2.51 5 N 1780 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10798 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "B" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "C" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "D" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Unusual residues: {' K': 4, '805': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'805': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'805': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'805': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALYS A 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 449 " occ=0.50 residue: pdb=" N ALYS B 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 449 " occ=0.50 residue: pdb=" N ALYS C 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 449 " occ=0.50 residue: pdb=" N ALYS D 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 449 " occ=0.50 Time building chain proxies: 11.69, per 1000 atoms: 1.08 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 - 3.50 Amino acid : False - 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: 3.95 Conformation dependent library (CDL) restraints added in 3.4 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 4 sheets defined 61.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.921A pdb=" N TRP A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 39' Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.662A pdb=" N TYR A 87 " --> pdb=" O CYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.691A pdb=" N GLN A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 211 removed outlier: 4.544A pdb=" N PHE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 260 removed outlier: 3.945A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 removed outlier: 4.033A pdb=" N TYR A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.926A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.582A pdb=" N ARG A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 370 removed outlier: 4.075A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.847A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 removed outlier: 3.906A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 451 removed outlier: 3.828A pdb=" N ASN A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.921A pdb=" N TRP B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 32 through 39' Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.662A pdb=" N TYR B 87 " --> pdb=" O CYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.691A pdb=" N GLN B 111 " --> pdb=" O MET B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 211 removed outlier: 4.544A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 260 removed outlier: 3.946A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 4.033A pdb=" N TYR B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.925A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.582A pdb=" N ARG B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 370 removed outlier: 4.076A pdb=" N LEU B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 399 removed outlier: 3.847A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 removed outlier: 3.905A pdb=" N LEU B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 451 removed outlier: 3.827A pdb=" N ASN B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.920A pdb=" N TRP C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 32 through 39' Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.662A pdb=" N TYR C 87 " --> pdb=" O CYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.690A pdb=" N GLN C 111 " --> pdb=" O MET C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 211 removed outlier: 4.544A pdb=" N PHE C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 260 removed outlier: 3.945A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 4.032A pdb=" N TYR C 290 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.925A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 removed outlier: 3.583A pdb=" N ARG C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 370 removed outlier: 4.076A pdb=" N LEU C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 removed outlier: 3.848A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 removed outlier: 3.906A pdb=" N LEU C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 451 removed outlier: 3.828A pdb=" N ASN C 438 " --> pdb=" O VAL C 434 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.921A pdb=" N TRP D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 32 through 39' Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 83 through 95 removed outlier: 3.662A pdb=" N TYR D 87 " --> pdb=" O CYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 111 removed outlier: 3.691A pdb=" N GLN D 111 " --> pdb=" O MET D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 211 removed outlier: 4.544A pdb=" N PHE D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 260 removed outlier: 3.945A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 removed outlier: 4.033A pdb=" N TYR D 290 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 320 through 325 removed outlier: 3.926A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.582A pdb=" N ARG D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 370 removed outlier: 4.076A pdb=" N LEU D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 399 removed outlier: 3.847A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 removed outlier: 3.906A pdb=" N LEU D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 451 removed outlier: 3.827A pdb=" N ASN D 438 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 439 " --> pdb=" O ILE D 435 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.903A pdb=" N THR A 17 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 14 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 47 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.903A pdb=" N THR B 17 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 14 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP B 47 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.903A pdb=" N THR C 17 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 14 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP C 47 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.904A pdb=" N THR D 17 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 14 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP D 47 " --> pdb=" O PHE D 56 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 4.32 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: 99.79 - 106.66: 376 106.66 - 113.54: 5949 113.54 - 120.42: 4699 120.42 - 127.30: 3908 127.30 - 134.18: 172 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 2.440 nonbonded pdb=" O HOH A 702 " pdb=" O HOH A 703 " model vdw 0.057 2.440 nonbonded pdb=" O HOH A 701 " pdb=" O HOH A 702 " model vdw 0.066 2.440 nonbonded pdb=" O HOH B 701 " pdb=" O HOH B 702 " model vdw 0.076 2.440 nonbonded pdb=" O HOH D 702 " pdb=" O HOH D 703 " model vdw 0.079 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) selection = (chain 'B' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) selection = (chain 'C' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) selection = (chain 'D' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 37.170 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 11100 Z= 0.517 Angle : 0.904 13.038 15104 Z= 0.468 Chirality : 0.047 0.197 1664 Planarity : 0.005 0.046 1876 Dihedral : 17.235 86.809 3908 Min Nonbonded Distance : 0.051 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.91 % Favored : 92.01 % Rotamer: Outliers : 5.14 % Allowed : 21.90 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.21), residues: 1272 helix: -2.39 (0.15), residues: 772 sheet: None (None), residues: 0 loop : -2.81 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 94 HIS 0.003 0.001 HIS D 19 PHE 0.010 0.002 PHE C 359 TYR 0.017 0.002 TYR B 22 ARG 0.003 0.001 ARG D 320 *********************** 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 fitting. rotamer outliers: 58 poor density : 200 time to evaluate : 1.169 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: 0.3008 time to fit residues: 100.6644 Evaluate side-chains 240 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 43 HIS A 60 HIS A 111 GLN A 450 GLN B 19 HIS B 60 HIS B 111 GLN C 19 HIS C 43 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11100 Z= 0.247 Angle : 0.606 8.211 15104 Z= 0.311 Chirality : 0.043 0.215 1664 Planarity : 0.006 0.063 1876 Dihedral : 9.637 55.065 1611 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.59 % Allowed : 21.99 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.23), residues: 1272 helix: -1.21 (0.17), residues: 800 sheet: None (None), residues: 0 loop : -2.70 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 94 HIS 0.004 0.001 HIS A 19 PHE 0.016 0.001 PHE D 289 TYR 0.015 0.001 TYR C 247 ARG 0.006 0.000 ARG B 311 *********************** 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 253 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 190 time to evaluate : 1.194 Fit side-chains REVERT: A 71 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: A 255 TRP cc_start: 0.7801 (t60) cc_final: 0.7583 (t-100) REVERT: A 281 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7194 (tp) REVERT: A 310 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6391 (tp) REVERT: B 71 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.8040 (m-10) REVERT: B 210 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6650 (mp0) REVERT: B 310 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6471 (tp) REVERT: C 71 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7983 (m-10) REVERT: C 255 TRP cc_start: 0.7774 (t60) cc_final: 0.7566 (t-100) REVERT: D 71 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.8056 (m-10) outliers start: 63 outliers final: 40 residues processed: 244 average time/residue: 0.2439 time to fit residues: 81.7788 Evaluate side-chains 237 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 71 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 17 THR 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 338 LEU Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 17 THR 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 338 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 103 optimal weight: 0.0470 chunk 115 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 450 GLN C 111 GLN D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1641 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= 0.209 Angle : 0.557 8.560 15104 Z= 0.286 Chirality : 0.042 0.189 1664 Planarity : 0.006 0.067 1876 Dihedral : 7.196 57.291 1550 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.41 % Allowed : 21.19 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.23), residues: 1272 helix: -0.64 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.39 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 94 HIS 0.003 0.000 HIS C 19 PHE 0.011 0.001 PHE C 289 TYR 0.016 0.001 TYR C 247 ARG 0.005 0.000 ARG B 311 *********************** 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 258 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 197 time to evaluate : 1.239 Fit side-chains REVERT: A 18 ARG cc_start: 0.7588 (ptp90) cc_final: 0.7386 (ptp-170) REVERT: A 71 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8019 (m-10) REVERT: A 247 TYR cc_start: 0.7855 (m-80) cc_final: 0.7091 (m-80) REVERT: B 18 ARG cc_start: 0.7621 (ptp90) cc_final: 0.7347 (ptp90) REVERT: B 71 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8051 (m-10) REVERT: B 210 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6544 (mt-10) REVERT: B 247 TYR cc_start: 0.7893 (m-80) cc_final: 0.7068 (m-80) REVERT: C 71 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.8035 (m-10) REVERT: D 71 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.8063 (m-10) REVERT: D 247 TYR cc_start: 0.7816 (m-80) cc_final: 0.7078 (m-80) outliers start: 61 outliers final: 40 residues processed: 244 average time/residue: 0.2471 time to fit residues: 83.0722 Evaluate side-chains 220 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 287 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 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 17 THR 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 310 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 43 HIS B 111 GLN C 111 GLN C 327 HIS D 43 HIS D 111 GLN D 327 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11100 Z= 0.225 Angle : 0.553 8.403 15104 Z= 0.283 Chirality : 0.042 0.170 1664 Planarity : 0.005 0.070 1876 Dihedral : 6.481 58.290 1538 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.67 % Allowed : 21.72 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1272 helix: -0.36 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -2.16 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 392 HIS 0.003 0.000 HIS A 19 PHE 0.008 0.001 PHE D 359 TYR 0.031 0.001 TYR D 70 ARG 0.003 0.000 ARG C 339 *********************** 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 244 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 180 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6744 (ttp-170) REVERT: A 71 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8015 (m-10) REVERT: A 86 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7588 (tt) REVERT: A 247 TYR cc_start: 0.7841 (m-80) cc_final: 0.7065 (m-80) REVERT: A 281 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7211 (tp) REVERT: B 18 ARG cc_start: 0.7644 (ptp90) cc_final: 0.7363 (ptp90) REVERT: B 86 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7563 (tt) REVERT: B 210 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6529 (mt-10) REVERT: B 247 TYR cc_start: 0.7876 (m-80) cc_final: 0.7077 (m-80) REVERT: B 255 TRP cc_start: 0.7725 (t-100) cc_final: 0.7501 (t-100) REVERT: C 18 ARG cc_start: 0.7624 (ptp90) cc_final: 0.7309 (ptp90) REVERT: C 71 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.8013 (m-10) REVERT: C 255 TRP cc_start: 0.7613 (t60) cc_final: 0.7397 (t-100) REVERT: D 247 TYR cc_start: 0.7786 (m-80) cc_final: 0.7038 (m-80) outliers start: 64 outliers final: 46 residues processed: 231 average time/residue: 0.2614 time to fit residues: 82.9693 Evaluate side-chains 229 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 177 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 33 ARG 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 240 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 262 MET 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 386 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 33 ARG 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 310 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN 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 103 optimal weight: 0.0040 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 112 HIS B 111 GLN B 112 HIS C 111 GLN C 409 GLN D 111 GLN D 327 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1894 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= 0.295 Angle : 0.578 8.521 15104 Z= 0.297 Chirality : 0.044 0.155 1664 Planarity : 0.005 0.062 1876 Dihedral : 6.669 59.670 1538 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.56 % Allowed : 21.19 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1272 helix: -0.34 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.00 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.003 0.001 HIS B 19 PHE 0.012 0.001 PHE B 258 TYR 0.029 0.002 TYR D 70 ARG 0.003 0.000 ARG B 311 *********************** 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 260 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 186 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8031 (m-10) REVERT: A 116 GLU cc_start: 0.5523 (OUTLIER) cc_final: 0.5167 (pp20) REVERT: A 281 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7258 (tp) REVERT: B 210 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6574 (mt-10) REVERT: C 71 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: C 116 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5645 (pp20) outliers start: 74 outliers final: 58 residues processed: 247 average time/residue: 0.2584 time to fit residues: 88.1879 Evaluate side-chains 245 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 182 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 33 ARG Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 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 419 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 33 ARG 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 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 49 ASP 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 269 ASN Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11100 Z= 0.186 Angle : 0.534 7.800 15104 Z= 0.273 Chirality : 0.041 0.171 1664 Planarity : 0.005 0.077 1876 Dihedral : 6.162 59.696 1538 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.59 % Allowed : 22.70 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.24), residues: 1272 helix: 0.00 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.85 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 392 HIS 0.002 0.000 HIS A 19 PHE 0.012 0.001 PHE B 258 TYR 0.021 0.001 TYR D 70 ARG 0.003 0.000 ARG B 311 *********************** 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 245 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 182 time to evaluate : 1.136 Fit side-chains REVERT: A 33 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6744 (ttp-170) REVERT: A 86 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7556 (tt) REVERT: A 116 GLU cc_start: 0.5579 (OUTLIER) cc_final: 0.5187 (pp20) REVERT: A 247 TYR cc_start: 0.7887 (m-80) cc_final: 0.7117 (m-80) REVERT: A 281 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7270 (tp) REVERT: B 18 ARG cc_start: 0.7606 (ptp90) cc_final: 0.7343 (ptp90) REVERT: B 71 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: B 86 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7558 (tt) REVERT: B 210 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6567 (mt-10) REVERT: B 247 TYR cc_start: 0.7898 (m-80) cc_final: 0.7119 (m-80) REVERT: B 255 TRP cc_start: 0.7636 (t-100) cc_final: 0.7364 (t-100) REVERT: C 33 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6998 (ttp-170) REVERT: C 71 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: C 116 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5646 (pp20) REVERT: D 71 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: D 247 TYR cc_start: 0.7836 (m-80) cc_final: 0.7109 (m-80) REVERT: D 325 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8318 (m) outliers start: 63 outliers final: 42 residues processed: 230 average time/residue: 0.2514 time to fit residues: 78.6571 Evaluate side-chains 236 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 183 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 33 ARG Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 412 SER 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 49 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 33 ARG 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 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 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 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN C 112 HIS D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11100 Z= 0.251 Angle : 0.560 8.017 15104 Z= 0.287 Chirality : 0.043 0.177 1664 Planarity : 0.005 0.068 1876 Dihedral : 6.170 59.476 1536 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.23 % Allowed : 22.52 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1272 helix: -0.04 (0.19), residues: 820 sheet: None (None), residues: 0 loop : -1.63 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.003 0.001 HIS A 19 PHE 0.013 0.001 PHE A 244 TYR 0.031 0.002 TYR A 70 ARG 0.005 0.000 ARG D 18 *********************** 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 240 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 181 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6723 (ttp-170) REVERT: A 86 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7551 (tt) REVERT: A 116 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.5127 (pp20) REVERT: A 247 TYR cc_start: 0.7894 (m-80) cc_final: 0.7124 (m-80) REVERT: A 281 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7290 (tp) REVERT: B 18 ARG cc_start: 0.7645 (ptp90) cc_final: 0.7342 (ptp90) REVERT: B 71 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8062 (m-10) REVERT: B 86 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7576 (tt) REVERT: B 210 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6533 (mt-10) REVERT: B 247 TYR cc_start: 0.7904 (m-80) cc_final: 0.7123 (m-80) REVERT: C 116 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5598 (pp20) REVERT: D 71 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: D 247 TYR cc_start: 0.7878 (m-80) cc_final: 0.7136 (m-80) REVERT: D 325 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8228 (m) outliers start: 59 outliers final: 47 residues processed: 227 average time/residue: 0.2750 time to fit residues: 84.9739 Evaluate side-chains 237 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 181 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 33 ARG Chi-restraints excluded: chain A residue 49 ASP 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 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain 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 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 0.0020 chunk 11 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2325 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= 0.202 Angle : 0.539 7.682 15104 Z= 0.274 Chirality : 0.042 0.174 1664 Planarity : 0.005 0.065 1876 Dihedral : 5.950 59.877 1536 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.14 % Allowed : 22.52 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.24), residues: 1272 helix: 0.17 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -1.60 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 255 HIS 0.003 0.000 HIS C 19 PHE 0.009 0.001 PHE A 199 TYR 0.023 0.001 TYR C 70 ARG 0.005 0.000 ARG A 18 *********************** 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 241 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 183 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7520 (tt) REVERT: A 116 GLU cc_start: 0.5534 (OUTLIER) cc_final: 0.5118 (pp20) REVERT: A 199 PHE cc_start: 0.8203 (m-80) cc_final: 0.7627 (m-10) REVERT: A 247 TYR cc_start: 0.7870 (m-80) cc_final: 0.7111 (m-80) REVERT: A 281 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7292 (tp) REVERT: B 71 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8059 (m-10) REVERT: B 86 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7557 (tt) REVERT: B 210 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6549 (mt-10) REVERT: B 247 TYR cc_start: 0.7923 (m-80) cc_final: 0.7149 (m-80) REVERT: C 116 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5610 (pp20) REVERT: D 71 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8241 (m-10) REVERT: D 247 TYR cc_start: 0.7885 (m-80) cc_final: 0.7121 (m-80) REVERT: D 325 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8193 (m) outliers start: 58 outliers final: 47 residues processed: 228 average time/residue: 0.2540 time to fit residues: 79.2339 Evaluate side-chains 235 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 180 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 33 ARG Chi-restraints excluded: chain A residue 49 ASP 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 254 VAL Chi-restraints excluded: chain A residue 281 ILE 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 386 ASN Chi-restraints excluded: chain A residue 412 SER 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 49 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain 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 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 0.0570 chunk 121 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 327 HIS C 111 GLN D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2435 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= 0.195 Angle : 0.539 7.677 15104 Z= 0.273 Chirality : 0.042 0.175 1664 Planarity : 0.005 0.063 1876 Dihedral : 5.808 59.632 1536 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.14 % Allowed : 22.87 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.24), residues: 1272 helix: 0.27 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -1.50 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 255 HIS 0.002 0.000 HIS B 19 PHE 0.010 0.001 PHE A 199 TYR 0.020 0.001 TYR C 70 ARG 0.005 0.000 ARG D 18 *********************** 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 245 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 187 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7496 (tt) REVERT: A 116 GLU cc_start: 0.5610 (OUTLIER) cc_final: 0.5146 (pp20) REVERT: A 199 PHE cc_start: 0.8133 (m-80) cc_final: 0.7534 (m-10) REVERT: A 247 TYR cc_start: 0.7923 (m-80) cc_final: 0.7163 (m-80) REVERT: A 281 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7231 (tp) REVERT: B 71 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.8073 (m-10) REVERT: B 86 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7537 (tt) REVERT: B 210 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6576 (mt-10) REVERT: B 247 TYR cc_start: 0.7956 (m-80) cc_final: 0.7191 (m-80) REVERT: C 116 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5577 (pp20) REVERT: D 71 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8146 (m-10) REVERT: D 199 PHE cc_start: 0.8136 (m-80) cc_final: 0.7544 (m-10) REVERT: D 247 TYR cc_start: 0.7926 (m-80) cc_final: 0.7216 (m-80) REVERT: D 325 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8182 (m) outliers start: 58 outliers final: 44 residues processed: 232 average time/residue: 0.2433 time to fit residues: 77.5812 Evaluate side-chains 237 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 185 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 33 ARG Chi-restraints excluded: chain A residue 49 ASP 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 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 49 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain 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 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 80 optimal weight: 0.0070 chunk 108 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11100 Z= 0.184 Angle : 0.533 7.663 15104 Z= 0.270 Chirality : 0.042 0.176 1664 Planarity : 0.005 0.062 1876 Dihedral : 5.651 59.588 1535 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.79 % Allowed : 23.14 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1272 helix: 0.39 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -1.39 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 255 HIS 0.002 0.000 HIS B 19 PHE 0.010 0.001 PHE A 199 TYR 0.019 0.001 TYR C 70 ARG 0.004 0.000 ARG B 18 ********************** 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 244 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 190 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7472 (tt) REVERT: A 116 GLU cc_start: 0.5552 (OUTLIER) cc_final: 0.5070 (pp20) REVERT: A 199 PHE cc_start: 0.8096 (m-80) cc_final: 0.7455 (m-10) REVERT: A 247 TYR cc_start: 0.7944 (m-80) cc_final: 0.7230 (m-80) REVERT: A 255 TRP cc_start: 0.7547 (t-100) cc_final: 0.7141 (t-100) REVERT: A 258 PHE cc_start: 0.7904 (t80) cc_final: 0.7585 (t80) REVERT: A 281 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7232 (tp) REVERT: B 71 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: B 86 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7510 (tt) REVERT: B 210 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6497 (mt-10) REVERT: B 247 TYR cc_start: 0.7949 (m-80) cc_final: 0.7199 (m-80) REVERT: C 116 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5552 (pp20) REVERT: D 71 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.8200 (m-10) REVERT: D 199 PHE cc_start: 0.8122 (m-80) cc_final: 0.7540 (m-10) REVERT: D 247 TYR cc_start: 0.7952 (m-80) cc_final: 0.7243 (m-80) REVERT: D 255 TRP cc_start: 0.7561 (t-100) cc_final: 0.7194 (t-100) REVERT: D 325 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8150 (m) outliers start: 54 outliers final: 43 residues processed: 232 average time/residue: 0.2532 time to fit residues: 80.6494 Evaluate side-chains 238 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 187 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 33 ARG Chi-restraints excluded: chain A residue 49 ASP 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 386 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 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 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain 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 386 ASN Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 0.0570 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 104 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101867 restraints weight = 50151.193| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.29 r_work: 0.3205 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11100 Z= 0.169 Angle : 0.524 6.969 15104 Z= 0.265 Chirality : 0.041 0.176 1664 Planarity : 0.005 0.061 1876 Dihedral : 5.285 59.214 1533 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.17 % Allowed : 23.67 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1272 helix: 0.52 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -1.28 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 255 HIS 0.002 0.000 HIS B 19 PHE 0.012 0.001 PHE B 258 TYR 0.017 0.001 TYR C 247 ARG 0.004 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2740.15 seconds wall clock time: 49 minutes 34.34 seconds (2974.34 seconds total)