Starting phenix.real_space_refine on Fri Mar 15 06:01:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/03_2024/7pqu_13605_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/03_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_13605/03_2024/7pqu_13605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/03_2024/7pqu_13605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/03_2024/7pqu_13605_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/03_2024/7pqu_13605_updated.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.80, per 1000 atoms: 1.00 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: 4.25 Conformation dependent library (CDL) restraints added in 3.5 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... running ksdssp... Secondary structure from input PDB file: 64 helices and 4 sheets defined 55.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 removed outlier: 4.414A pdb=" N THR A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 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) No H-bonds generated for 'chain 'A' and resid 33 through 38' Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.862A pdb=" N ASN A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 192 through 210 removed outlier: 4.544A pdb=" N PHE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.631A pdb=" N PHE A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.895A pdb=" N ARG A 320 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 321 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.582A pdb=" N ARG A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 369 removed outlier: 3.706A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 3.847A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.906A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 450 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 28 removed outlier: 4.414A pdb=" N THR B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 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) No H-bonds generated for 'chain 'B' and resid 33 through 38' Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.863A pdb=" N ASN B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 70 " --> pdb=" O HIS B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 192 through 210 removed outlier: 4.544A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 261 removed outlier: 3.631A pdb=" N PHE B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.896A pdb=" N ARG B 320 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 321 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.582A pdb=" N ARG B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 369 removed outlier: 3.706A pdb=" N LEU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 3.847A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 429 removed outlier: 3.905A pdb=" N LEU B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 450 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 28 removed outlier: 4.414A pdb=" N THR C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 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) No H-bonds generated for 'chain 'C' and resid 33 through 38' Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 64 through 70 removed outlier: 3.862A pdb=" N ASN C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 107 through 110 No H-bonds generated for 'chain 'C' and resid 107 through 110' Processing helix chain 'C' and resid 192 through 210 removed outlier: 4.544A pdb=" N PHE C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 261 removed outlier: 3.631A pdb=" N PHE C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 311 through 314 No H-bonds generated for 'chain 'C' and resid 311 through 314' Processing helix chain 'C' and resid 316 through 324 removed outlier: 3.895A pdb=" N ARG C 320 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 321 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 removed outlier: 3.583A pdb=" N ARG C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 369 removed outlier: 3.706A pdb=" N LEU C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 398 removed outlier: 3.848A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.906A pdb=" N LEU C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 450 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 28 removed outlier: 4.414A pdb=" N THR D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 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) No H-bonds generated for 'chain 'D' and resid 33 through 38' Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.862A pdb=" N ASN D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR D 70 " --> pdb=" O HIS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 107 through 110 No H-bonds generated for 'chain 'D' and resid 107 through 110' Processing helix chain 'D' and resid 192 through 210 removed outlier: 4.544A pdb=" N PHE D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 261 removed outlier: 3.631A pdb=" N PHE D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 311 through 314 No H-bonds generated for 'chain 'D' and resid 311 through 314' Processing helix chain 'D' and resid 316 through 324 removed outlier: 3.895A pdb=" N ARG D 320 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 321 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.582A pdb=" N ARG D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 369 removed outlier: 3.706A pdb=" N LEU D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 398 removed outlier: 3.847A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 429 removed outlier: 3.906A pdb=" N LEU D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 450 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= A, 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: 4.012A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 47 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing sheet with id= B, 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: 4.012A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP B 47 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing sheet with id= C, 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: 4.013A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP C 47 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing sheet with id= D, 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: 4.013A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP D 47 " --> pdb=" O PHE D 56 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 4.63 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: 8077 3.10 - 4.12: 29641 4.12 - 5.14: 64988 Warning: very small nonbonded interaction distances. Nonbonded interactions: 102717 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 102712 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: 2.300 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: 8.250 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 39.820 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.230 ------------------------------------------------------------------------------- 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 : 1.174 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: 0.2927 time to fit residues: 97.2805 Evaluate side-chains 240 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 60 HIS A 111 GLN A 450 GLN B 19 HIS B 60 HIS B 111 GLN C 19 HIS C 60 HIS C 111 GLN D 19 HIS D 60 HIS D 111 GLN D 409 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1138 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= 0.250 Angle : 0.607 8.175 15104 Z= 0.310 Chirality : 0.043 0.205 1664 Planarity : 0.006 0.062 1876 Dihedral : 9.754 55.405 1611 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.32 % Allowed : 21.99 % Favored : 72.70 % 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: -2.61 (0.23), residues: 1272 helix: -1.21 (0.17), residues: 792 sheet: None (None), residues: 0 loop : -2.49 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 392 HIS 0.004 0.001 HIS A 19 PHE 0.014 0.001 PHE D 289 TYR 0.014 0.001 TYR D 22 ARG 0.008 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 250 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 190 time to evaluate : 1.271 Fit side-chains REVERT: A 71 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: A 281 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7155 (tp) REVERT: A 310 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6273 (tp) REVERT: B 71 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8044 (m-10) REVERT: B 210 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6667 (mp0) REVERT: C 71 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7989 (m-10) REVERT: C 255 TRP cc_start: 0.7774 (t60) cc_final: 0.7572 (t-100) REVERT: D 71 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8080 (m-10) outliers start: 60 outliers final: 41 residues processed: 240 average time/residue: 0.2524 time to fit residues: 82.8821 Evaluate side-chains 233 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 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 54 GLU Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU 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 54 GLU 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 310 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 54 GLU 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 312 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7559 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11100 Z= 0.228 Angle : 0.559 8.635 15104 Z= 0.286 Chirality : 0.042 0.182 1664 Planarity : 0.005 0.065 1876 Dihedral : 7.523 58.763 1552 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.12 % Allowed : 21.63 % 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: -1.94 (0.24), residues: 1272 helix: -0.65 (0.18), residues: 788 sheet: None (None), residues: 0 loop : -2.27 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 94 HIS 0.003 0.001 HIS C 19 PHE 0.013 0.001 PHE C 289 TYR 0.015 0.001 TYR C 247 ARG 0.005 0.000 ARG C 339 *********************** 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 261 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 192 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8045 (m-10) REVERT: A 86 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7610 (tt) REVERT: A 247 TYR cc_start: 0.7831 (m-80) cc_final: 0.7059 (m-80) REVERT: B 71 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8046 (m-10) REVERT: B 210 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6586 (mt-10) REVERT: B 247 TYR cc_start: 0.7875 (m-80) cc_final: 0.7047 (m-80) REVERT: B 325 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7964 (m) REVERT: C 71 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: C 325 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7902 (m) REVERT: D 71 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: D 247 TYR cc_start: 0.7785 (m-80) cc_final: 0.7025 (m-80) REVERT: D 325 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.7837 (p) outliers start: 69 outliers final: 38 residues processed: 248 average time/residue: 0.2645 time to fit residues: 88.8689 Evaluate side-chains 228 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 182 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 33 ARG 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 262 MET 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 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 71 TYR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU 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 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 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN 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 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 262 MET 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 310 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 C 409 GLN D 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11100 Z= 0.315 Angle : 0.585 8.902 15104 Z= 0.301 Chirality : 0.044 0.184 1664 Planarity : 0.006 0.069 1876 Dihedral : 7.142 59.966 1541 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 6.29 % Allowed : 22.16 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.24), residues: 1272 helix: -0.58 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -2.38 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 94 HIS 0.004 0.001 HIS A 19 PHE 0.011 0.001 PHE A 315 TYR 0.016 0.002 TYR C 247 ARG 0.005 0.000 ARG A 18 *********************** 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 251 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 180 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: A 247 TYR cc_start: 0.7836 (m-80) cc_final: 0.7082 (m-80) REVERT: A 281 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7204 (tp) REVERT: B 71 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8009 (m-10) REVERT: B 210 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6607 (mt-10) REVERT: B 247 TYR cc_start: 0.7921 (m-80) cc_final: 0.7099 (m-80) REVERT: B 255 TRP cc_start: 0.7681 (t60) cc_final: 0.7473 (t-100) REVERT: B 325 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8034 (m) REVERT: C 71 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8022 (m-10) REVERT: C 325 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8000 (m) REVERT: D 71 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8027 (m-10) REVERT: D 240 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6806 (mt-10) REVERT: D 325 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8270 (m) outliers start: 71 outliers final: 50 residues processed: 236 average time/residue: 0.2408 time to fit residues: 77.6762 Evaluate side-chains 239 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 180 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 71 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 262 MET 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 386 ASN Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 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 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 262 MET 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 419 LEU 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 97 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 445 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7534 moved from start: 0.2023 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 : 0.533 7.960 15104 Z= 0.272 Chirality : 0.041 0.168 1664 Planarity : 0.005 0.074 1876 Dihedral : 6.542 59.248 1541 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.76 % Allowed : 22.34 % Favored : 71.90 % 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: -1.46 (0.24), residues: 1272 helix: -0.21 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -2.21 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 392 HIS 0.002 0.000 HIS D 19 PHE 0.011 0.001 PHE B 258 TYR 0.016 0.001 TYR C 247 ARG 0.004 0.000 ARG A 18 *********************** 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 252 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 187 time to evaluate : 1.099 Fit side-chains REVERT: A 33 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6814 (ttp-170) REVERT: A 71 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8041 (m-10) REVERT: A 86 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7585 (tt) REVERT: A 281 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7220 (tp) REVERT: B 71 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: B 86 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7579 (tt) REVERT: B 210 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6587 (mt-10) REVERT: B 247 TYR cc_start: 0.7878 (m-80) cc_final: 0.7089 (m-80) REVERT: C 71 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.8036 (m-10) REVERT: C 325 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7937 (m) REVERT: D 71 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8020 (m-10) REVERT: D 86 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7569 (tt) REVERT: D 247 TYR cc_start: 0.7843 (m-80) cc_final: 0.7108 (m-80) REVERT: D 325 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8257 (m) outliers start: 65 outliers final: 44 residues processed: 237 average time/residue: 0.2600 time to fit residues: 84.9891 Evaluate side-chains 231 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 176 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 71 TYR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 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 419 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 21 THR 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 262 MET Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11100 Z= 0.171 Angle : 0.525 7.871 15104 Z= 0.267 Chirality : 0.041 0.161 1664 Planarity : 0.005 0.076 1876 Dihedral : 5.857 59.354 1536 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.79 % Allowed : 22.96 % 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: -1.01 (0.24), residues: 1272 helix: 0.09 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -1.94 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 392 HIS 0.002 0.000 HIS C 19 PHE 0.011 0.001 PHE A 244 TYR 0.028 0.001 TYR B 70 ARG 0.004 0.000 ARG B 18 *********************** 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 242 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 1.316 Fit side-chains REVERT: A 86 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7535 (tt) REVERT: A 116 GLU cc_start: 0.5568 (OUTLIER) cc_final: 0.5159 (pp20) REVERT: A 199 PHE cc_start: 0.8213 (m-80) cc_final: 0.7651 (m-10) REVERT: A 247 TYR cc_start: 0.7901 (m-80) cc_final: 0.7140 (m-80) REVERT: A 281 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7228 (tp) REVERT: B 86 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7487 (tt) REVERT: B 210 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6585 (mt-10) REVERT: B 247 TYR cc_start: 0.7880 (m-80) cc_final: 0.7097 (m-80) REVERT: C 116 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5616 (pp20) REVERT: C 199 PHE cc_start: 0.7992 (m-80) cc_final: 0.7397 (m-10) REVERT: D 86 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7512 (tt) REVERT: D 199 PHE cc_start: 0.8025 (m-80) cc_final: 0.7463 (m-10) REVERT: D 247 TYR cc_start: 0.7822 (m-80) cc_final: 0.7076 (m-80) REVERT: D 325 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8199 (m) outliers start: 54 outliers final: 33 residues processed: 233 average time/residue: 0.2436 time to fit residues: 78.5824 Evaluate side-chains 222 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 419 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 THR 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=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: 0.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 327 HIS C 111 GLN C 112 HIS D 111 GLN D 450 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11100 Z= 0.255 Angle : 0.561 8.106 15104 Z= 0.284 Chirality : 0.043 0.157 1664 Planarity : 0.006 0.079 1876 Dihedral : 5.851 59.607 1531 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.70 % Allowed : 22.87 % 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: -0.99 (0.24), residues: 1272 helix: -0.01 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -1.74 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 94 HIS 0.003 0.001 HIS B 19 PHE 0.013 0.001 PHE B 258 TYR 0.025 0.002 TYR A 70 ARG 0.004 0.000 ARG B 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 233 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 180 time to evaluate : 1.099 Fit side-chains REVERT: A 33 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6766 (ttp-170) REVERT: A 86 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7593 (tt) REVERT: A 116 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.5139 (pp20) REVERT: A 247 TYR cc_start: 0.7907 (m-80) cc_final: 0.7147 (m-80) REVERT: A 281 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7268 (tp) REVERT: B 86 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7526 (tt) REVERT: B 210 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6533 (mt-10) REVERT: C 86 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7551 (tt) REVERT: C 116 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5548 (pp20) REVERT: C 199 PHE cc_start: 0.8113 (m-80) cc_final: 0.7503 (m-10) REVERT: D 86 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7549 (tt) REVERT: D 199 PHE cc_start: 0.8113 (m-80) cc_final: 0.7544 (m-10) REVERT: D 325 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8211 (m) outliers start: 53 outliers final: 37 residues processed: 223 average time/residue: 0.2506 time to fit residues: 77.2528 Evaluate side-chains 225 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 179 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 419 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 291 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 419 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 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 419 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 112 HIS B 327 HIS C 111 GLN D 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2339 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= 0.249 Angle : 0.557 7.958 15104 Z= 0.282 Chirality : 0.043 0.154 1664 Planarity : 0.006 0.078 1876 Dihedral : 5.935 59.580 1531 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.34 % Allowed : 23.40 % 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: -0.88 (0.24), residues: 1272 helix: 0.05 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.56 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 255 HIS 0.003 0.001 HIS B 19 PHE 0.012 0.001 PHE B 258 TYR 0.023 0.002 TYR C 70 ARG 0.004 0.000 ARG C 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 229 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 180 time to evaluate : 1.179 Fit side-chains REVERT: A 33 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6715 (ttp-170) REVERT: A 86 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7586 (tt) REVERT: A 116 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5118 (pp20) REVERT: A 199 PHE cc_start: 0.8069 (m-80) cc_final: 0.7479 (m-10) REVERT: A 247 TYR cc_start: 0.7958 (m-80) cc_final: 0.7159 (m-80) REVERT: A 281 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7210 (tp) REVERT: B 86 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7576 (tt) REVERT: B 210 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6565 (mt-10) REVERT: C 116 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5554 (pp20) REVERT: C 199 PHE cc_start: 0.8073 (m-80) cc_final: 0.7424 (m-10) REVERT: D 199 PHE cc_start: 0.8148 (m-80) cc_final: 0.7567 (m-10) REVERT: D 247 TYR cc_start: 0.7909 (m-80) cc_final: 0.7191 (m-80) REVERT: D 325 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8089 (m) outliers start: 49 outliers final: 37 residues processed: 220 average time/residue: 0.2348 time to fit residues: 71.2841 Evaluate side-chains 224 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 180 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 33 ARG 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 419 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 325 THR 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 B residue 445 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 291 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 419 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 445 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 0.0870 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 chunk 103 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- 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 43 HIS C 111 GLN D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11100 Z= 0.177 Angle : 0.529 7.396 15104 Z= 0.266 Chirality : 0.041 0.152 1664 Planarity : 0.005 0.080 1876 Dihedral : 5.432 59.456 1530 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.72 % Allowed : 24.20 % 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: -0.52 (0.25), residues: 1272 helix: 0.42 (0.20), residues: 776 sheet: None (None), residues: 0 loop : -1.52 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 392 HIS 0.002 0.000 HIS A 19 PHE 0.012 0.001 PHE B 258 TYR 0.024 0.001 TYR B 247 ARG 0.004 0.000 ARG C 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 223 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7516 (tt) REVERT: A 116 GLU cc_start: 0.5588 (OUTLIER) cc_final: 0.5069 (pp20) REVERT: A 199 PHE cc_start: 0.7993 (m-80) cc_final: 0.7419 (m-10) REVERT: A 247 TYR cc_start: 0.7968 (m-80) cc_final: 0.7257 (m-80) REVERT: A 281 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7253 (tp) REVERT: B 86 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7472 (tt) REVERT: B 210 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6533 (mt-10) REVERT: C 86 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7451 (tt) REVERT: C 116 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5573 (pp20) REVERT: C 199 PHE cc_start: 0.8016 (m-80) cc_final: 0.7349 (m-10) REVERT: D 86 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7449 (tt) REVERT: D 199 PHE cc_start: 0.8073 (m-80) cc_final: 0.7476 (m-10) REVERT: D 247 TYR cc_start: 0.7945 (m-80) cc_final: 0.7180 (m-80) outliers start: 42 outliers final: 30 residues processed: 216 average time/residue: 0.2464 time to fit residues: 72.6816 Evaluate side-chains 214 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 33 ARG 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 291 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 386 ASN 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: 2.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 43 HIS D 111 GLN D 112 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11100 Z= 0.273 Angle : 0.567 7.870 15104 Z= 0.289 Chirality : 0.044 0.152 1664 Planarity : 0.006 0.081 1876 Dihedral : 5.693 59.280 1528 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.28 % Allowed : 24.47 % 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: -0.74 (0.24), residues: 1272 helix: 0.26 (0.19), residues: 776 sheet: -2.68 (0.60), residues: 40 loop : -1.49 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 255 HIS 0.004 0.001 HIS A 19 PHE 0.011 0.001 PHE B 258 TYR 0.029 0.002 TYR B 247 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 212 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 1.116 Fit side-chains REVERT: A 33 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6760 (ttp-170) REVERT: A 86 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7579 (tt) REVERT: A 199 PHE cc_start: 0.8030 (m-80) cc_final: 0.7455 (m-10) REVERT: A 247 TYR cc_start: 0.7958 (m-80) cc_final: 0.7170 (m-80) REVERT: A 281 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7210 (tp) REVERT: B 75 LYS cc_start: 0.8508 (mttp) cc_final: 0.8308 (mttp) REVERT: B 86 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7530 (tt) REVERT: B 210 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6455 (mt-10) REVERT: C 116 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5505 (pp20) REVERT: C 199 PHE cc_start: 0.8092 (m-80) cc_final: 0.7423 (m-10) REVERT: D 199 PHE cc_start: 0.8122 (m-80) cc_final: 0.7521 (m-10) REVERT: D 247 TYR cc_start: 0.7930 (m-80) cc_final: 0.7181 (m-80) outliers start: 37 outliers final: 31 residues processed: 206 average time/residue: 0.2420 time to fit residues: 68.7163 Evaluate side-chains 211 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 33 ARG 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 240 GLU Chi-restraints excluded: chain A residue 246 THR 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 419 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 246 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 327 HIS C 111 GLN D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098866 restraints weight = 50730.124| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.40 r_work: 0.3144 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11100 Z= 0.207 Angle : 0.540 7.369 15104 Z= 0.274 Chirality : 0.042 0.150 1664 Planarity : 0.006 0.080 1876 Dihedral : 5.492 59.964 1528 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.37 % Allowed : 24.38 % 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: -0.55 (0.24), residues: 1272 helix: 0.44 (0.20), residues: 772 sheet: -2.60 (0.59), residues: 40 loop : -1.46 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 255 HIS 0.002 0.000 HIS C 19 PHE 0.013 0.001 PHE B 258 TYR 0.033 0.002 TYR B 247 ARG 0.004 0.000 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2734.11 seconds wall clock time: 49 minutes 43.32 seconds (2983.32 seconds total)