Starting phenix.real_space_refine on Thu Jul 31 13:13:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnz_33331/07_2025/7xnz_33331_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnz_33331/07_2025/7xnz_33331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xnz_33331/07_2025/7xnz_33331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnz_33331/07_2025/7xnz_33331.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnz_33331/07_2025/7xnz_33331_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnz_33331/07_2025/7xnz_33331_trim.cif" } resolution = 3.6 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= -0.000 sd= 0.009 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 P 4 5.49 5 S 60 5.16 5 C 8484 2.51 5 N 2336 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13524 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "A" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "C" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "D" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 7.83, per 1000 atoms: 0.58 Number of scatterers: 13524 At special positions: 0 Unit cell: (86.67, 146.59, 84.53, 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) S 60 16.00 P 4 15.00 O 2640 8.00 N 2336 7.00 C 8484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 20 sheets defined 42.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.732A pdb=" N LEU B 10 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 removed outlier: 4.383A pdb=" N ILE B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.913A pdb=" N ARG B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.667A pdb=" N ARG B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.600A pdb=" N VAL B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.638A pdb=" N HIS B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.776A pdb=" N THR B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 196 removed outlier: 4.086A pdb=" N TYR B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 262 removed outlier: 3.624A pdb=" N SER B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 281 removed outlier: 3.742A pdb=" N GLY B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.434A pdb=" N SER B 303 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.503A pdb=" N TYR B 314 " --> pdb=" O TRP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.906A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 334' Processing helix chain 'B' and resid 335 through 338 Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.746A pdb=" N SER B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.732A pdb=" N LEU A 10 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 58 removed outlier: 4.383A pdb=" N ILE A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.913A pdb=" N ARG A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.667A pdb=" N ARG A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.600A pdb=" N VAL A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.638A pdb=" N HIS A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.776A pdb=" N THR A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 4.086A pdb=" N TYR A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 262 removed outlier: 3.623A pdb=" N SER A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.742A pdb=" N GLY A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 removed outlier: 4.434A pdb=" N SER A 303 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.503A pdb=" N TYR A 314 " --> pdb=" O TRP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.906A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 335 through 338 Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.746A pdb=" N SER A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.733A pdb=" N LEU C 10 " --> pdb=" O ILE C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 removed outlier: 4.383A pdb=" N ILE C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.913A pdb=" N ARG C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.668A pdb=" N ARG C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 139 removed outlier: 3.601A pdb=" N VAL C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.637A pdb=" N HIS C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.776A pdb=" N THR C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 removed outlier: 4.086A pdb=" N TYR C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 262 removed outlier: 3.623A pdb=" N SER C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 removed outlier: 3.742A pdb=" N GLY C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 removed outlier: 4.434A pdb=" N SER C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.503A pdb=" N TYR C 314 " --> pdb=" O TRP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.907A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 334' Processing helix chain 'C' and resid 335 through 338 Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 388 through 397 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.746A pdb=" N SER C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.732A pdb=" N LEU D 10 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 58 removed outlier: 4.383A pdb=" N ILE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.913A pdb=" N ARG D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.667A pdb=" N ARG D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.601A pdb=" N VAL D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 161 removed outlier: 3.638A pdb=" N HIS D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.777A pdb=" N THR D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 196 removed outlier: 4.086A pdb=" N TYR D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 262 removed outlier: 3.623A pdb=" N SER D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 281 removed outlier: 3.742A pdb=" N GLY D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 removed outlier: 4.434A pdb=" N SER D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 removed outlier: 3.502A pdb=" N TYR D 314 " --> pdb=" O TRP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 338 removed outlier: 4.222A pdb=" N ARG D 336 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS D 337 " --> pdb=" O LEU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.746A pdb=" N SER D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.781A pdb=" N VAL B 30 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 29 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 292 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 31 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 69 removed outlier: 5.883A pdb=" N ILE B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 93 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU B 69 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS B 90 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL B 114 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE B 92 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS B 116 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS B 94 " --> pdb=" O CYS B 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 175 through 179 removed outlier: 5.888A pdb=" N PHE B 176 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA B 206 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA B 178 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL B 246 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASP B 207 " --> pdb=" O VAL B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 367 through 370 Processing sheet with id=AA5, first strand: chain 'B' and resid 416 through 418 removed outlier: 4.245A pdb=" N GLY B 446 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU B 440 " --> pdb=" O PRO B 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 17 through 19 removed outlier: 4.781A pdb=" N VAL A 30 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 29 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 292 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A 31 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 67 through 69 removed outlier: 5.883A pdb=" N ILE A 67 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL A 93 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU A 69 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS A 90 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 114 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE A 92 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N CYS A 116 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS A 94 " --> pdb=" O CYS A 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 175 through 179 removed outlier: 5.889A pdb=" N PHE A 176 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ALA A 206 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 178 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 246 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASP A 207 " --> pdb=" O VAL A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 367 through 370 Processing sheet with id=AB1, first strand: chain 'A' and resid 416 through 418 removed outlier: 4.244A pdb=" N GLY A 446 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU A 440 " --> pdb=" O PRO A 444 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 19 removed outlier: 4.781A pdb=" N VAL C 30 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 29 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 292 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA C 31 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 67 through 69 removed outlier: 5.884A pdb=" N ILE C 67 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL C 93 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU C 69 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS C 90 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 114 " --> pdb=" O CYS C 90 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE C 92 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS C 116 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS C 94 " --> pdb=" O CYS C 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 179 removed outlier: 5.888A pdb=" N PHE C 176 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA C 206 " --> pdb=" O PHE C 176 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA C 178 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL C 246 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP C 207 " --> pdb=" O VAL C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 370 Processing sheet with id=AB6, first strand: chain 'C' and resid 416 through 418 removed outlier: 4.244A pdb=" N GLY C 446 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU C 440 " --> pdb=" O PRO C 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 17 through 19 removed outlier: 4.782A pdb=" N VAL D 30 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR D 29 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL D 292 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA D 31 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 67 through 69 removed outlier: 5.883A pdb=" N ILE D 67 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL D 93 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU D 69 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS D 90 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL D 114 " --> pdb=" O CYS D 90 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE D 92 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N CYS D 116 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS D 94 " --> pdb=" O CYS D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 175 through 179 removed outlier: 5.888A pdb=" N PHE D 176 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ALA D 206 " --> pdb=" O PHE D 176 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA D 178 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL D 246 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASP D 207 " --> pdb=" O VAL D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 367 through 370 Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 418 removed outlier: 4.245A pdb=" N GLY D 446 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU D 440 " --> pdb=" O PRO D 444 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1332 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: 4.13 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4493 1.34 - 1.45: 1552 1.45 - 1.57: 7643 1.57 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 13796 Sorted by residual: bond pdb=" N THR D 329 " pdb=" CA THR D 329 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.20e+00 bond pdb=" N LEU D 344 " pdb=" CA LEU D 344 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.12e+00 bond pdb=" N VAL C 345 " pdb=" CA VAL C 345 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.24e+00 bond pdb=" N HIS C 346 " pdb=" CA HIS C 346 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.26e-02 6.30e+03 6.19e+00 bond pdb=" N ALA B 343 " pdb=" CA ALA B 343 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.10e+00 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 18498 2.14 - 4.28: 264 4.28 - 6.42: 1 6.42 - 8.55: 3 8.55 - 10.69: 2 Bond angle restraints: 18768 Sorted by residual: angle pdb=" C SER B 328 " pdb=" N THR B 329 " pdb=" CA THR B 329 " ideal model delta sigma weight residual 122.92 133.61 -10.69 1.76e+00 3.23e-01 3.69e+01 angle pdb=" C SER C 328 " pdb=" N THR C 329 " pdb=" CA THR C 329 " ideal model delta sigma weight residual 122.92 133.35 -10.43 1.76e+00 3.23e-01 3.51e+01 angle pdb=" CA PRO B 342 " pdb=" C PRO B 342 " pdb=" O PRO B 342 " ideal model delta sigma weight residual 121.31 117.17 4.14 7.40e-01 1.83e+00 3.13e+01 angle pdb=" CA PRO D 342 " pdb=" C PRO D 342 " pdb=" O PRO D 342 " ideal model delta sigma weight residual 121.38 117.24 4.14 7.70e-01 1.69e+00 2.89e+01 angle pdb=" C SER A 328 " pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 122.92 130.73 -7.81 1.76e+00 3.23e-01 1.97e+01 ... (remaining 18763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 8076 33.07 - 66.15: 136 66.15 - 99.22: 6 99.22 - 132.30: 0 132.30 - 165.37: 2 Dihedral angle restraints: 8220 sinusoidal: 3124 harmonic: 5096 Sorted by residual: dihedral pdb=" C5A PLP D 501 " pdb=" O4P PLP D 501 " pdb=" P PLP D 501 " pdb=" O1P PLP D 501 " ideal model delta sinusoidal sigma weight residual 76.43 -118.20 -165.37 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5A PLP A 501 " pdb=" O4P PLP A 501 " pdb=" P PLP A 501 " pdb=" O1P PLP A 501 " ideal model delta sinusoidal sigma weight residual 76.43 -118.24 -165.33 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5A PLP C 501 " pdb=" O4P PLP C 501 " pdb=" P PLP C 501 " pdb=" O1P PLP C 501 " ideal model delta sinusoidal sigma weight residual 76.43 1.22 75.20 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 8217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1474 0.041 - 0.083: 433 0.083 - 0.124: 184 0.124 - 0.165: 9 0.165 - 0.207: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA LEU A 341 " pdb=" N LEU A 341 " pdb=" C LEU A 341 " pdb=" CB LEU A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL C 345 " pdb=" N VAL C 345 " pdb=" C VAL C 345 " pdb=" CB VAL C 345 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ALA A 343 " pdb=" N ALA A 343 " pdb=" C ALA A 343 " pdb=" CB ALA A 343 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 2101 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C GLN B 327 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN B 327 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 328 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 327 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C GLN C 327 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN C 327 " 0.012 2.00e-02 2.50e+03 pdb=" N SER C 328 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 340 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ALA C 340 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA C 340 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU C 341 " 0.009 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 447 2.70 - 3.25: 14878 3.25 - 3.80: 20654 3.80 - 4.35: 27125 4.35 - 4.90: 44982 Nonbonded interactions: 108086 Sorted by model distance: nonbonded pdb=" O PRO A 145 " pdb=" ND2 ASN A 150 " model vdw 2.146 3.120 nonbonded pdb=" O PRO C 145 " pdb=" ND2 ASN C 150 " model vdw 2.146 3.120 nonbonded pdb=" O PRO D 145 " pdb=" ND2 ASN D 150 " model vdw 2.146 3.120 nonbonded pdb=" O PRO B 145 " pdb=" ND2 ASN B 150 " model vdw 2.147 3.120 nonbonded pdb=" O LEU C 265 " pdb=" N GLY C 298 " model vdw 2.152 3.120 ... (remaining 108081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.820 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.004 0.042 13800 Z= 0.221 Angle : 0.597 10.692 18768 Z= 0.337 Chirality : 0.044 0.207 2104 Planarity : 0.004 0.034 2472 Dihedral : 13.119 165.370 5012 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 35.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.01 % Favored : 87.72 % Rotamer: Outliers : 3.42 % Allowed : 5.56 % Favored : 91.03 % 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: -3.94 (0.17), residues: 1824 helix: -1.98 (0.18), residues: 684 sheet: -3.33 (0.28), residues: 180 loop : -3.00 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 310 HIS 0.002 0.001 HIS A 175 PHE 0.004 0.001 PHE A 316 TYR 0.014 0.001 TYR B 128 ARG 0.002 0.000 ARG D 399 Details of bonding type rmsd hydrogen bonds : bond 0.15257 ( 479) hydrogen bonds : angle 7.34663 ( 1332) covalent geometry : bond 0.00406 (13796) covalent geometry : angle 0.59660 (18768) Misc. bond : bond 0.03868 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 320 time to evaluate : 1.366 Fit side-chains REVERT: B 278 LEU cc_start: 0.9272 (mt) cc_final: 0.9002 (mp) REVERT: B 311 MET cc_start: 0.9084 (tpp) cc_final: 0.8045 (tpt) REVERT: B 437 MET cc_start: 0.8404 (ptp) cc_final: 0.8140 (ptt) REVERT: A 172 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7333 (tptt) REVERT: C 311 MET cc_start: 0.9077 (tpp) cc_final: 0.8017 (tpt) REVERT: C 437 MET cc_start: 0.8393 (ptp) cc_final: 0.8145 (ptt) REVERT: D 172 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7346 (tptt) outliers start: 48 outliers final: 17 residues processed: 349 average time/residue: 0.2731 time to fit residues: 135.2944 Evaluate side-chains 216 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.125583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.101373 restraints weight = 17438.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.103828 restraints weight = 12198.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.105526 restraints weight = 9591.461| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13800 Z= 0.181 Angle : 0.650 9.043 18768 Z= 0.331 Chirality : 0.048 0.184 2104 Planarity : 0.005 0.059 2472 Dihedral : 8.378 158.953 2028 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 4.99 % Allowed : 12.82 % Favored : 82.19 % 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: -2.67 (0.19), residues: 1824 helix: -0.93 (0.20), residues: 688 sheet: -2.55 (0.31), residues: 180 loop : -2.28 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 310 HIS 0.009 0.002 HIS D 409 PHE 0.005 0.001 PHE A 92 TYR 0.019 0.002 TYR D 129 ARG 0.004 0.001 ARG C 431 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 479) hydrogen bonds : angle 5.05028 ( 1332) covalent geometry : bond 0.00440 (13796) covalent geometry : angle 0.65031 (18768) Misc. bond : bond 0.00043 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 227 time to evaluate : 1.372 Fit side-chains REVERT: B 150 ASN cc_start: 0.8710 (t0) cc_final: 0.8436 (m-40) REVERT: B 279 LYS cc_start: 0.8555 (tptm) cc_final: 0.8025 (mttt) REVERT: A 146 ASP cc_start: 0.8096 (t0) cc_final: 0.7726 (t70) REVERT: A 172 LYS cc_start: 0.7686 (ttpp) cc_final: 0.7467 (tptt) REVERT: C 150 ASN cc_start: 0.8724 (t0) cc_final: 0.8422 (m-40) REVERT: D 172 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7428 (tptt) outliers start: 70 outliers final: 36 residues processed: 277 average time/residue: 0.2072 time to fit residues: 89.4733 Evaluate side-chains 237 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN D 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.126140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102107 restraints weight = 17710.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.104441 restraints weight = 12391.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.106275 restraints weight = 9730.693| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13800 Z= 0.141 Angle : 0.593 8.580 18768 Z= 0.300 Chirality : 0.046 0.215 2104 Planarity : 0.005 0.047 2472 Dihedral : 7.583 141.421 2020 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 5.91 % Allowed : 16.31 % Favored : 77.78 % 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: -1.98 (0.19), residues: 1824 helix: -0.28 (0.20), residues: 692 sheet: -2.07 (0.33), residues: 180 loop : -1.97 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 310 HIS 0.007 0.001 HIS A 409 PHE 0.004 0.001 PHE C 316 TYR 0.017 0.001 TYR A 451 ARG 0.003 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 479) hydrogen bonds : angle 4.76371 ( 1332) covalent geometry : bond 0.00338 (13796) covalent geometry : angle 0.59283 (18768) Misc. bond : bond 0.00037 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 197 time to evaluate : 1.362 Fit side-chains REVERT: B 279 LYS cc_start: 0.8579 (tptm) cc_final: 0.7928 (mttt) REVERT: A 146 ASP cc_start: 0.8102 (t0) cc_final: 0.7649 (t0) REVERT: A 172 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7390 (tptt) REVERT: C 279 LYS cc_start: 0.8468 (tptm) cc_final: 0.7886 (mttt) REVERT: D 172 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7417 (tptt) outliers start: 83 outliers final: 48 residues processed: 259 average time/residue: 0.2303 time to fit residues: 90.0029 Evaluate side-chains 236 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 chunk 72 optimal weight: 1.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.126286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.101472 restraints weight = 17532.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.104168 restraints weight = 11959.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.105989 restraints weight = 9246.671| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13800 Z= 0.143 Angle : 0.581 9.090 18768 Z= 0.295 Chirality : 0.045 0.178 2104 Planarity : 0.005 0.052 2472 Dihedral : 7.101 134.397 2018 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.87 % Favored : 94.08 % Rotamer: Outliers : 4.99 % Allowed : 18.45 % Favored : 76.57 % 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: -1.61 (0.19), residues: 1824 helix: 0.09 (0.20), residues: 692 sheet: -2.24 (0.31), residues: 196 loop : -1.71 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.008 0.001 HIS D 409 PHE 0.004 0.001 PHE C 316 TYR 0.021 0.001 TYR A 129 ARG 0.003 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 479) hydrogen bonds : angle 4.62077 ( 1332) covalent geometry : bond 0.00343 (13796) covalent geometry : angle 0.58143 (18768) Misc. bond : bond 0.00029 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 204 time to evaluate : 2.377 Fit side-chains REVERT: B 279 LYS cc_start: 0.8552 (tptm) cc_final: 0.7698 (mttt) REVERT: A 146 ASP cc_start: 0.8094 (t0) cc_final: 0.7596 (t70) REVERT: A 172 LYS cc_start: 0.7923 (ttpp) cc_final: 0.7565 (tptt) REVERT: A 368 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8669 (mtp) REVERT: C 279 LYS cc_start: 0.8456 (tptm) cc_final: 0.7629 (mttt) REVERT: D 172 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7465 (tptt) REVERT: D 368 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8653 (mtp) outliers start: 70 outliers final: 47 residues processed: 254 average time/residue: 0.2269 time to fit residues: 89.7161 Evaluate side-chains 227 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 165 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 29 optimal weight: 0.0570 chunk 25 optimal weight: 4.9990 chunk 146 optimal weight: 0.0570 chunk 94 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.129448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.105325 restraints weight = 17505.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.107811 restraints weight = 12219.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.109452 restraints weight = 9598.904| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13800 Z= 0.107 Angle : 0.546 7.908 18768 Z= 0.276 Chirality : 0.044 0.170 2104 Planarity : 0.005 0.051 2472 Dihedral : 6.472 115.964 2018 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 4.77 % Allowed : 19.23 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1824 helix: 0.43 (0.20), residues: 708 sheet: -1.71 (0.33), residues: 196 loop : -1.42 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 166 HIS 0.006 0.001 HIS D 409 PHE 0.006 0.001 PHE D 316 TYR 0.015 0.001 TYR D 451 ARG 0.003 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 479) hydrogen bonds : angle 4.51577 ( 1332) covalent geometry : bond 0.00246 (13796) covalent geometry : angle 0.54611 (18768) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 215 time to evaluate : 1.193 Fit side-chains REVERT: B 279 LYS cc_start: 0.8396 (tptm) cc_final: 0.7608 (mttt) REVERT: A 146 ASP cc_start: 0.8059 (t0) cc_final: 0.7633 (t70) REVERT: A 221 TYR cc_start: 0.8570 (m-80) cc_final: 0.8196 (m-80) REVERT: A 332 ASP cc_start: 0.7875 (m-30) cc_final: 0.7372 (t0) REVERT: A 368 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8549 (mtp) REVERT: C 279 LYS cc_start: 0.8376 (tptm) cc_final: 0.7566 (mttt) REVERT: D 172 LYS cc_start: 0.7649 (ttpp) cc_final: 0.7371 (tptt) REVERT: D 221 TYR cc_start: 0.8552 (m-80) cc_final: 0.8179 (m-80) REVERT: D 287 ASP cc_start: 0.6976 (m-30) cc_final: 0.6763 (t70) outliers start: 67 outliers final: 43 residues processed: 265 average time/residue: 0.2915 time to fit residues: 115.2576 Evaluate side-chains 238 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 0.0670 chunk 157 optimal weight: 6.9990 chunk 110 optimal weight: 0.0770 chunk 137 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.129021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104530 restraints weight = 17650.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107235 restraints weight = 11942.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.109116 restraints weight = 9184.591| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13800 Z= 0.117 Angle : 0.558 7.248 18768 Z= 0.280 Chirality : 0.045 0.184 2104 Planarity : 0.005 0.051 2472 Dihedral : 6.071 100.536 2018 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 5.48 % Allowed : 17.66 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1824 helix: 0.61 (0.20), residues: 704 sheet: -1.44 (0.34), residues: 196 loop : -1.13 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 310 HIS 0.006 0.001 HIS D 409 PHE 0.006 0.001 PHE D 176 TYR 0.020 0.001 TYR D 129 ARG 0.004 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 479) hydrogen bonds : angle 4.45926 ( 1332) covalent geometry : bond 0.00277 (13796) covalent geometry : angle 0.55779 (18768) Misc. bond : bond 0.00017 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 200 time to evaluate : 2.318 Fit side-chains REVERT: B 279 LYS cc_start: 0.8376 (tptm) cc_final: 0.7502 (mttt) REVERT: A 106 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8554 (mt) REVERT: A 146 ASP cc_start: 0.8056 (t0) cc_final: 0.7657 (t70) REVERT: A 332 ASP cc_start: 0.7953 (m-30) cc_final: 0.7433 (t0) REVERT: C 164 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: C 279 LYS cc_start: 0.8383 (tptm) cc_final: 0.7566 (mttt) REVERT: D 106 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8518 (mt) REVERT: D 172 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7419 (tptt) REVERT: D 287 ASP cc_start: 0.6952 (m-30) cc_final: 0.6735 (t70) outliers start: 77 outliers final: 51 residues processed: 255 average time/residue: 0.3102 time to fit residues: 125.4510 Evaluate side-chains 242 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.126470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102396 restraints weight = 17630.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104749 restraints weight = 12580.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.106406 restraints weight = 10022.147| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13800 Z= 0.167 Angle : 0.599 11.168 18768 Z= 0.300 Chirality : 0.046 0.172 2104 Planarity : 0.005 0.051 2472 Dihedral : 6.066 89.998 2018 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 5.63 % Allowed : 18.16 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1824 helix: 0.61 (0.20), residues: 700 sheet: -1.10 (0.33), residues: 204 loop : -1.09 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 310 HIS 0.009 0.001 HIS D 409 PHE 0.019 0.001 PHE D 230 TYR 0.017 0.002 TYR A 451 ARG 0.004 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 479) hydrogen bonds : angle 4.53567 ( 1332) covalent geometry : bond 0.00408 (13796) covalent geometry : angle 0.59880 (18768) Misc. bond : bond 0.00049 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 184 time to evaluate : 2.513 Fit side-chains REVERT: B 164 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: B 279 LYS cc_start: 0.8425 (tptm) cc_final: 0.7540 (mttt) REVERT: A 106 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8607 (mt) REVERT: A 146 ASP cc_start: 0.8036 (t0) cc_final: 0.7597 (t70) REVERT: A 332 ASP cc_start: 0.8026 (m-30) cc_final: 0.7505 (t0) REVERT: C 164 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: C 279 LYS cc_start: 0.8433 (tptm) cc_final: 0.7501 (mttt) REVERT: D 106 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8592 (mt) REVERT: D 172 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7554 (tptt) REVERT: D 221 TYR cc_start: 0.8573 (m-80) cc_final: 0.8154 (m-80) REVERT: D 287 ASP cc_start: 0.7060 (m-30) cc_final: 0.6813 (t70) outliers start: 79 outliers final: 67 residues processed: 245 average time/residue: 0.3236 time to fit residues: 124.9498 Evaluate side-chains 245 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 174 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 172 optimal weight: 0.0970 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.106667 restraints weight = 17613.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.109112 restraints weight = 12390.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.110830 restraints weight = 9785.804| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13800 Z= 0.105 Angle : 0.561 10.813 18768 Z= 0.279 Chirality : 0.044 0.139 2104 Planarity : 0.004 0.050 2472 Dihedral : 5.575 70.625 2018 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 4.77 % Allowed : 19.80 % Favored : 75.43 % 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: -0.37 (0.20), residues: 1824 helix: 0.87 (0.20), residues: 704 sheet: -1.05 (0.34), residues: 196 loop : -0.92 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 310 HIS 0.006 0.001 HIS A 409 PHE 0.015 0.001 PHE D 230 TYR 0.019 0.001 TYR D 129 ARG 0.003 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 479) hydrogen bonds : angle 4.47694 ( 1332) covalent geometry : bond 0.00239 (13796) covalent geometry : angle 0.56140 (18768) Misc. bond : bond 0.00023 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 2.112 Fit side-chains REVERT: B 164 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: B 279 LYS cc_start: 0.8271 (tptm) cc_final: 0.7418 (mttt) REVERT: B 301 TYR cc_start: 0.8569 (m-80) cc_final: 0.8294 (m-80) REVERT: A 84 GLN cc_start: 0.8741 (tt0) cc_final: 0.8521 (tp40) REVERT: A 106 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 146 ASP cc_start: 0.7967 (t0) cc_final: 0.7535 (t70) REVERT: A 332 ASP cc_start: 0.7999 (m-30) cc_final: 0.7460 (t0) REVERT: C 60 GLN cc_start: 0.7425 (mt0) cc_final: 0.7118 (mt0) REVERT: C 164 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: C 279 LYS cc_start: 0.8352 (tptm) cc_final: 0.7458 (mttt) REVERT: C 397 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6584 (mt-10) REVERT: D 84 GLN cc_start: 0.8801 (tt0) cc_final: 0.8525 (tp40) REVERT: D 138 ASP cc_start: 0.8190 (m-30) cc_final: 0.7985 (m-30) REVERT: D 172 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7481 (tptt) REVERT: D 221 TYR cc_start: 0.8616 (m-80) cc_final: 0.8277 (m-80) REVERT: D 287 ASP cc_start: 0.7004 (m-30) cc_final: 0.6775 (t70) outliers start: 67 outliers final: 54 residues processed: 251 average time/residue: 0.2939 time to fit residues: 112.9917 Evaluate side-chains 245 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 116 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 118 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.127202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101527 restraints weight = 17596.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.104357 restraints weight = 11801.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.106369 restraints weight = 9000.677| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13800 Z= 0.148 Angle : 0.596 12.022 18768 Z= 0.296 Chirality : 0.045 0.160 2104 Planarity : 0.005 0.050 2472 Dihedral : 5.384 58.060 2018 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 5.27 % Allowed : 18.87 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1824 helix: 0.88 (0.20), residues: 704 sheet: -0.81 (0.34), residues: 204 loop : -0.95 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.007 0.001 HIS A 409 PHE 0.007 0.001 PHE C 316 TYR 0.018 0.001 TYR D 451 ARG 0.004 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 479) hydrogen bonds : angle 4.49343 ( 1332) covalent geometry : bond 0.00361 (13796) covalent geometry : angle 0.59601 (18768) Misc. bond : bond 0.00082 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 188 time to evaluate : 3.502 Fit side-chains REVERT: B 60 GLN cc_start: 0.7636 (mt0) cc_final: 0.7372 (mt0) REVERT: B 164 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: B 279 LYS cc_start: 0.8434 (tptm) cc_final: 0.7452 (mttt) REVERT: B 332 ASP cc_start: 0.8434 (m-30) cc_final: 0.8205 (m-30) REVERT: A 138 ASP cc_start: 0.8147 (m-30) cc_final: 0.7916 (m-30) REVERT: A 146 ASP cc_start: 0.8073 (t0) cc_final: 0.7524 (t70) REVERT: A 332 ASP cc_start: 0.8133 (m-30) cc_final: 0.7468 (t0) REVERT: C 60 GLN cc_start: 0.7617 (mt0) cc_final: 0.7257 (mt0) REVERT: C 164 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: C 279 LYS cc_start: 0.8436 (tptm) cc_final: 0.7431 (mttt) REVERT: C 397 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6722 (mt-10) REVERT: D 138 ASP cc_start: 0.8076 (m-30) cc_final: 0.7840 (m-30) REVERT: D 172 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7452 (tptt) REVERT: D 221 TYR cc_start: 0.8597 (m-80) cc_final: 0.8237 (m-80) REVERT: D 287 ASP cc_start: 0.7099 (m-30) cc_final: 0.6787 (t70) outliers start: 74 outliers final: 60 residues processed: 246 average time/residue: 0.3330 time to fit residues: 125.6261 Evaluate side-chains 242 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.126222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.102205 restraints weight = 17660.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104534 restraints weight = 12608.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.106195 restraints weight = 10065.649| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13800 Z= 0.166 Angle : 0.606 11.441 18768 Z= 0.304 Chirality : 0.046 0.155 2104 Planarity : 0.005 0.050 2472 Dihedral : 5.651 67.726 2018 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 4.56 % Allowed : 19.37 % Favored : 76.07 % 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: -0.40 (0.20), residues: 1824 helix: 0.82 (0.20), residues: 704 sheet: -0.83 (0.34), residues: 204 loop : -0.96 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 310 HIS 0.008 0.001 HIS D 409 PHE 0.016 0.001 PHE A 230 TYR 0.018 0.002 TYR D 451 ARG 0.005 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 479) hydrogen bonds : angle 4.54435 ( 1332) covalent geometry : bond 0.00407 (13796) covalent geometry : angle 0.60633 (18768) Misc. bond : bond 0.00075 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 2.494 Fit side-chains REVERT: B 60 GLN cc_start: 0.7500 (mt0) cc_final: 0.7245 (mt0) REVERT: B 164 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: B 279 LYS cc_start: 0.8406 (tptm) cc_final: 0.7508 (mttt) REVERT: A 138 ASP cc_start: 0.8119 (m-30) cc_final: 0.7886 (m-30) REVERT: A 146 ASP cc_start: 0.8086 (t0) cc_final: 0.7633 (t70) REVERT: A 332 ASP cc_start: 0.7957 (m-30) cc_final: 0.7426 (t0) REVERT: C 60 GLN cc_start: 0.7538 (mt0) cc_final: 0.7262 (mt0) REVERT: C 164 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: C 279 LYS cc_start: 0.8420 (tptm) cc_final: 0.7470 (mttt) REVERT: C 397 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6619 (mt-10) REVERT: D 138 ASP cc_start: 0.8054 (m-30) cc_final: 0.7816 (m-30) REVERT: D 221 TYR cc_start: 0.8656 (m-80) cc_final: 0.8302 (m-80) REVERT: D 287 ASP cc_start: 0.7070 (m-30) cc_final: 0.6835 (t70) outliers start: 64 outliers final: 59 residues processed: 236 average time/residue: 0.3372 time to fit residues: 122.1547 Evaluate side-chains 237 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 118 optimal weight: 0.0270 chunk 169 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.105663 restraints weight = 17640.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.108101 restraints weight = 12492.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109848 restraints weight = 9903.517| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13800 Z= 0.113 Angle : 0.577 11.838 18768 Z= 0.288 Chirality : 0.045 0.145 2104 Planarity : 0.005 0.049 2472 Dihedral : 5.430 58.984 2018 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 4.20 % Allowed : 20.09 % Favored : 75.71 % 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: -0.26 (0.20), residues: 1824 helix: 0.98 (0.20), residues: 704 sheet: -0.92 (0.35), residues: 196 loop : -0.89 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 310 HIS 0.007 0.001 HIS D 409 PHE 0.016 0.001 PHE A 230 TYR 0.017 0.001 TYR D 451 ARG 0.005 0.000 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 479) hydrogen bonds : angle 4.49822 ( 1332) covalent geometry : bond 0.00267 (13796) covalent geometry : angle 0.57685 (18768) Misc. bond : bond 0.00050 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4990.88 seconds wall clock time: 96 minutes 37.99 seconds (5797.99 seconds total)