Starting phenix.real_space_refine on Sun Jul 21 06:08:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/07_2024/7xnz_33331_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/07_2024/7xnz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/07_2024/7xnz_33331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/07_2024/7xnz_33331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/07_2024/7xnz_33331_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/07_2024/7xnz_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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 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: 7.88, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.16 Conformation dependent library (CDL) restraints added in 2.8 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: 1.53 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: 3.77 Time building geometry restraints manager: 6.69 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: 100.01 - 106.82: 563 106.82 - 113.63: 7698 113.63 - 120.44: 5203 120.44 - 127.25: 5136 127.25 - 134.06: 168 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 2.520 nonbonded pdb=" O PRO C 145 " pdb=" ND2 ASN C 150 " model vdw 2.146 2.520 nonbonded pdb=" O PRO D 145 " pdb=" ND2 ASN D 150 " model vdw 2.146 2.520 nonbonded pdb=" O PRO B 145 " pdb=" ND2 ASN B 150 " model vdw 2.147 2.520 nonbonded pdb=" O LEU C 265 " pdb=" N GLY C 298 " model vdw 2.152 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.580 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 38.630 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.640 ------------------------------------------------------------------------------- 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 13796 Z= 0.272 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 *********************** 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 fitting. rotamer outliers: 48 poor density : 320 time to evaluate : 1.533 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: 0.2627 time to fit residues: 129.9617 Evaluate side-chains 216 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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: 0.0570 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13796 Z= 0.222 Angle : 0.608 8.720 18768 Z= 0.309 Chirality : 0.046 0.177 2104 Planarity : 0.005 0.057 2472 Dihedral : 8.636 174.420 2028 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 4.42 % Allowed : 12.25 % Favored : 83.33 % 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: -2.60 (0.19), residues: 1824 helix: -0.87 (0.20), residues: 688 sheet: -2.45 (0.31), residues: 180 loop : -2.24 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 310 HIS 0.006 0.001 HIS D 409 PHE 0.005 0.001 PHE A 306 TYR 0.018 0.001 TYR D 129 ARG 0.004 0.000 ARG B 431 *********************** 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 291 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 229 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: B 279 LYS cc_start: 0.8589 (tptm) cc_final: 0.7898 (mttt) REVERT: A 146 ASP cc_start: 0.8112 (t0) cc_final: 0.7609 (t70) REVERT: A 172 LYS cc_start: 0.7329 (ttpp) cc_final: 0.7007 (tptt) REVERT: D 172 LYS cc_start: 0.7337 (ttpp) cc_final: 0.6848 (tptt) REVERT: D 289 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8270 (tp) outliers start: 62 outliers final: 35 residues processed: 271 average time/residue: 0.2171 time to fit residues: 91.7006 Evaluate side-chains 240 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 290 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 174 THR 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 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL 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 290 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 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 174 THR 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 289 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL 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 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.0060 chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13796 Z= 0.203 Angle : 0.569 8.673 18768 Z= 0.287 Chirality : 0.045 0.214 2104 Planarity : 0.005 0.049 2472 Dihedral : 8.204 174.807 2020 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.19 % Rotamer: Outliers : 5.41 % Allowed : 16.60 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.19), residues: 1824 helix: -0.19 (0.20), residues: 692 sheet: -2.09 (0.32), residues: 176 loop : -1.89 (0.20), residues: 956 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 D 451 ARG 0.004 0.000 ARG C 256 *********************** 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 279 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 203 time to evaluate : 1.431 Fit side-chains REVERT: B 279 LYS cc_start: 0.8620 (tptm) cc_final: 0.7880 (mttt) REVERT: A 146 ASP cc_start: 0.8127 (t0) cc_final: 0.7609 (t70) REVERT: A 172 LYS cc_start: 0.7505 (ttpp) cc_final: 0.7080 (tptt) REVERT: C 279 LYS cc_start: 0.8619 (tptm) cc_final: 0.7799 (mttt) REVERT: D 172 LYS cc_start: 0.7378 (ttpp) cc_final: 0.7025 (tptt) outliers start: 76 outliers final: 49 residues processed: 261 average time/residue: 0.2145 time to fit residues: 85.9099 Evaluate side-chains 238 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 189 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 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 71 THR 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 174 THR 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 246 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 291 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 185 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 290 ILE Chi-restraints excluded: chain C residue 292 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 71 THR 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 174 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13796 Z= 0.240 Angle : 0.571 9.195 18768 Z= 0.289 Chirality : 0.046 0.187 2104 Planarity : 0.005 0.052 2472 Dihedral : 8.012 172.823 2020 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 5.48 % Allowed : 17.74 % Favored : 76.78 % 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: -1.55 (0.19), residues: 1824 helix: 0.10 (0.20), residues: 692 sheet: -1.79 (0.32), residues: 204 loop : -1.74 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 310 HIS 0.008 0.001 HIS A 409 PHE 0.005 0.001 PHE B 316 TYR 0.020 0.001 TYR A 129 ARG 0.003 0.000 ARG C 256 *********************** 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 262 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 185 time to evaluate : 1.588 Fit side-chains REVERT: B 279 LYS cc_start: 0.8533 (tptm) cc_final: 0.7617 (mttt) REVERT: A 146 ASP cc_start: 0.8091 (t0) cc_final: 0.7581 (t70) REVERT: A 172 LYS cc_start: 0.7596 (ttpp) cc_final: 0.7196 (tptt) REVERT: C 279 LYS cc_start: 0.8626 (tptm) cc_final: 0.7802 (mttt) REVERT: D 172 LYS cc_start: 0.7578 (ttpp) cc_final: 0.7142 (tptt) outliers start: 77 outliers final: 54 residues processed: 242 average time/residue: 0.2277 time to fit residues: 82.8068 Evaluate side-chains 227 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 196 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 290 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain A residue 71 THR 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 118 THR Chi-restraints excluded: chain A residue 174 THR 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 291 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 91 VAL 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 196 VAL 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 290 ILE Chi-restraints excluded: chain C residue 292 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 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 174 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 291 VAL 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 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 144 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 156 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13796 Z= 0.197 Angle : 0.545 9.818 18768 Z= 0.274 Chirality : 0.045 0.199 2104 Planarity : 0.004 0.051 2472 Dihedral : 7.570 167.435 2018 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 5.63 % Allowed : 18.73 % Favored : 75.64 % 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: -1.11 (0.20), residues: 1824 helix: 0.41 (0.20), residues: 700 sheet: -1.41 (0.33), residues: 204 loop : -1.47 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 310 HIS 0.006 0.001 HIS A 409 PHE 0.006 0.001 PHE C 316 TYR 0.014 0.001 TYR A 451 ARG 0.004 0.000 ARG A 103 *********************** 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 272 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 193 time to evaluate : 1.432 Fit side-chains REVERT: B 279 LYS cc_start: 0.8475 (tptm) cc_final: 0.7537 (mttt) REVERT: A 20 ASN cc_start: 0.8707 (p0) cc_final: 0.8433 (p0) REVERT: A 146 ASP cc_start: 0.8079 (t0) cc_final: 0.7524 (t70) REVERT: A 172 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7065 (tptt) REVERT: C 35 GLU cc_start: 0.8089 (tt0) cc_final: 0.7868 (tt0) REVERT: C 279 LYS cc_start: 0.8547 (tptm) cc_final: 0.7498 (mttt) REVERT: D 172 LYS cc_start: 0.7492 (ttpp) cc_final: 0.7027 (tptt) REVERT: D 441 GLU cc_start: 0.8192 (mp0) cc_final: 0.7149 (pt0) outliers start: 79 outliers final: 62 residues processed: 252 average time/residue: 0.2007 time to fit residues: 78.7359 Evaluate side-chains 243 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 181 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain B residue 197 SER 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 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 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 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 174 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 292 VAL 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 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL 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 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 292 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 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 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ILE 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 345 VAL 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 414 LEU Chi-restraints excluded: chain D residue 424 SER 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 58 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13796 Z= 0.158 Angle : 0.526 8.982 18768 Z= 0.263 Chirality : 0.044 0.161 2104 Planarity : 0.004 0.051 2472 Dihedral : 7.503 169.444 2018 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 4.77 % Allowed : 19.44 % Favored : 75.78 % 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: -0.75 (0.20), residues: 1824 helix: 0.66 (0.20), residues: 704 sheet: -1.18 (0.34), residues: 196 loop : -1.25 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 310 HIS 0.006 0.001 HIS A 409 PHE 0.006 0.001 PHE C 316 TYR 0.019 0.001 TYR D 129 ARG 0.003 0.000 ARG C 256 *********************** 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 273 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 206 time to evaluate : 1.423 Fit side-chains REVERT: B 56 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7162 (mt-10) REVERT: B 279 LYS cc_start: 0.8414 (tptm) cc_final: 0.7442 (mttt) REVERT: A 89 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8408 (ptpp) REVERT: A 146 ASP cc_start: 0.8008 (t0) cc_final: 0.7459 (t70) REVERT: A 172 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7327 (tptt) REVERT: C 35 GLU cc_start: 0.7996 (tt0) cc_final: 0.7792 (tt0) REVERT: C 279 LYS cc_start: 0.8523 (tptm) cc_final: 0.7481 (mttt) REVERT: D 172 LYS cc_start: 0.7410 (ttpp) cc_final: 0.7045 (tptt) REVERT: D 441 GLU cc_start: 0.8099 (mp0) cc_final: 0.6968 (pt0) outliers start: 67 outliers final: 56 residues processed: 258 average time/residue: 0.2056 time to fit residues: 82.1644 Evaluate side-chains 249 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 193 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain B residue 197 SER 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 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 173 VAL Chi-restraints excluded: chain A residue 174 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 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 197 SER 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 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 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE 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 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 167 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13796 Z= 0.162 Angle : 0.534 11.585 18768 Z= 0.265 Chirality : 0.044 0.150 2104 Planarity : 0.004 0.050 2472 Dihedral : 7.305 165.344 2016 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 5.06 % Allowed : 19.30 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1824 helix: 0.85 (0.20), residues: 704 sheet: -0.92 (0.34), residues: 196 loop : -1.11 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 310 HIS 0.007 0.001 HIS D 409 PHE 0.006 0.001 PHE C 316 TYR 0.017 0.001 TYR D 451 ARG 0.004 0.000 ARG C 256 *********************** 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 275 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 204 time to evaluate : 1.477 Fit side-chains REVERT: B 279 LYS cc_start: 0.8342 (tptm) cc_final: 0.7453 (mttt) REVERT: A 89 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8435 (ptpp) REVERT: A 146 ASP cc_start: 0.7875 (t0) cc_final: 0.7316 (t70) REVERT: A 172 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7322 (tptt) REVERT: A 441 GLU cc_start: 0.8152 (mp0) cc_final: 0.7064 (pt0) REVERT: C 35 GLU cc_start: 0.7957 (tt0) cc_final: 0.7754 (tt0) REVERT: C 185 THR cc_start: 0.8416 (m) cc_final: 0.8080 (m) REVERT: C 279 LYS cc_start: 0.8472 (tptm) cc_final: 0.7420 (mttt) REVERT: D 89 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8393 (ptpp) REVERT: D 172 LYS cc_start: 0.7370 (ttpp) cc_final: 0.6992 (tptt) REVERT: D 287 ASP cc_start: 0.6881 (m-30) cc_final: 0.6651 (t70) REVERT: D 441 GLU cc_start: 0.8024 (mp0) cc_final: 0.6920 (pt0) outliers start: 71 outliers final: 55 residues processed: 255 average time/residue: 0.2144 time to fit residues: 83.5624 Evaluate side-chains 245 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 190 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 SER 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 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 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 174 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 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 91 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 292 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 42 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 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** ** C 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13796 Z= 0.424 Angle : 0.662 10.478 18768 Z= 0.333 Chirality : 0.049 0.199 2104 Planarity : 0.005 0.050 2472 Dihedral : 7.665 167.995 2016 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 5.70 % Allowed : 18.95 % Favored : 75.36 % 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: -0.89 (0.20), residues: 1824 helix: 0.43 (0.20), residues: 688 sheet: -0.87 (0.34), residues: 204 loop : -1.29 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 310 HIS 0.012 0.001 HIS D 409 PHE 0.019 0.001 PHE D 230 TYR 0.019 0.002 TYR D 451 ARG 0.005 0.001 ARG C 336 *********************** 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 251 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 171 time to evaluate : 1.422 Fit side-chains REVERT: B 56 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7290 (mt-10) REVERT: B 279 LYS cc_start: 0.8509 (tptm) cc_final: 0.7543 (mttt) REVERT: A 146 ASP cc_start: 0.8080 (t0) cc_final: 0.7503 (t70) REVERT: C 35 GLU cc_start: 0.8177 (tt0) cc_final: 0.7955 (tt0) REVERT: C 279 LYS cc_start: 0.8557 (tptm) cc_final: 0.7566 (mttt) outliers start: 80 outliers final: 71 residues processed: 234 average time/residue: 0.2167 time to fit residues: 77.6544 Evaluate side-chains 231 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 160 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE 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 177 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 SER 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 B residue 445 VAL Chi-restraints excluded: chain A residue 42 SER 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 118 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 292 VAL 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 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 177 VAL 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 246 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 293 LEU 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 C residue 445 VAL Chi-restraints excluded: chain D residue 42 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 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 292 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 424 SER 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 157 optimal weight: 0.0370 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13796 Z= 0.162 Angle : 0.565 12.080 18768 Z= 0.278 Chirality : 0.045 0.154 2104 Planarity : 0.004 0.050 2472 Dihedral : 7.574 171.400 2016 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 3.99 % Allowed : 20.87 % Favored : 75.14 % 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: -0.48 (0.20), residues: 1824 helix: 0.81 (0.20), residues: 700 sheet: -0.81 (0.35), residues: 196 loop : -1.07 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 310 HIS 0.005 0.001 HIS D 409 PHE 0.015 0.001 PHE D 230 TYR 0.017 0.001 TYR A 451 ARG 0.003 0.000 ARG C 256 *********************** 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 240 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 184 time to evaluate : 1.315 Fit side-chains REVERT: B 279 LYS cc_start: 0.8314 (tptm) cc_final: 0.7401 (mttt) REVERT: B 437 MET cc_start: 0.8318 (ptm) cc_final: 0.8107 (ttp) REVERT: A 89 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8481 (ptpp) REVERT: A 146 ASP cc_start: 0.8073 (t0) cc_final: 0.7528 (t70) REVERT: C 279 LYS cc_start: 0.8444 (tptm) cc_final: 0.7435 (mttt) REVERT: C 437 MET cc_start: 0.8254 (ptm) cc_final: 0.7994 (ttp) REVERT: D 89 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8486 (ptpp) REVERT: D 287 ASP cc_start: 0.6947 (m-30) cc_final: 0.6738 (t70) outliers start: 56 outliers final: 42 residues processed: 230 average time/residue: 0.2342 time to fit residues: 81.3872 Evaluate side-chains 221 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 177 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 385 SER 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 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 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 212 VAL 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 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 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 223 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 chunk 165 optimal weight: 0.6980 chunk 142 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 0.1980 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13796 Z= 0.170 Angle : 0.565 11.184 18768 Z= 0.279 Chirality : 0.044 0.168 2104 Planarity : 0.004 0.049 2472 Dihedral : 7.529 173.072 2016 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 3.42 % Allowed : 21.01 % Favored : 75.57 % 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: -0.33 (0.20), residues: 1824 helix: 0.94 (0.21), residues: 700 sheet: -0.64 (0.35), residues: 196 loop : -1.02 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 310 HIS 0.005 0.001 HIS A 409 PHE 0.016 0.001 PHE A 230 TYR 0.017 0.001 TYR D 451 ARG 0.004 0.000 ARG B 256 ********************** 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 230 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 1.507 Fit side-chains REVERT: B 279 LYS cc_start: 0.8376 (tptm) cc_final: 0.7440 (mttt) REVERT: A 89 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8466 (ptpp) REVERT: A 146 ASP cc_start: 0.8017 (t0) cc_final: 0.7490 (t70) REVERT: C 279 LYS cc_start: 0.8469 (tptm) cc_final: 0.7469 (mttt) REVERT: C 437 MET cc_start: 0.8266 (ptm) cc_final: 0.8031 (ttp) REVERT: D 89 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8469 (ptpp) outliers start: 48 outliers final: 46 residues processed: 221 average time/residue: 0.2321 time to fit residues: 77.4209 Evaluate side-chains 222 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 177 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 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 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 289 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR 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 42 SER Chi-restraints excluded: chain C residue 91 VAL 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 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 118 THR Chi-restraints excluded: chain D residue 173 VAL 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 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 152 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.0270 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.130336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.107139 restraints weight = 17407.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109600 restraints weight = 12219.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.111293 restraints weight = 9600.795| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13796 Z= 0.164 Angle : 0.557 11.105 18768 Z= 0.275 Chirality : 0.044 0.159 2104 Planarity : 0.004 0.049 2472 Dihedral : 7.623 178.401 2016 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 3.70 % Allowed : 20.87 % 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: -0.22 (0.20), residues: 1824 helix: 0.99 (0.20), residues: 704 sheet: -0.50 (0.36), residues: 196 loop : -0.94 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 310 HIS 0.006 0.001 HIS A 409 PHE 0.007 0.001 PHE D 230 TYR 0.016 0.001 TYR A 451 ARG 0.004 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2587.84 seconds wall clock time: 47 minutes 16.71 seconds (2836.71 seconds total)