Starting phenix.real_space_refine on Thu Sep 26 15:53:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/09_2024/7xnz_33331_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/09_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_33331/09_2024/7xnz_33331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/09_2024/7xnz_33331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/09_2024/7xnz_33331_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/09_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.93, per 1000 atoms: 0.59 Number of scatterers: 13524 At special positions: 0 Unit cell: (86.67, 146.59, 84.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 4 15.00 O 2640 8.00 N 2336 7.00 C 8484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.8 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 20 sheets defined 42.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 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: 3.66 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4493 1.34 - 1.45: 1552 1.45 - 1.57: 7643 1.57 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 13796 Sorted by residual: bond pdb=" N THR D 329 " pdb=" CA THR D 329 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.20e+00 bond pdb=" N LEU D 344 " pdb=" CA LEU D 344 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.12e+00 bond pdb=" N VAL C 345 " pdb=" CA VAL C 345 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.24e+00 bond pdb=" N HIS C 346 " pdb=" CA HIS C 346 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.26e-02 6.30e+03 6.19e+00 bond pdb=" N ALA B 343 " pdb=" CA ALA B 343 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.10e+00 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 18498 2.14 - 4.28: 264 4.28 - 6.42: 1 6.42 - 8.55: 3 8.55 - 10.69: 2 Bond angle restraints: 18768 Sorted by residual: angle pdb=" C SER B 328 " pdb=" N THR B 329 " pdb=" CA THR B 329 " ideal model delta sigma weight residual 122.92 133.61 -10.69 1.76e+00 3.23e-01 3.69e+01 angle pdb=" C SER C 328 " pdb=" N THR C 329 " pdb=" CA THR C 329 " ideal model delta sigma weight residual 122.92 133.35 -10.43 1.76e+00 3.23e-01 3.51e+01 angle pdb=" CA PRO B 342 " pdb=" C PRO B 342 " pdb=" O PRO B 342 " ideal model delta sigma weight residual 121.31 117.17 4.14 7.40e-01 1.83e+00 3.13e+01 angle pdb=" CA PRO D 342 " pdb=" C PRO D 342 " pdb=" O PRO D 342 " ideal model delta sigma weight residual 121.38 117.24 4.14 7.70e-01 1.69e+00 2.89e+01 angle pdb=" C SER A 328 " pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 122.92 130.73 -7.81 1.76e+00 3.23e-01 1.97e+01 ... (remaining 18763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 8076 33.07 - 66.15: 136 66.15 - 99.22: 6 99.22 - 132.30: 0 132.30 - 165.37: 2 Dihedral angle restraints: 8220 sinusoidal: 3124 harmonic: 5096 Sorted by residual: dihedral pdb=" C5A PLP D 501 " pdb=" O4P PLP D 501 " pdb=" P PLP D 501 " pdb=" O1P PLP D 501 " ideal model delta sinusoidal sigma weight residual 76.43 -118.20 -165.37 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5A PLP A 501 " pdb=" O4P PLP A 501 " pdb=" P PLP A 501 " pdb=" O1P PLP A 501 " ideal model delta sinusoidal sigma weight residual 76.43 -118.24 -165.33 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5A PLP C 501 " pdb=" O4P PLP C 501 " pdb=" P PLP C 501 " pdb=" O1P PLP C 501 " ideal model delta sinusoidal sigma weight residual 76.43 1.22 75.20 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 8217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1474 0.041 - 0.083: 433 0.083 - 0.124: 184 0.124 - 0.165: 9 0.165 - 0.207: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA LEU A 341 " pdb=" N LEU A 341 " pdb=" C LEU A 341 " pdb=" CB LEU A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL C 345 " pdb=" N VAL C 345 " pdb=" C VAL C 345 " pdb=" CB VAL C 345 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ALA A 343 " pdb=" N ALA A 343 " pdb=" C ALA A 343 " pdb=" CB ALA A 343 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 2101 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C GLN B 327 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN B 327 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 328 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 327 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C GLN C 327 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN C 327 " 0.012 2.00e-02 2.50e+03 pdb=" N SER C 328 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 340 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ALA C 340 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA C 340 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU C 341 " 0.009 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 447 2.70 - 3.25: 14878 3.25 - 3.80: 20654 3.80 - 4.35: 27125 4.35 - 4.90: 44982 Nonbonded interactions: 108086 Sorted by model distance: nonbonded pdb=" O PRO A 145 " pdb=" ND2 ASN A 150 " model vdw 2.146 3.120 nonbonded pdb=" O PRO C 145 " pdb=" ND2 ASN C 150 " model vdw 2.146 3.120 nonbonded pdb=" O PRO D 145 " pdb=" ND2 ASN D 150 " model vdw 2.146 3.120 nonbonded pdb=" O PRO B 145 " pdb=" ND2 ASN B 150 " model vdw 2.147 3.120 nonbonded pdb=" O LEU C 265 " pdb=" N GLY C 298 " model vdw 2.152 3.120 ... (remaining 108081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.340 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- 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 : 1.328 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: 0.2628 time to fit residues: 131.5640 Evaluate side-chains 216 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13796 Z= 0.292 Angle : 0.650 9.043 18768 Z= 0.331 Chirality : 0.048 0.184 2104 Planarity : 0.005 0.059 2472 Dihedral : 8.378 158.953 2028 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 4.99 % Allowed : 12.82 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.19), residues: 1824 helix: -0.93 (0.20), residues: 688 sheet: -2.55 (0.31), residues: 180 loop : -2.28 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 310 HIS 0.009 0.002 HIS D 409 PHE 0.005 0.001 PHE A 92 TYR 0.019 0.002 TYR D 129 ARG 0.004 0.001 ARG C 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 227 time to evaluate : 1.606 Fit side-chains REVERT: B 150 ASN cc_start: 0.8691 (t0) cc_final: 0.8400 (m-40) REVERT: B 279 LYS cc_start: 0.8631 (tptm) cc_final: 0.7944 (mttt) REVERT: A 146 ASP cc_start: 0.8203 (t0) cc_final: 0.7669 (t70) REVERT: A 172 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7263 (tptt) REVERT: C 150 ASN cc_start: 0.8709 (t0) cc_final: 0.8392 (m-40) REVERT: D 172 LYS cc_start: 0.7603 (ttpp) cc_final: 0.7229 (tptt) outliers start: 70 outliers final: 36 residues processed: 277 average time/residue: 0.2080 time to fit residues: 90.8199 Evaluate side-chains 237 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN D 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13796 Z= 0.243 Angle : 0.596 8.232 18768 Z= 0.302 Chirality : 0.046 0.216 2104 Planarity : 0.005 0.047 2472 Dihedral : 7.483 137.838 2020 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 5.77 % Allowed : 16.52 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.19), residues: 1824 helix: -0.28 (0.20), residues: 692 sheet: -2.07 (0.33), residues: 180 loop : -1.94 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 310 HIS 0.007 0.001 HIS D 409 PHE 0.004 0.001 PHE C 316 TYR 0.018 0.001 TYR A 451 ARG 0.003 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 286 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 205 time to evaluate : 1.324 Fit side-chains REVERT: B 279 LYS cc_start: 0.8590 (tptm) cc_final: 0.7719 (mttt) REVERT: A 146 ASP cc_start: 0.8203 (t0) cc_final: 0.7664 (t0) REVERT: A 172 LYS cc_start: 0.7671 (ttpp) cc_final: 0.7286 (tptt) REVERT: C 279 LYS cc_start: 0.8493 (tptm) cc_final: 0.7883 (mttt) REVERT: D 172 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7384 (tptt) outliers start: 81 outliers final: 48 residues processed: 268 average time/residue: 0.2190 time to fit residues: 88.6608 Evaluate side-chains 234 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 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 305 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 104 ASN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 66 THR 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 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.8100 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13796 Z= 0.170 Angle : 0.560 9.463 18768 Z= 0.283 Chirality : 0.045 0.202 2104 Planarity : 0.005 0.051 2472 Dihedral : 6.861 129.176 2018 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer: Outliers : 4.34 % Allowed : 19.16 % Favored : 76.50 % 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: -1.45 (0.20), residues: 1824 helix: 0.25 (0.21), residues: 692 sheet: -2.08 (0.32), residues: 196 loop : -1.66 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 310 HIS 0.007 0.001 HIS D 409 PHE 0.005 0.001 PHE D 176 TYR 0.021 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 278 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 217 time to evaluate : 1.824 Fit side-chains REVERT: B 103 ARG cc_start: 0.7782 (ptt180) cc_final: 0.7527 (ptm-80) REVERT: B 279 LYS cc_start: 0.8493 (tptm) cc_final: 0.7595 (mttt) REVERT: B 289 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8835 (tt) REVERT: A 146 ASP cc_start: 0.8177 (t0) cc_final: 0.7654 (t70) REVERT: A 172 LYS cc_start: 0.7595 (ttpp) cc_final: 0.7226 (tptt) REVERT: A 221 TYR cc_start: 0.8494 (m-80) cc_final: 0.8134 (m-80) REVERT: A 279 LYS cc_start: 0.8763 (tptp) cc_final: 0.8203 (tppt) REVERT: C 103 ARG cc_start: 0.7752 (ptt180) cc_final: 0.7531 (ptm-80) REVERT: C 279 LYS cc_start: 0.8468 (tptm) cc_final: 0.7597 (mttt) REVERT: D 172 LYS cc_start: 0.7650 (ttpp) cc_final: 0.7304 (tptt) outliers start: 61 outliers final: 39 residues processed: 261 average time/residue: 0.2268 time to fit residues: 90.8193 Evaluate side-chains 231 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL 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 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL 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: 0.0970 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13796 Z= 0.326 Angle : 0.616 8.290 18768 Z= 0.312 Chirality : 0.047 0.211 2104 Planarity : 0.005 0.051 2472 Dihedral : 6.837 125.494 2018 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 6.41 % Allowed : 17.59 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1824 helix: 0.19 (0.20), residues: 692 sheet: -1.64 (0.33), residues: 204 loop : -1.58 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 310 HIS 0.008 0.001 HIS A 409 PHE 0.006 0.001 PHE B 316 TYR 0.017 0.002 TYR D 451 ARG 0.005 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 192 time to evaluate : 1.353 Fit side-chains REVERT: B 279 LYS cc_start: 0.8529 (tptm) cc_final: 0.7622 (mttt) REVERT: B 289 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8825 (tt) REVERT: A 106 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8582 (mt) REVERT: A 146 ASP cc_start: 0.8192 (t0) cc_final: 0.7634 (t70) REVERT: A 172 LYS cc_start: 0.7884 (ttpp) cc_final: 0.7499 (tptt) REVERT: A 311 MET cc_start: 0.8627 (mmm) cc_final: 0.8278 (tpt) REVERT: A 332 ASP cc_start: 0.7969 (m-30) cc_final: 0.7442 (t0) REVERT: C 279 LYS cc_start: 0.8490 (tptm) cc_final: 0.7585 (mttt) REVERT: D 311 MET cc_start: 0.8616 (mmm) cc_final: 0.8254 (tpt) outliers start: 90 outliers final: 66 residues processed: 258 average time/residue: 0.2385 time to fit residues: 93.8661 Evaluate side-chains 246 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 178 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 290 ILE 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 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 278 LEU 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 47 ILE Chi-restraints excluded: chain C residue 66 THR 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 196 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE 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 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 177 VAL Chi-restraints excluded: chain D residue 187 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 14 optimal weight: 0.0060 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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** ** D 84 GLN ** 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: 0.8141 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13796 Z= 0.219 Angle : 0.572 10.217 18768 Z= 0.287 Chirality : 0.045 0.184 2104 Planarity : 0.005 0.051 2472 Dihedral : 6.463 112.577 2018 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 5.77 % Allowed : 18.16 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1824 helix: 0.40 (0.20), residues: 704 sheet: -1.63 (0.34), residues: 196 loop : -1.31 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 310 HIS 0.006 0.001 HIS D 409 PHE 0.006 0.001 PHE B 316 TYR 0.022 0.002 TYR A 129 ARG 0.004 0.000 ARG B 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 270 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 189 time to evaluate : 1.444 Fit side-chains REVERT: B 9 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7568 (mm-30) REVERT: B 164 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: B 279 LYS cc_start: 0.8463 (tptm) cc_final: 0.7522 (mttt) REVERT: B 289 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8859 (tt) REVERT: A 146 ASP cc_start: 0.8151 (t0) cc_final: 0.7599 (t70) REVERT: A 172 LYS cc_start: 0.7867 (ttpp) cc_final: 0.7489 (tptt) REVERT: C 9 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7557 (mm-30) REVERT: C 103 ARG cc_start: 0.7731 (ptt180) cc_final: 0.7467 (ptm-80) REVERT: C 164 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: C 279 LYS cc_start: 0.8474 (tptm) cc_final: 0.7489 (mttt) REVERT: D 287 ASP cc_start: 0.7129 (m-30) cc_final: 0.6839 (t70) outliers start: 81 outliers final: 58 residues processed: 250 average time/residue: 0.2380 time to fit residues: 91.7288 Evaluate side-chains 244 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 183 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 150 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 LEU 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 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 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 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 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 424 SER 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: 0.9990 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13796 Z= 0.180 Angle : 0.564 9.536 18768 Z= 0.283 Chirality : 0.044 0.163 2104 Planarity : 0.005 0.051 2472 Dihedral : 6.036 95.234 2018 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 5.20 % Allowed : 18.30 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1824 helix: 0.66 (0.20), residues: 700 sheet: -1.40 (0.35), residues: 196 loop : -1.07 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 310 HIS 0.007 0.001 HIS A 409 PHE 0.006 0.001 PHE D 176 TYR 0.014 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 278 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 205 time to evaluate : 1.376 Fit side-chains REVERT: B 279 LYS cc_start: 0.8361 (tptm) cc_final: 0.7460 (mttt) REVERT: B 289 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8746 (tt) REVERT: B 301 TYR cc_start: 0.8724 (m-80) cc_final: 0.8339 (m-80) REVERT: B 397 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6673 (mt-10) REVERT: A 146 ASP cc_start: 0.8135 (t0) cc_final: 0.7582 (t70) REVERT: A 172 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7470 (tptt) REVERT: C 164 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: C 279 LYS cc_start: 0.8405 (tptm) cc_final: 0.7455 (mttt) REVERT: D 172 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7337 (tptt) REVERT: D 221 TYR cc_start: 0.8578 (m-80) cc_final: 0.8146 (m-80) REVERT: D 287 ASP cc_start: 0.7088 (m-30) cc_final: 0.6754 (t70) outliers start: 73 outliers final: 60 residues processed: 258 average time/residue: 0.2394 time to fit residues: 91.7729 Evaluate side-chains 255 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 193 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 150 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 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 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 278 LEU 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 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 293 LEU 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 17 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 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: 2.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 136 optimal weight: 4.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- 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 84 GLN ** 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: 0.8149 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13796 Z= 0.265 Angle : 0.600 9.042 18768 Z= 0.300 Chirality : 0.046 0.172 2104 Planarity : 0.005 0.051 2472 Dihedral : 5.951 88.170 2018 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer: Outliers : 5.91 % Allowed : 18.16 % Favored : 75.93 % 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: -0.62 (0.20), residues: 1824 helix: 0.66 (0.20), residues: 700 sheet: -1.10 (0.35), residues: 204 loop : -1.06 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 310 HIS 0.010 0.001 HIS A 409 PHE 0.007 0.001 PHE C 316 TYR 0.019 0.002 TYR D 129 ARG 0.004 0.000 ARG B 256 *********************** 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 274 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 191 time to evaluate : 1.506 Fit side-chains REVERT: B 9 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7586 (mm-30) REVERT: B 60 GLN cc_start: 0.7507 (mt0) cc_final: 0.7183 (mt0) REVERT: B 164 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: B 279 LYS cc_start: 0.8444 (tptm) cc_final: 0.7495 (mttt) REVERT: B 289 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8751 (tt) REVERT: B 296 ASP cc_start: 0.8477 (t0) cc_final: 0.8276 (t0) REVERT: B 332 ASP cc_start: 0.8343 (m-30) cc_final: 0.8139 (m-30) REVERT: A 146 ASP cc_start: 0.8199 (t0) cc_final: 0.7654 (t70) REVERT: A 332 ASP cc_start: 0.7941 (m-30) cc_final: 0.7381 (t0) REVERT: C 9 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7592 (mm-30) REVERT: C 60 GLN cc_start: 0.7528 (mt0) cc_final: 0.7210 (mt0) REVERT: C 164 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: C 279 LYS cc_start: 0.8484 (tptm) cc_final: 0.7509 (mttt) REVERT: C 437 MET cc_start: 0.8185 (ptm) cc_final: 0.7914 (ttp) REVERT: D 287 ASP cc_start: 0.7140 (m-30) cc_final: 0.6819 (t70) outliers start: 83 outliers final: 75 residues processed: 254 average time/residue: 0.2196 time to fit residues: 85.4655 Evaluate side-chains 257 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 179 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 278 LEU 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 355 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 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 385 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 355 ASP 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 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.3980 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 0.0770 chunk 161 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.5942 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13796 Z= 0.166 Angle : 0.573 11.326 18768 Z= 0.285 Chirality : 0.044 0.146 2104 Planarity : 0.004 0.051 2472 Dihedral : 5.531 69.808 2018 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Rotamer: Outliers : 5.13 % Allowed : 19.02 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1824 helix: 0.88 (0.20), residues: 704 sheet: -1.13 (0.36), residues: 196 loop : -0.93 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 310 HIS 0.008 0.001 HIS D 409 PHE 0.008 0.001 PHE D 316 TYR 0.017 0.001 TYR A 451 ARG 0.004 0.000 ARG B 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 274 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 202 time to evaluate : 1.465 Fit side-chains REVERT: B 60 GLN cc_start: 0.7513 (mt0) cc_final: 0.7245 (mt0) REVERT: B 164 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: B 279 LYS cc_start: 0.8336 (tptm) cc_final: 0.7416 (mttt) REVERT: B 289 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8629 (tt) REVERT: B 301 TYR cc_start: 0.8698 (m-80) cc_final: 0.8265 (m-80) REVERT: B 397 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6655 (mt-10) REVERT: A 146 ASP cc_start: 0.8114 (t0) cc_final: 0.7565 (t70) REVERT: A 172 LYS cc_start: 0.7850 (ttpp) cc_final: 0.7459 (tptt) REVERT: A 221 TYR cc_start: 0.8565 (m-80) cc_final: 0.8163 (m-80) REVERT: A 287 ASP cc_start: 0.7155 (m-30) cc_final: 0.6777 (t70) REVERT: A 332 ASP cc_start: 0.7960 (m-30) cc_final: 0.7382 (t0) REVERT: C 60 GLN cc_start: 0.7535 (mt0) cc_final: 0.7273 (mt0) REVERT: C 164 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: C 279 LYS cc_start: 0.8396 (tptm) cc_final: 0.7390 (mttt) REVERT: C 397 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6667 (mt-10) REVERT: D 146 ASP cc_start: 0.8054 (t0) cc_final: 0.7481 (t70) REVERT: D 221 TYR cc_start: 0.8612 (m-80) cc_final: 0.8216 (m-80) REVERT: D 287 ASP cc_start: 0.7099 (m-30) cc_final: 0.6852 (t70) outliers start: 72 outliers final: 62 residues processed: 253 average time/residue: 0.2255 time to fit residues: 85.8929 Evaluate side-chains 254 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 189 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 150 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 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 385 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 355 ASP 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: 0.9990 chunk 104 optimal weight: 0.0040 chunk 81 optimal weight: 0.9980 chunk 118 optimal weight: 0.0570 chunk 179 optimal weight: 0.4980 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5110 ------------------------------------------------------------------------------- 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: 0.8069 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13796 Z= 0.163 Angle : 0.583 12.325 18768 Z= 0.289 Chirality : 0.044 0.149 2104 Planarity : 0.005 0.050 2472 Dihedral : 5.245 57.426 2018 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Rotamer: Outliers : 4.77 % Allowed : 19.23 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1824 helix: 0.99 (0.20), residues: 704 sheet: -1.01 (0.36), residues: 196 loop : -0.86 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 310 HIS 0.009 0.001 HIS D 409 PHE 0.007 0.001 PHE D 316 TYR 0.018 0.001 TYR D 129 ARG 0.007 0.000 ARG D 361 ********************** 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 263 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 196 time to evaluate : 1.434 Fit side-chains REVERT: B 60 GLN cc_start: 0.7549 (mt0) cc_final: 0.7267 (mt0) REVERT: B 164 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: B 279 LYS cc_start: 0.8301 (tptm) cc_final: 0.7397 (mttt) REVERT: B 289 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8600 (tt) REVERT: B 301 TYR cc_start: 0.8632 (m-80) cc_final: 0.8246 (m-80) REVERT: B 397 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6654 (mt-10) REVERT: A 138 ASP cc_start: 0.8113 (m-30) cc_final: 0.7855 (m-30) REVERT: A 146 ASP cc_start: 0.8064 (t0) cc_final: 0.7528 (t70) REVERT: A 172 LYS cc_start: 0.7857 (ttpp) cc_final: 0.7513 (tptt) REVERT: A 221 TYR cc_start: 0.8605 (m-80) cc_final: 0.8204 (m-80) REVERT: A 287 ASP cc_start: 0.7133 (m-30) cc_final: 0.6781 (t70) REVERT: A 332 ASP cc_start: 0.7942 (m-30) cc_final: 0.7383 (t0) REVERT: C 60 GLN cc_start: 0.7554 (mt0) cc_final: 0.7269 (mt0) REVERT: C 164 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: C 279 LYS cc_start: 0.8393 (tptm) cc_final: 0.7440 (mttt) REVERT: C 437 MET cc_start: 0.8153 (ptm) cc_final: 0.7929 (ttp) REVERT: D 146 ASP cc_start: 0.7990 (t0) cc_final: 0.7463 (t70) REVERT: D 221 TYR cc_start: 0.8602 (m-80) cc_final: 0.8254 (m-80) REVERT: D 287 ASP cc_start: 0.7092 (m-30) cc_final: 0.6849 (t70) outliers start: 67 outliers final: 58 residues processed: 246 average time/residue: 0.2108 time to fit residues: 79.3666 Evaluate side-chains 250 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 189 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 355 ASP 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 91 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 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 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 414 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR 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: 4.9990 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 0.0470 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 overall best weight: 1.6882 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.126102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.102046 restraints weight = 17534.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104471 restraints weight = 12473.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.106155 restraints weight = 9906.117| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13796 Z= 0.284 Angle : 0.618 11.543 18768 Z= 0.309 Chirality : 0.046 0.153 2104 Planarity : 0.005 0.051 2472 Dihedral : 5.548 65.970 2016 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 4.99 % Allowed : 19.09 % Favored : 75.93 % 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: -0.38 (0.20), residues: 1824 helix: 0.86 (0.20), residues: 700 sheet: -0.88 (0.36), residues: 204 loop : -0.95 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 310 HIS 0.010 0.001 HIS A 409 PHE 0.007 0.001 PHE C 316 TYR 0.018 0.002 TYR D 451 ARG 0.006 0.000 ARG D 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2700.39 seconds wall clock time: 49 minutes 11.25 seconds (2951.25 seconds total)