Starting phenix.real_space_refine on Sat Mar 16 11:57:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/03_2024/7u9g_26397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/03_2024/7u9g_26397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/03_2024/7u9g_26397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/03_2024/7u9g_26397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/03_2024/7u9g_26397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/03_2024/7u9g_26397.pdb" } resolution = 3.39 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= 0.002 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 9198 2.51 5 N 2457 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14553 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3041 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 25, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3041 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 25, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3041 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 25, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "G" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "I" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.96, per 1000 atoms: 0.55 Number of scatterers: 14553 At special positions: 0 Unit cell: (122.1, 115.5, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2802 8.00 N 2457 7.00 C 9198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 207 " distance=2.02 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 283 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 207 " distance=2.02 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 207 " distance=2.02 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 228 " distance=2.03 Simple disulfide: pdb=" SG CYS C 223 " - pdb=" SG CYS C 252 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 239 " - pdb=" SG CYS G 312 " distance=2.04 Simple disulfide: pdb=" SG CYS H 239 " - pdb=" SG CYS H 312 " distance=2.04 Simple disulfide: pdb=" SG CYS I 239 " - pdb=" SG CYS I 312 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 319 " " NAG A 502 " - " ASN A 158 " " NAG A 503 " - " ASN A 247 " " NAG B 501 " - " ASN B 319 " " NAG B 502 " - " ASN B 158 " " NAG B 503 " - " ASN B 247 " " NAG C 501 " - " ASN C 319 " " NAG C 502 " - " ASN C 247 " " NAG C 503 " - " ASN C 158 " Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.5 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 42 sheets defined 17.1% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.671A pdb=" N GLU A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.150A pdb=" N ASN A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 276 through 294 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.262A pdb=" N ILE A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.784A pdb=" N SER A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.033A pdb=" N LEU A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 90 through 104 Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.671A pdb=" N GLU B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 4.151A pdb=" N ASN B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 276 through 294 Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 334 through 339 removed outlier: 4.263A pdb=" N ILE B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.785A pdb=" N SER B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.034A pdb=" N LEU B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.671A pdb=" N GLU C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 removed outlier: 4.150A pdb=" N ASN C 158 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 Processing helix chain 'C' and resid 276 through 294 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 334 through 339 removed outlier: 4.262A pdb=" N ILE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 380 removed outlier: 3.785A pdb=" N SER C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.034A pdb=" N LEU C 388 " --> pdb=" O HIS C 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.917A pdb=" N GLU D 84 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.916A pdb=" N GLU E 84 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.916A pdb=" N GLU F 84 " --> pdb=" O SER F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 281 Processing helix chain 'G' and resid 290 through 292 No H-bonds generated for 'chain 'G' and resid 290 through 292' Processing helix chain 'G' and resid 303 through 307 Processing helix chain 'H' and resid 278 through 281 Processing helix chain 'H' and resid 290 through 292 No H-bonds generated for 'chain 'H' and resid 290 through 292' Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'I' and resid 278 through 281 Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 218 removed outlier: 5.068A pdb=" N THR A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A 202 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 37 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET A 44 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 46 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TRP A 240 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 87 removed outlier: 3.530A pdb=" N GLY A 63 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 126 through 134 Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA7, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AA8, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 216 through 218 removed outlier: 5.067A pdb=" N THR B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 202 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 37 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET B 44 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 46 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TRP B 240 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 82 through 87 removed outlier: 3.530A pdb=" N GLY B 63 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 126 through 134 Processing sheet with id=AB5, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AB6, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AB7, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB8, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 216 through 218 removed outlier: 5.067A pdb=" N THR C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS C 202 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 37 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET C 44 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 46 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TRP C 240 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 82 through 87 removed outlier: 3.530A pdb=" N GLY C 63 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 126 through 134 Processing sheet with id=AC4, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AC5, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AC6, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AC7, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AC9, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.720A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AD3, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.720A pdb=" N GLY E 98 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AD5, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AD6, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.721A pdb=" N GLY F 98 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 220 through 224 Processing sheet with id=AD8, first strand: chain 'G' and resid 228 through 229 removed outlier: 3.824A pdb=" N GLY G 266 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG G 255 " --> pdb=" O TRP G 264 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP G 264 " --> pdb=" O ARG G 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 228 through 229 removed outlier: 4.457A pdb=" N VAL G 329 " --> pdb=" O ARG G 314 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER G 316 " --> pdb=" O MET G 327 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N MET G 327 " --> pdb=" O SER G 316 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 220 through 224 Processing sheet with id=AE2, first strand: chain 'H' and resid 228 through 229 removed outlier: 3.824A pdb=" N GLY H 266 " --> pdb=" O TRP H 253 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG H 255 " --> pdb=" O TRP H 264 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP H 264 " --> pdb=" O ARG H 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 228 through 229 removed outlier: 4.456A pdb=" N VAL H 329 " --> pdb=" O ARG H 314 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER H 316 " --> pdb=" O MET H 327 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N MET H 327 " --> pdb=" O SER H 316 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 220 through 224 Processing sheet with id=AE5, first strand: chain 'I' and resid 228 through 229 removed outlier: 3.824A pdb=" N GLY I 266 " --> pdb=" O TRP I 253 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG I 255 " --> pdb=" O TRP I 264 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP I 264 " --> pdb=" O ARG I 255 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 228 through 229 removed outlier: 4.457A pdb=" N VAL I 329 " --> pdb=" O ARG I 314 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER I 316 " --> pdb=" O MET I 327 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N MET I 327 " --> pdb=" O SER I 316 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1467 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: 5.08 Time building geometry restraints manager: 5.89 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: 4638 1.34 - 1.46: 3521 1.46 - 1.58: 6619 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 14916 Sorted by residual: bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.92e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C1 NAG B 503 " pdb=" O5 NAG B 503 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.65e+00 ... (remaining 14911 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.69: 573 106.69 - 113.54: 8284 113.54 - 120.39: 5312 120.39 - 127.23: 5880 127.23 - 134.08: 210 Bond angle restraints: 20259 Sorted by residual: angle pdb=" N HIS C 113 " pdb=" CA HIS C 113 " pdb=" C HIS C 113 " ideal model delta sigma weight residual 111.28 115.33 -4.05 1.09e+00 8.42e-01 1.38e+01 angle pdb=" N HIS B 113 " pdb=" CA HIS B 113 " pdb=" C HIS B 113 " ideal model delta sigma weight residual 111.28 115.27 -3.99 1.09e+00 8.42e-01 1.34e+01 angle pdb=" N HIS A 113 " pdb=" CA HIS A 113 " pdb=" C HIS A 113 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.32e+01 angle pdb=" N GLU A 267 " pdb=" CA GLU A 267 " pdb=" C GLU A 267 " ideal model delta sigma weight residual 111.14 114.57 -3.43 1.08e+00 8.57e-01 1.01e+01 angle pdb=" N GLU B 267 " pdb=" CA GLU B 267 " pdb=" C GLU B 267 " ideal model delta sigma weight residual 111.14 114.48 -3.34 1.08e+00 8.57e-01 9.57e+00 ... (remaining 20254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 8398 17.30 - 34.60: 512 34.60 - 51.90: 99 51.90 - 69.20: 21 69.20 - 86.51: 3 Dihedral angle restraints: 9033 sinusoidal: 3696 harmonic: 5337 Sorted by residual: dihedral pdb=" CB CYS A 24 " pdb=" SG CYS A 24 " pdb=" SG CYS A 283 " pdb=" CB CYS A 283 " ideal model delta sinusoidal sigma weight residual 93.00 146.41 -53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 283 " pdb=" CB CYS B 283 " ideal model delta sinusoidal sigma weight residual 93.00 146.40 -53.40 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 283 " pdb=" CB CYS C 283 " ideal model delta sinusoidal sigma weight residual 93.00 146.39 -53.39 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 9030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1500 0.040 - 0.080: 477 0.080 - 0.120: 226 0.120 - 0.160: 41 0.160 - 0.200: 9 Chirality restraints: 2253 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 158 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 158 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 2250 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 308 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.06e+00 pdb=" N PRO B 309 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 308 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO C 309 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 309 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 309 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 308 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO A 309 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " 0.034 5.00e-02 4.00e+02 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4190 2.81 - 3.34: 12376 3.34 - 3.86: 22701 3.86 - 4.38: 26055 4.38 - 4.90: 45596 Nonbonded interactions: 110918 Sorted by model distance: nonbonded pdb=" O PRO G 231 " pdb=" OG SER G 232 " model vdw 2.293 2.440 nonbonded pdb=" O PRO H 231 " pdb=" OG SER H 232 " model vdw 2.294 2.440 nonbonded pdb=" O PRO I 231 " pdb=" OG SER I 232 " model vdw 2.294 2.440 nonbonded pdb=" OG SER C 15 " pdb=" OE2 GLU C 324 " model vdw 2.389 2.440 nonbonded pdb=" OG SER B 15 " pdb=" OE2 GLU B 324 " model vdw 2.389 2.440 ... (remaining 110913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 4.230 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 40.070 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.007 0.052 14916 Z= 0.443 Angle : 0.771 7.143 20259 Z= 0.449 Chirality : 0.049 0.200 2253 Planarity : 0.005 0.062 2568 Dihedral : 11.019 86.505 5550 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: 0.29 (0.19), residues: 1830 helix: 0.19 (0.36), residues: 225 sheet: 0.84 (0.21), residues: 534 loop : -0.07 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 253 HIS 0.008 0.001 HIS A 113 PHE 0.022 0.002 PHE I 295 TYR 0.016 0.002 TYR G 322 ARG 0.005 0.001 ARG C 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7954 (mt) cc_final: 0.7746 (mm) REVERT: A 244 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8050 (tm-30) REVERT: A 323 MET cc_start: 0.8939 (mmt) cc_final: 0.8277 (mmt) REVERT: B 244 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8321 (tm-30) REVERT: B 323 MET cc_start: 0.8874 (mmt) cc_final: 0.8412 (mmt) REVERT: C 244 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8205 (tm-30) REVERT: D 79 LEU cc_start: 0.8590 (tp) cc_final: 0.8208 (tt) REVERT: D 86 ASP cc_start: 0.8727 (m-30) cc_final: 0.7932 (p0) REVERT: F 79 LEU cc_start: 0.8399 (tp) cc_final: 0.8143 (tt) REVERT: F 86 ASP cc_start: 0.8596 (m-30) cc_final: 0.7850 (p0) REVERT: G 233 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8537 (mm-30) REVERT: H 233 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8461 (mm-30) REVERT: H 244 ASP cc_start: 0.8341 (t70) cc_final: 0.8008 (t70) REVERT: H 246 MET cc_start: 0.8534 (mtp) cc_final: 0.8123 (mtp) REVERT: H 328 ASP cc_start: 0.8465 (m-30) cc_final: 0.8162 (m-30) REVERT: I 233 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8473 (mm-30) REVERT: I 244 ASP cc_start: 0.8438 (t70) cc_final: 0.8201 (t70) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2913 time to fit residues: 108.0115 Evaluate side-chains 164 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14916 Z= 0.257 Angle : 0.574 7.660 20259 Z= 0.304 Chirality : 0.042 0.209 2253 Planarity : 0.005 0.048 2568 Dihedral : 4.418 21.434 2205 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.05 % Allowed : 8.41 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1830 helix: 0.48 (0.37), residues: 210 sheet: 0.97 (0.20), residues: 576 loop : -0.15 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 36 HIS 0.003 0.001 HIS G 220 PHE 0.021 0.002 PHE G 295 TYR 0.015 0.001 TYR I 322 ARG 0.006 0.000 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8663 (mmp) cc_final: 0.8403 (mmm) REVERT: A 323 MET cc_start: 0.8867 (mmt) cc_final: 0.8425 (mmt) REVERT: B 244 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8267 (tm-30) REVERT: B 323 MET cc_start: 0.8809 (mmt) cc_final: 0.8583 (mmt) REVERT: C 179 MET cc_start: 0.8396 (mmm) cc_final: 0.8139 (mmm) REVERT: C 323 MET cc_start: 0.8731 (mmt) cc_final: 0.8186 (mmm) REVERT: D 80 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7010 (mmm-85) REVERT: E 50 TYR cc_start: 0.8144 (p90) cc_final: 0.7941 (p90) REVERT: F 76 ILE cc_start: 0.8703 (mp) cc_final: 0.8186 (mt) REVERT: F 80 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7821 (mmm-85) REVERT: G 233 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8458 (mm-30) REVERT: H 233 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8540 (mm-30) REVERT: H 244 ASP cc_start: 0.8295 (t70) cc_final: 0.8016 (t70) REVERT: I 218 GLN cc_start: 0.8602 (tp40) cc_final: 0.8335 (tp40) REVERT: I 233 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8361 (mm-30) REVERT: I 244 ASP cc_start: 0.8328 (t70) cc_final: 0.8127 (t70) outliers start: 17 outliers final: 12 residues processed: 180 average time/residue: 0.2679 time to fit residues: 70.4085 Evaluate side-chains 156 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 HIS B 261 HIS C 261 HIS E 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 14916 Z= 0.445 Angle : 0.638 7.079 20259 Z= 0.337 Chirality : 0.044 0.169 2253 Planarity : 0.005 0.046 2568 Dihedral : 4.660 25.406 2205 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.47 % Allowed : 9.03 % Favored : 88.50 % 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: -0.00 (0.19), residues: 1830 helix: 0.44 (0.37), residues: 207 sheet: 0.94 (0.22), residues: 510 loop : -0.54 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 36 HIS 0.004 0.001 HIS B 384 PHE 0.021 0.002 PHE G 295 TYR 0.020 0.002 TYR H 311 ARG 0.006 0.001 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8771 (p) REVERT: A 244 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8135 (tm-30) REVERT: A 323 MET cc_start: 0.8784 (mmt) cc_final: 0.8307 (mmt) REVERT: B 244 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8358 (tm-30) REVERT: C 102 MET cc_start: 0.9062 (mmm) cc_final: 0.8853 (mmm) REVERT: C 244 GLN cc_start: 0.9014 (mm110) cc_final: 0.8118 (tm-30) REVERT: C 323 MET cc_start: 0.8673 (mmt) cc_final: 0.8344 (mmt) REVERT: D 17 ARG cc_start: 0.9012 (mmm-85) cc_final: 0.8573 (ttm-80) REVERT: D 61 ASP cc_start: 0.8873 (m-30) cc_final: 0.8367 (t0) REVERT: E 17 ARG cc_start: 0.8939 (mmm-85) cc_final: 0.8554 (ttm-80) REVERT: E 79 LEU cc_start: 0.8978 (tt) cc_final: 0.8629 (tt) REVERT: E 106 LYS cc_start: 0.9312 (tttm) cc_final: 0.8931 (tptm) REVERT: F 80 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.7939 (mmm-85) REVERT: G 233 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8622 (mm-30) REVERT: H 233 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8617 (mm-30) REVERT: H 244 ASP cc_start: 0.8708 (t70) cc_final: 0.8450 (t70) REVERT: I 233 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8592 (mm-30) REVERT: I 244 ASP cc_start: 0.8434 (t70) cc_final: 0.8176 (t70) REVERT: I 246 MET cc_start: 0.8651 (mtp) cc_final: 0.8323 (mtp) outliers start: 40 outliers final: 28 residues processed: 179 average time/residue: 0.2722 time to fit residues: 71.5102 Evaluate side-chains 167 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 300 ASN Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain I residue 328 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14916 Z= 0.157 Angle : 0.511 6.270 20259 Z= 0.267 Chirality : 0.041 0.176 2253 Planarity : 0.004 0.044 2568 Dihedral : 4.087 19.006 2205 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.55 % Allowed : 10.58 % Favored : 87.88 % 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: 0.18 (0.19), residues: 1830 helix: 0.50 (0.38), residues: 192 sheet: 0.85 (0.21), residues: 570 loop : -0.32 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 330 HIS 0.002 0.000 HIS C 261 PHE 0.011 0.001 PHE I 295 TYR 0.016 0.001 TYR B 168 ARG 0.006 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.8787 (mmm) cc_final: 0.8521 (mmm) REVERT: A 244 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8150 (tm-30) REVERT: A 323 MET cc_start: 0.8779 (mmt) cc_final: 0.8351 (mmt) REVERT: B 171 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8573 (p) REVERT: B 244 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8503 (tm-30) REVERT: C 244 GLN cc_start: 0.9013 (mm110) cc_final: 0.8200 (tm-30) REVERT: C 323 MET cc_start: 0.8712 (mmt) cc_final: 0.8217 (mmm) REVERT: D 17 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8609 (ttm-80) REVERT: D 80 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7834 (mmm-85) REVERT: E 17 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.8524 (ttm-80) REVERT: E 54 LYS cc_start: 0.9321 (mttm) cc_final: 0.8965 (mmmm) REVERT: E 79 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8715 (tt) REVERT: F 80 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7826 (mmm-85) REVERT: G 233 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8569 (mm-30) REVERT: H 233 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8576 (mm-30) REVERT: H 244 ASP cc_start: 0.8478 (t70) cc_final: 0.8164 (t70) REVERT: I 218 GLN cc_start: 0.8602 (tp40) cc_final: 0.8350 (tp40) REVERT: I 233 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8652 (mm-30) REVERT: I 244 ASP cc_start: 0.8374 (t70) cc_final: 0.8121 (t70) REVERT: I 246 MET cc_start: 0.8436 (mtp) cc_final: 0.8181 (mtp) outliers start: 25 outliers final: 16 residues processed: 170 average time/residue: 0.2597 time to fit residues: 64.7918 Evaluate side-chains 166 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 300 ASN Chi-restraints excluded: chain H residue 328 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 14916 Z= 0.541 Angle : 0.673 6.719 20259 Z= 0.351 Chirality : 0.044 0.152 2253 Planarity : 0.005 0.046 2568 Dihedral : 4.688 23.774 2205 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.15 % Allowed : 10.02 % Favored : 86.83 % 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: -0.09 (0.19), residues: 1830 helix: 0.24 (0.37), residues: 207 sheet: 0.82 (0.21), residues: 558 loop : -0.59 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 36 HIS 0.005 0.001 HIS C 20 PHE 0.021 0.002 PHE G 295 TYR 0.020 0.002 TYR F 87 ARG 0.004 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 140 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.8854 (mmm) cc_final: 0.8557 (mmm) REVERT: A 323 MET cc_start: 0.8738 (mmt) cc_final: 0.8231 (mmt) REVERT: B 244 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8489 (tm-30) REVERT: C 244 GLN cc_start: 0.9065 (mm110) cc_final: 0.8173 (tm-30) REVERT: C 323 MET cc_start: 0.8686 (mmt) cc_final: 0.8311 (mmt) REVERT: D 17 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8569 (ttm-80) REVERT: E 17 ARG cc_start: 0.8941 (mmm-85) cc_final: 0.8478 (ttm-80) REVERT: E 79 LEU cc_start: 0.9137 (tt) cc_final: 0.8924 (tt) REVERT: F 12 ASP cc_start: 0.8202 (t70) cc_final: 0.7963 (t70) REVERT: G 233 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8726 (mm-30) REVERT: H 233 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8617 (mm-30) REVERT: H 244 ASP cc_start: 0.8793 (t70) cc_final: 0.8578 (t70) REVERT: H 292 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8833 (mtmm) REVERT: I 233 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8629 (mm-30) REVERT: I 281 LYS cc_start: 0.9400 (ttmm) cc_final: 0.9161 (ttmm) outliers start: 51 outliers final: 40 residues processed: 183 average time/residue: 0.2617 time to fit residues: 70.6912 Evaluate side-chains 174 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 300 ASN Chi-restraints excluded: chain H residue 320 VAL Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain I residue 239 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14916 Z= 0.144 Angle : 0.510 7.224 20259 Z= 0.263 Chirality : 0.041 0.170 2253 Planarity : 0.004 0.045 2568 Dihedral : 4.002 16.522 2205 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.67 % Allowed : 12.31 % Favored : 86.02 % 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: 0.14 (0.19), residues: 1830 helix: 0.44 (0.38), residues: 192 sheet: 0.77 (0.21), residues: 612 loop : -0.35 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 251 HIS 0.002 0.000 HIS B 21 PHE 0.011 0.001 PHE A 263 TYR 0.019 0.001 TYR C 168 ARG 0.004 0.000 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.336 Fit side-chains REVERT: A 102 MET cc_start: 0.8891 (mmm) cc_final: 0.8601 (mmm) REVERT: A 244 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8201 (tm-30) REVERT: A 323 MET cc_start: 0.8746 (mmt) cc_final: 0.8301 (mmt) REVERT: B 244 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8490 (tm-30) REVERT: C 179 MET cc_start: 0.8430 (mmm) cc_final: 0.8171 (mmm) REVERT: C 244 GLN cc_start: 0.9016 (mm110) cc_final: 0.8278 (tm-30) REVERT: C 323 MET cc_start: 0.8705 (mmt) cc_final: 0.8210 (mmm) REVERT: D 17 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8476 (ttm-80) REVERT: E 17 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8447 (ttm-80) REVERT: E 54 LYS cc_start: 0.9325 (mttm) cc_final: 0.8921 (mmmm) REVERT: E 79 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8663 (tt) REVERT: F 17 ARG cc_start: 0.9146 (mmm-85) cc_final: 0.8836 (tpp80) REVERT: G 233 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8587 (mm-30) REVERT: H 233 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8608 (mm-30) REVERT: H 244 ASP cc_start: 0.8525 (t70) cc_final: 0.8222 (t70) REVERT: I 233 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8567 (mm-30) outliers start: 27 outliers final: 17 residues processed: 177 average time/residue: 0.2621 time to fit residues: 68.5958 Evaluate side-chains 162 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 328 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14916 Z= 0.308 Angle : 0.568 10.043 20259 Z= 0.292 Chirality : 0.042 0.154 2253 Planarity : 0.004 0.044 2568 Dihedral : 4.192 18.352 2205 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.92 % Allowed : 12.86 % Favored : 85.22 % 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: 0.18 (0.20), residues: 1830 helix: 0.51 (0.38), residues: 207 sheet: 0.79 (0.21), residues: 591 loop : -0.32 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 251 HIS 0.002 0.001 HIS C 328 PHE 0.016 0.002 PHE I 295 TYR 0.020 0.001 TYR A 168 ARG 0.004 0.000 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.524 Fit side-chains REVERT: A 102 MET cc_start: 0.8899 (mmm) cc_final: 0.8604 (mmm) REVERT: A 244 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8231 (tm-30) REVERT: A 323 MET cc_start: 0.8745 (mmt) cc_final: 0.8254 (mmt) REVERT: B 244 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8518 (tm-30) REVERT: C 244 GLN cc_start: 0.9040 (mm110) cc_final: 0.8276 (tm-30) REVERT: C 323 MET cc_start: 0.8678 (mmt) cc_final: 0.8354 (mmt) REVERT: D 17 ARG cc_start: 0.8939 (mmm-85) cc_final: 0.8545 (ttm-80) REVERT: E 17 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8462 (ttm-80) REVERT: E 54 LYS cc_start: 0.9389 (mttm) cc_final: 0.9042 (mmmm) REVERT: E 79 LEU cc_start: 0.9112 (tt) cc_final: 0.8851 (tt) REVERT: G 233 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8632 (mm-30) REVERT: H 233 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8554 (mm-30) REVERT: H 244 ASP cc_start: 0.8716 (t70) cc_final: 0.8485 (t70) REVERT: H 292 LYS cc_start: 0.9277 (mtmm) cc_final: 0.8968 (mtmm) REVERT: I 233 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8582 (mm-30) outliers start: 31 outliers final: 28 residues processed: 166 average time/residue: 0.2692 time to fit residues: 65.6475 Evaluate side-chains 166 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain I residue 328 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14916 Z= 0.236 Angle : 0.544 9.479 20259 Z= 0.278 Chirality : 0.041 0.156 2253 Planarity : 0.004 0.046 2568 Dihedral : 4.092 18.141 2205 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.29 % Allowed : 12.74 % Favored : 84.97 % 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: 0.18 (0.20), residues: 1830 helix: 0.56 (0.39), residues: 189 sheet: 0.81 (0.21), residues: 612 loop : -0.35 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 251 HIS 0.004 0.001 HIS B 397 PHE 0.014 0.001 PHE I 295 TYR 0.020 0.001 TYR C 168 ARG 0.004 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.628 Fit side-chains REVERT: A 102 MET cc_start: 0.8930 (mmm) cc_final: 0.8655 (mmm) REVERT: A 244 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8218 (tm-30) REVERT: A 323 MET cc_start: 0.8721 (mmt) cc_final: 0.8235 (mmt) REVERT: A 385 MET cc_start: 0.8120 (tpt) cc_final: 0.7629 (tpt) REVERT: B 244 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8550 (tm-30) REVERT: C 179 MET cc_start: 0.8344 (mmm) cc_final: 0.8114 (mmm) REVERT: C 244 GLN cc_start: 0.9044 (mm110) cc_final: 0.8310 (tm-30) REVERT: C 323 MET cc_start: 0.8687 (mmt) cc_final: 0.8360 (mmt) REVERT: D 17 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8682 (ttm-80) REVERT: E 17 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8399 (ttm-80) REVERT: E 79 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8811 (tt) REVERT: F 17 ARG cc_start: 0.9159 (mmm-85) cc_final: 0.8741 (ttm-80) REVERT: G 233 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8652 (mm-30) REVERT: H 233 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8590 (mm-30) REVERT: H 244 ASP cc_start: 0.8659 (t70) cc_final: 0.8426 (t70) REVERT: I 233 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8575 (mm-30) REVERT: I 281 LYS cc_start: 0.9355 (ttmm) cc_final: 0.9120 (ttmm) outliers start: 37 outliers final: 31 residues processed: 170 average time/residue: 0.2593 time to fit residues: 65.3156 Evaluate side-chains 170 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 328 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14916 Z= 0.164 Angle : 0.515 9.330 20259 Z= 0.261 Chirality : 0.041 0.157 2253 Planarity : 0.004 0.045 2568 Dihedral : 3.869 16.824 2205 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.86 % Allowed : 13.30 % Favored : 84.85 % 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: 0.30 (0.20), residues: 1830 helix: 0.11 (0.36), residues: 228 sheet: 0.93 (0.21), residues: 612 loop : -0.19 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 251 HIS 0.003 0.000 HIS B 397 PHE 0.013 0.001 PHE A 263 TYR 0.021 0.001 TYR A 168 ARG 0.004 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.547 Fit side-chains REVERT: A 102 MET cc_start: 0.8932 (mmm) cc_final: 0.8638 (mmm) REVERT: A 244 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8317 (tm-30) REVERT: A 323 MET cc_start: 0.8734 (mmt) cc_final: 0.8277 (mmt) REVERT: B 244 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8554 (tm-30) REVERT: C 179 MET cc_start: 0.8389 (mmm) cc_final: 0.8117 (mmm) REVERT: C 244 GLN cc_start: 0.9039 (mm110) cc_final: 0.8334 (tm-30) REVERT: C 323 MET cc_start: 0.8682 (mmt) cc_final: 0.8172 (mmm) REVERT: D 17 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8657 (ttm-80) REVERT: E 17 ARG cc_start: 0.8835 (mmm-85) cc_final: 0.8374 (ttm-80) REVERT: E 54 LYS cc_start: 0.9386 (mttm) cc_final: 0.8929 (mmmm) REVERT: E 79 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8809 (tt) REVERT: F 17 ARG cc_start: 0.9137 (mmm-85) cc_final: 0.8739 (ttm-80) REVERT: F 86 ASP cc_start: 0.8663 (m-30) cc_final: 0.8432 (m-30) REVERT: G 233 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8552 (mm-30) REVERT: H 233 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8537 (mm-30) REVERT: H 244 ASP cc_start: 0.8556 (t70) cc_final: 0.8268 (t70) REVERT: H 292 LYS cc_start: 0.9542 (mtmt) cc_final: 0.9302 (mtmm) REVERT: I 233 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8565 (mm-30) outliers start: 30 outliers final: 28 residues processed: 165 average time/residue: 0.2653 time to fit residues: 64.8107 Evaluate side-chains 169 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 328 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 0.0370 chunk 87 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14916 Z= 0.284 Angle : 0.555 9.000 20259 Z= 0.283 Chirality : 0.041 0.150 2253 Planarity : 0.004 0.046 2568 Dihedral : 4.057 15.327 2205 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.10 % Allowed : 13.23 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1830 helix: 0.07 (0.36), residues: 225 sheet: 0.91 (0.21), residues: 612 loop : -0.25 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 251 HIS 0.002 0.001 HIS B 397 PHE 0.015 0.001 PHE A 263 TYR 0.021 0.001 TYR A 168 ARG 0.004 0.000 ARG D 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.846 Fit side-chains REVERT: A 244 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8299 (tm-30) REVERT: A 323 MET cc_start: 0.8727 (mmt) cc_final: 0.8250 (mmt) REVERT: B 244 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8561 (tm-30) REVERT: C 179 MET cc_start: 0.8412 (mmm) cc_final: 0.8136 (mmm) REVERT: C 244 GLN cc_start: 0.9061 (mm110) cc_final: 0.8348 (tm-30) REVERT: C 323 MET cc_start: 0.8683 (mmt) cc_final: 0.8354 (mmt) REVERT: D 17 ARG cc_start: 0.8888 (mmm-85) cc_final: 0.8643 (ttm-80) REVERT: E 12 ASP cc_start: 0.8187 (t70) cc_final: 0.7942 (t70) REVERT: E 17 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8350 (ttm-80) REVERT: E 79 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8779 (tt) REVERT: F 17 ARG cc_start: 0.9168 (mmm-85) cc_final: 0.8718 (ttm-80) REVERT: G 233 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8592 (mm-30) REVERT: H 233 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8509 (mm-30) REVERT: H 244 ASP cc_start: 0.8685 (t70) cc_final: 0.8448 (t70) REVERT: H 292 LYS cc_start: 0.9500 (mtmt) cc_final: 0.9145 (mtmm) REVERT: I 233 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8570 (mm-30) REVERT: I 281 LYS cc_start: 0.9310 (ttmm) cc_final: 0.9062 (mtpp) outliers start: 34 outliers final: 32 residues processed: 164 average time/residue: 0.2635 time to fit residues: 63.9674 Evaluate side-chains 169 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 300 ASN Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 328 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.050784 restraints weight = 43497.841| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 4.85 r_work: 0.2501 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14916 Z= 0.213 Angle : 0.535 8.936 20259 Z= 0.271 Chirality : 0.041 0.153 2253 Planarity : 0.004 0.046 2568 Dihedral : 3.963 15.435 2205 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.35 % Allowed : 12.93 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1830 helix: 0.05 (0.36), residues: 225 sheet: 0.94 (0.21), residues: 612 loop : -0.22 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 251 HIS 0.003 0.000 HIS B 397 PHE 0.016 0.001 PHE A 263 TYR 0.020 0.001 TYR A 168 ARG 0.003 0.000 ARG D 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2745.03 seconds wall clock time: 50 minutes 45.24 seconds (3045.24 seconds total)