Starting phenix.real_space_refine on Sun Oct 13 10:11:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/10_2024/7u9g_26397.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/10_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_26397/10_2024/7u9g_26397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/10_2024/7u9g_26397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/10_2024/7u9g_26397.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9g_26397/10_2024/7u9g_26397.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 8.65, per 1000 atoms: 0.59 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 - 3.00 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=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: 3.48 Conformation dependent library (CDL) restraints added in 2.3 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: 2.78 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: 5.89 Time building geometry restraints manager: 4.08 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: 0.00 - 1.43: 18869 1.43 - 2.86: 1186 2.86 - 4.29: 163 4.29 - 5.71: 29 5.71 - 7.14: 12 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 3.040 nonbonded pdb=" O PRO H 231 " pdb=" OG SER H 232 " model vdw 2.294 3.040 nonbonded pdb=" O PRO I 231 " pdb=" OG SER I 232 " model vdw 2.294 3.040 nonbonded pdb=" OG SER C 15 " pdb=" OE2 GLU C 324 " model vdw 2.389 3.040 nonbonded pdb=" OG SER B 15 " pdb=" OE2 GLU B 324 " model vdw 2.389 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.850 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.950 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- 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 : 1.730 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: 0.3696 time to fit residues: 137.3615 Evaluate side-chains 164 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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: 3.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 0.0980 chunk 85 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN E 6 GLN F 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14916 Z= 0.209 Angle : 0.565 7.418 20259 Z= 0.300 Chirality : 0.042 0.210 2253 Planarity : 0.005 0.050 2568 Dihedral : 4.275 20.301 2205 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.80 % Allowed : 7.79 % Favored : 91.40 % 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: 0.41 (0.19), residues: 1830 helix: 0.49 (0.36), residues: 210 sheet: 0.91 (0.20), residues: 570 loop : -0.07 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 36 HIS 0.003 0.001 HIS G 220 PHE 0.019 0.001 PHE G 295 TYR 0.012 0.001 TYR I 322 ARG 0.005 0.001 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 188 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8866 (mmt) cc_final: 0.8448 (mmt) REVERT: B 244 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8259 (tm-30) REVERT: B 323 MET cc_start: 0.8836 (mmt) cc_final: 0.8599 (mmt) REVERT: C 179 MET cc_start: 0.8375 (mmm) cc_final: 0.8120 (mmm) REVERT: C 323 MET cc_start: 0.8757 (mmt) cc_final: 0.8259 (mmm) REVERT: D 80 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7078 (mmm-85) REVERT: E 54 LYS cc_start: 0.9300 (mttp) cc_final: 0.8938 (mmmm) REVERT: F 76 ILE cc_start: 0.8723 (mp) cc_final: 0.8196 (mt) REVERT: F 80 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7700 (mmm-85) REVERT: G 233 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8212 (mm-30) REVERT: H 233 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8266 (mm-30) REVERT: H 244 ASP cc_start: 0.8238 (t70) cc_final: 0.7932 (t70) REVERT: I 218 GLN cc_start: 0.8563 (tp40) cc_final: 0.8319 (tp40) REVERT: I 233 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8263 (mm-30) REVERT: I 244 ASP cc_start: 0.8300 (t70) cc_final: 0.8060 (t70) outliers start: 13 outliers final: 6 residues processed: 184 average time/residue: 0.3711 time to fit residues: 98.3407 Evaluate side-chains 156 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E 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: 6.9990 chunk 50 optimal weight: 8.9990 chunk 136 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 163 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14916 Z= 0.210 Angle : 0.531 8.473 20259 Z= 0.278 Chirality : 0.042 0.179 2253 Planarity : 0.004 0.047 2568 Dihedral : 4.106 21.394 2205 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.86 % Allowed : 8.16 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1830 helix: 0.74 (0.37), residues: 207 sheet: 0.82 (0.20), residues: 573 loop : -0.08 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 36 HIS 0.002 0.000 HIS C 328 PHE 0.016 0.001 PHE I 295 TYR 0.023 0.001 TYR E 50 ARG 0.011 0.000 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 188 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8091 (tm-30) REVERT: A 323 MET cc_start: 0.8828 (mmt) cc_final: 0.8426 (mmt) REVERT: B 244 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8321 (tm-30) REVERT: C 102 MET cc_start: 0.9045 (mmm) cc_final: 0.8831 (mmm) REVERT: C 244 GLN cc_start: 0.8994 (mm110) cc_final: 0.8064 (tm-30) REVERT: C 323 MET cc_start: 0.8708 (mmt) cc_final: 0.8443 (mmt) REVERT: D 17 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8504 (ttm-80) REVERT: D 80 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7642 (mmm-85) REVERT: E 17 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8467 (ttm-80) REVERT: E 50 TYR cc_start: 0.8073 (p90) cc_final: 0.7823 (p90) REVERT: E 54 LYS cc_start: 0.9313 (mttp) cc_final: 0.8924 (mmmm) REVERT: E 61 ASP cc_start: 0.8901 (m-30) cc_final: 0.8494 (t0) REVERT: E 79 LEU cc_start: 0.8534 (tt) cc_final: 0.8256 (tt) REVERT: F 80 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7352 (mmm-85) REVERT: G 233 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8288 (mm-30) REVERT: G 292 LYS cc_start: 0.9492 (mtmt) cc_final: 0.9221 (mtmm) REVERT: G 318 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8561 (m-30) REVERT: H 233 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8291 (mm-30) REVERT: H 244 ASP cc_start: 0.8367 (t70) cc_final: 0.8070 (t70) REVERT: H 292 LYS cc_start: 0.9453 (mtmt) cc_final: 0.9126 (mtmm) REVERT: I 233 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8264 (mm-30) REVERT: I 244 ASP cc_start: 0.8369 (t70) cc_final: 0.8144 (t70) REVERT: I 292 LYS cc_start: 0.9241 (mtmm) cc_final: 0.9037 (mtmm) outliers start: 30 outliers final: 14 residues processed: 184 average time/residue: 0.2652 time to fit residues: 72.0596 Evaluate side-chains 164 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 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 393 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 318 ASP Chi-restraints excluded: chain I residue 297 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 0.0870 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 0.3980 chunk 46 optimal weight: 20.0000 overall best weight: 2.4964 ------------------------------------------------------------------------------- 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: 0.2975 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= 0.266 Angle : 0.547 5.917 20259 Z= 0.286 Chirality : 0.042 0.170 2253 Planarity : 0.004 0.046 2568 Dihedral : 4.149 20.549 2205 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.48 % Allowed : 9.34 % Favored : 89.18 % 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: 0.66 (0.37), residues: 207 sheet: 0.73 (0.20), residues: 603 loop : -0.17 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.003 0.001 HIS B 397 PHE 0.018 0.002 PHE I 295 TYR 0.018 0.001 TYR I 311 ARG 0.006 0.000 ARG F 17 *********************** 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 178 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8340 (mmm) cc_final: 0.8134 (mmm) REVERT: A 244 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8138 (tm-30) REVERT: A 323 MET cc_start: 0.8809 (mmt) cc_final: 0.8402 (mmt) REVERT: B 244 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8412 (tm-30) REVERT: C 244 GLN cc_start: 0.9004 (mm110) cc_final: 0.8096 (tm-30) REVERT: C 323 MET cc_start: 0.8707 (mmt) cc_final: 0.8433 (mmt) REVERT: D 80 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7990 (mmm-85) REVERT: E 17 ARG cc_start: 0.8928 (mmm-85) cc_final: 0.8486 (ttm-80) REVERT: E 61 ASP cc_start: 0.8851 (m-30) cc_final: 0.8452 (t0) REVERT: E 79 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8338 (tt) REVERT: F 12 ASP cc_start: 0.7904 (t70) cc_final: 0.7614 (t70) REVERT: F 17 ARG cc_start: 0.8879 (ttm-80) cc_final: 0.8502 (ttm-80) REVERT: F 80 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7731 (mmm-85) REVERT: F 82 GLU cc_start: 0.8436 (pm20) cc_final: 0.8075 (pm20) REVERT: G 233 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8277 (mm-30) REVERT: G 318 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8613 (m-30) REVERT: H 233 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8285 (mm-30) REVERT: H 244 ASP cc_start: 0.8548 (t70) cc_final: 0.8253 (t70) REVERT: I 218 GLN cc_start: 0.8535 (tp40) cc_final: 0.8277 (tp40) REVERT: I 233 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8273 (mm-30) REVERT: I 244 ASP cc_start: 0.8413 (t70) cc_final: 0.8176 (t70) REVERT: I 292 LYS cc_start: 0.9288 (mtmm) cc_final: 0.9024 (mtmm) outliers start: 24 outliers final: 20 residues processed: 172 average time/residue: 0.3105 time to fit residues: 78.2917 Evaluate side-chains 171 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL 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 272 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 79 LEU 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 318 ASP Chi-restraints excluded: chain I residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 0.0170 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- 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: 0.8639 moved from start: 0.3176 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= 0.237 Angle : 0.527 6.701 20259 Z= 0.274 Chirality : 0.041 0.166 2253 Planarity : 0.004 0.046 2568 Dihedral : 4.061 19.176 2205 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.61 % Allowed : 9.28 % Favored : 89.12 % 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: 0.60 (0.37), residues: 207 sheet: 0.81 (0.20), residues: 603 loop : -0.22 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.002 0.000 HIS C 328 PHE 0.015 0.001 PHE I 295 TYR 0.019 0.001 TYR A 168 ARG 0.005 0.000 ARG D 17 *********************** 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 180 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8798 (mmt) cc_final: 0.8387 (mmt) REVERT: B 244 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8527 (tm-30) REVERT: C 244 GLN cc_start: 0.8997 (mm110) cc_final: 0.8117 (tm-30) REVERT: C 323 MET cc_start: 0.8703 (mmt) cc_final: 0.8414 (mmt) REVERT: D 61 ASP cc_start: 0.8890 (m-30) cc_final: 0.8421 (t0) REVERT: E 17 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8435 (ttm-80) REVERT: E 61 ASP cc_start: 0.8836 (m-30) cc_final: 0.8472 (t0) REVERT: E 79 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8255 (tt) REVERT: F 12 ASP cc_start: 0.7941 (t70) cc_final: 0.7619 (t70) REVERT: F 17 ARG cc_start: 0.8856 (ttm-80) cc_final: 0.8496 (ttm-80) REVERT: F 80 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7696 (mmm-85) REVERT: F 82 GLU cc_start: 0.8511 (pm20) cc_final: 0.8172 (pm20) REVERT: F 84 GLU cc_start: 0.8147 (pm20) cc_final: 0.7935 (pm20) REVERT: G 233 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8346 (mm-30) REVERT: G 292 LYS cc_start: 0.9386 (mtmm) cc_final: 0.9113 (mtmm) REVERT: G 318 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: H 233 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8346 (mm-30) REVERT: H 244 ASP cc_start: 0.8554 (t70) cc_final: 0.8256 (t70) REVERT: H 292 LYS cc_start: 0.9418 (mtmm) cc_final: 0.9158 (mtmm) REVERT: I 233 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8286 (mm-30) REVERT: I 244 ASP cc_start: 0.8363 (t70) cc_final: 0.8154 (t70) outliers start: 26 outliers final: 21 residues processed: 176 average time/residue: 0.3148 time to fit residues: 80.4573 Evaluate side-chains 171 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 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 389 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 79 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 318 ASP Chi-restraints excluded: chain I residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.8654 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 : 0.004 0.048 14916 Z= 0.253 Angle : 0.532 6.795 20259 Z= 0.276 Chirality : 0.041 0.162 2253 Planarity : 0.004 0.048 2568 Dihedral : 4.060 18.449 2205 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.10 % Allowed : 9.34 % Favored : 88.56 % 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 (0.19), residues: 1830 helix: 0.60 (0.37), residues: 207 sheet: 0.74 (0.20), residues: 612 loop : -0.23 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 251 HIS 0.002 0.000 HIS C 328 PHE 0.015 0.001 PHE G 295 TYR 0.020 0.001 TYR C 168 ARG 0.006 0.000 ARG D 17 *********************** 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: 34 poor density : 150 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8240 (tm-30) REVERT: A 323 MET cc_start: 0.8791 (mmt) cc_final: 0.8374 (mmt) REVERT: B 244 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8539 (tm-30) REVERT: C 244 GLN cc_start: 0.8998 (mm110) cc_final: 0.8142 (tm-30) REVERT: C 323 MET cc_start: 0.8700 (mmt) cc_final: 0.8400 (mmt) REVERT: D 61 ASP cc_start: 0.8889 (m-30) cc_final: 0.8428 (t0) REVERT: E 12 ASP cc_start: 0.7622 (t70) cc_final: 0.7414 (t70) REVERT: E 17 ARG cc_start: 0.8843 (mmm-85) cc_final: 0.8340 (ttm-80) REVERT: E 61 ASP cc_start: 0.8798 (m-30) cc_final: 0.8477 (t0) REVERT: E 79 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8602 (tt) REVERT: F 12 ASP cc_start: 0.7995 (t70) cc_final: 0.7666 (t70) REVERT: F 80 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7767 (mmm-85) REVERT: F 82 GLU cc_start: 0.8535 (pm20) cc_final: 0.8224 (pm20) REVERT: F 84 GLU cc_start: 0.8210 (pm20) cc_final: 0.7942 (pm20) REVERT: G 233 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8478 (mm-30) REVERT: G 292 LYS cc_start: 0.9389 (mtmm) cc_final: 0.9151 (mtmm) REVERT: G 318 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8669 (m-30) REVERT: H 233 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8312 (mm-30) REVERT: H 244 ASP cc_start: 0.8598 (t70) cc_final: 0.8339 (t70) REVERT: I 233 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8333 (mm-30) REVERT: I 244 ASP cc_start: 0.8433 (t70) cc_final: 0.8133 (t70) outliers start: 34 outliers final: 28 residues processed: 177 average time/residue: 0.2994 time to fit residues: 78.8219 Evaluate side-chains 175 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 2.154 ------------------------------------------------------------------------------- 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 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 245 THR 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 162 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 317 ILE 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 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 221 LEU Chi-restraints excluded: chain G residue 318 ASP Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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: 0.8664 moved from start: 0.3464 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= 0.268 Angle : 0.539 7.727 20259 Z= 0.279 Chirality : 0.041 0.158 2253 Planarity : 0.004 0.046 2568 Dihedral : 4.099 17.952 2205 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.35 % Allowed : 9.89 % Favored : 87.76 % 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: 0.19 (0.19), residues: 1830 helix: 0.56 (0.37), residues: 207 sheet: 0.76 (0.20), residues: 612 loop : -0.32 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.003 0.001 HIS A 20 PHE 0.016 0.001 PHE I 295 TYR 0.021 0.001 TYR A 168 ARG 0.007 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 185 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8218 (tm-30) REVERT: A 323 MET cc_start: 0.8784 (mmt) cc_final: 0.8365 (mmt) REVERT: A 385 MET cc_start: 0.7894 (tpt) cc_final: 0.7190 (tpt) REVERT: B 244 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8467 (tm-30) REVERT: C 244 GLN cc_start: 0.8996 (mm110) cc_final: 0.8150 (tm-30) REVERT: C 323 MET cc_start: 0.8692 (mmt) cc_final: 0.8373 (mmt) REVERT: D 12 ASP cc_start: 0.7423 (t70) cc_final: 0.6730 (t0) REVERT: E 17 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8234 (ttm-80) REVERT: E 61 ASP cc_start: 0.8817 (m-30) cc_final: 0.8522 (t0) REVERT: F 12 ASP cc_start: 0.8016 (t70) cc_final: 0.7684 (t70) REVERT: F 80 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7786 (mmm-85) REVERT: F 82 GLU cc_start: 0.8616 (pm20) cc_final: 0.8314 (pm20) REVERT: F 84 GLU cc_start: 0.8219 (pm20) cc_final: 0.7900 (pm20) REVERT: F 96 LEU cc_start: 0.9615 (tp) cc_final: 0.9398 (tt) REVERT: G 233 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8457 (mm-30) REVERT: G 292 LYS cc_start: 0.9405 (mtmm) cc_final: 0.9141 (mtmm) REVERT: G 318 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8693 (m-30) REVERT: H 233 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8351 (mm-30) REVERT: H 244 ASP cc_start: 0.8645 (t70) cc_final: 0.8386 (t70) REVERT: I 233 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8406 (mm-30) REVERT: I 244 ASP cc_start: 0.8393 (t70) cc_final: 0.8126 (t70) REVERT: I 246 MET cc_start: 0.8555 (mtp) cc_final: 0.8222 (mtp) outliers start: 38 outliers final: 31 residues processed: 180 average time/residue: 0.3095 time to fit residues: 82.1027 Evaluate side-chains 175 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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 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 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 162 VAL Chi-restraints excluded: chain C residue 171 THR 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 389 VAL 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 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 318 ASP Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: