Starting phenix.real_space_refine on Mon Jun 16 00:32:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9duu_47179/06_2025/9duu_47179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9duu_47179/06_2025/9duu_47179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9duu_47179/06_2025/9duu_47179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9duu_47179/06_2025/9duu_47179.map" model { file = "/net/cci-nas-00/data/ceres_data/9duu_47179/06_2025/9duu_47179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9duu_47179/06_2025/9duu_47179_neut.cif" } resolution = 3.4 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= 0.003 sd= 0.148 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 133 5.16 5 C 11327 2.51 5 N 3020 2.21 5 O 3455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17953 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.68, per 1000 atoms: 0.65 Number of scatterers: 17953 At special positions: 0 Unit cell: (79.328, 100.64, 224.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 133 16.00 P 12 15.00 Mg 6 11.99 O 3455 8.00 N 3020 7.00 C 11327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP M 1 " - " ALA M 7 " " DTH M 4 " - " ALA M 3 " " TRP N 1 " - " ALA N 7 " " DTH N 4 " - " ALA N 3 " " TRP O 1 " - " ALA O 7 " " DTH O 4 " - " ALA O 3 " " TRP P 1 " - " ALA P 7 " " DTH P 4 " - " ALA P 3 " " TRP Q 1 " - " ALA Q 7 " " DTH Q 4 " - " ALA Q 3 " " TRP R 1 " - " ALA R 7 " " DTH R 4 " - " ALA R 3 " " TRP S 1 " - " ALA S 7 " " DTH S 4 " - " ALA S 3 " Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 2.3 seconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH M 4 " pdb=" CB DTH N 4 " pdb=" CB DTH O 4 " pdb=" CB DTH P 4 " pdb=" CB DTH Q 4 " pdb=" CB DTH R 4 " pdb=" CB DTH S 4 " Number of C-beta restraints generated: 4200 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 36 sheets defined 46.3% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.655A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.525A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.638A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.684A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.666A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.535A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.644A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.612A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.567A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.527A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.536A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.520A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.729A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.613A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.318A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.765A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.142A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.546A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.683A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.655A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.298A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.896A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.867A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.529A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.528A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.799A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.693A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 232 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.536A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 288 through 295 removed outlier: 4.510A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.866A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 removed outlier: 3.516A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.896A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 112 through 126 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 232 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 261 removed outlier: 3.583A pdb=" N LEU F 261 " --> pdb=" O PRO F 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 258 through 261' Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.758A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.575A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 351 through 355 removed outlier: 3.700A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.323A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.126A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.300A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 5.744A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.423A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.020A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.133A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 5.973A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.113A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.531A pdb=" N HIS E 161 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.233A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.800A pdb=" N THR F 160 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 5.860A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 821 hydrogen bonds defined for protein. 2154 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: 6.05 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2971 1.27 - 1.40: 4394 1.40 - 1.54: 10583 1.54 - 1.67: 167 1.67 - 1.81: 229 Bond restraints: 18344 Sorted by residual: bond pdb=" C LYS F 238 " pdb=" O LYS F 238 " ideal model delta sigma weight residual 1.234 1.135 0.099 1.25e-02 6.40e+03 6.23e+01 bond pdb=" C LYS B 238 " pdb=" O LYS B 238 " ideal model delta sigma weight residual 1.234 1.135 0.099 1.28e-02 6.10e+03 6.03e+01 bond pdb=" C LYS C 238 " pdb=" O LYS C 238 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.28e-02 6.10e+03 5.27e+01 bond pdb=" C LYS D 238 " pdb=" O LYS D 238 " ideal model delta sigma weight residual 1.235 1.155 0.080 1.30e-02 5.92e+03 3.79e+01 bond pdb=" C LYS A 238 " pdb=" O LYS A 238 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.25e-02 6.40e+03 3.04e+01 ... (remaining 18339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 24210 2.12 - 4.23: 548 4.23 - 6.35: 107 6.35 - 8.46: 23 8.46 - 10.58: 17 Bond angle restraints: 24905 Sorted by residual: angle pdb=" N LYS D 238 " pdb=" CA LYS D 238 " pdb=" CB LYS D 238 " ideal model delta sigma weight residual 111.08 102.59 8.49 1.71e+00 3.42e-01 2.47e+01 angle pdb=" C HYP N 6 " pdb=" N ALA N 7 " pdb=" CA ALA N 7 " ideal model delta sigma weight residual 121.70 113.20 8.50 1.80e+00 3.09e-01 2.23e+01 angle pdb=" C HYP S 6 " pdb=" N ALA S 7 " pdb=" CA ALA S 7 " ideal model delta sigma weight residual 121.70 113.22 8.48 1.80e+00 3.09e-01 2.22e+01 angle pdb=" C HYP Q 6 " pdb=" N ALA Q 7 " pdb=" CA ALA Q 7 " ideal model delta sigma weight residual 121.70 113.26 8.44 1.80e+00 3.09e-01 2.20e+01 angle pdb=" C HYP M 6 " pdb=" N ALA M 7 " pdb=" CA ALA M 7 " ideal model delta sigma weight residual 121.70 113.30 8.40 1.80e+00 3.09e-01 2.18e+01 ... (remaining 24900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 9916 24.12 - 48.25: 1004 48.25 - 72.37: 117 72.37 - 96.49: 18 96.49 - 120.62: 5 Dihedral angle restraints: 11060 sinusoidal: 4495 harmonic: 6565 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.61 -120.62 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 55.47 -115.47 1 2.00e+01 2.50e-03 3.43e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 54.29 -114.29 1 2.00e+01 2.50e-03 3.39e+01 ... (remaining 11057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2198 0.048 - 0.096: 397 0.096 - 0.144: 169 0.144 - 0.192: 10 0.192 - 0.240: 2 Chirality restraints: 2776 Sorted by residual: chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA CYS S 5 " pdb=" N CYS S 5 " pdb=" C CYS S 5 " pdb=" CB CYS S 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA CYS R 5 " pdb=" N CYS R 5 " pdb=" C CYS R 5 " pdb=" CB CYS R 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 2773 not shown) Planarity restraints: 3170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 237 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU D 237 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU D 237 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS D 238 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 237 " 0.012 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C GLU C 237 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU C 237 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS C 238 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 237 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLU A 237 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU A 237 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 238 " 0.012 2.00e-02 2.50e+03 ... (remaining 3167 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 97 2.38 - 3.01: 9806 3.01 - 3.64: 26491 3.64 - 4.27: 40851 4.27 - 4.90: 71403 Nonbonded interactions: 148648 Sorted by model distance: nonbonded pdb=" CD1 TRP S 1 " pdb=" SG CYS S 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP N 1 " pdb=" SG CYS N 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP M 1 " pdb=" SG CYS M 5 " model vdw 1.753 3.620 nonbonded pdb=" CD1 TRP R 1 " pdb=" SG CYS R 5 " model vdw 1.753 3.620 nonbonded pdb=" CD1 TRP P 1 " pdb=" SG CYS P 5 " model vdw 1.753 3.620 ... (remaining 148643 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 3.450 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: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.550 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.005 0.101 18358 Z= 0.274 Angle : 0.771 10.576 24947 Z= 0.391 Chirality : 0.045 0.240 2776 Planarity : 0.004 0.048 3156 Dihedral : 17.764 120.617 6818 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.37 % Favored : 95.36 % Rotamer: Outliers : 0.85 % Allowed : 29.70 % Favored : 69.45 % Cbeta Deviations : 0.14 % 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: 0.69 (0.19), residues: 2196 helix: 1.20 (0.18), residues: 930 sheet: 0.10 (0.34), residues: 282 loop : -0.04 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 1 HIS 0.001 0.000 HIS A 161 PHE 0.007 0.001 PHE B 200 TYR 0.009 0.001 TYR E 279 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd link_TRANS : bond 0.00345 ( 14) link_TRANS : angle 3.71896 ( 42) hydrogen bonds : bond 0.20464 ( 809) hydrogen bonds : angle 7.32226 ( 2154) covalent geometry : bond 0.00511 (18344) covalent geometry : angle 0.75614 (24905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 215 average time/residue: 0.2542 time to fit residues: 89.0222 Evaluate side-chains 209 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain M residue 5 CYS Chi-restraints excluded: chain N residue 5 CYS Chi-restraints excluded: chain O residue 5 CYS Chi-restraints excluded: chain P residue 5 CYS Chi-restraints excluded: chain Q residue 5 CYS Chi-restraints excluded: chain R residue 5 CYS Chi-restraints excluded: chain S residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 174 optimal weight: 0.0270 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 129 optimal weight: 0.4980 chunk 201 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN D 12 ASN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.101243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.090772 restraints weight = 22181.971| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.19 r_work: 0.2777 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18358 Z= 0.132 Angle : 0.587 6.475 24947 Z= 0.278 Chirality : 0.045 0.184 2776 Planarity : 0.004 0.033 3156 Dihedral : 9.269 118.803 2636 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.87 % Favored : 94.85 % Rotamer: Outliers : 3.17 % Allowed : 26.37 % Favored : 70.45 % 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: 0.77 (0.19), residues: 2196 helix: 1.13 (0.18), residues: 948 sheet: 0.16 (0.29), residues: 354 loop : 0.14 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 1 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE D 255 TYR 0.007 0.001 TYR A 198 ARG 0.002 0.000 ARG B 177 Details of bonding type rmsd link_TRANS : bond 0.00249 ( 14) link_TRANS : angle 0.63355 ( 42) hydrogen bonds : bond 0.03414 ( 809) hydrogen bonds : angle 5.43278 ( 2154) covalent geometry : bond 0.00306 (18344) covalent geometry : angle 0.58650 (24905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.6380 (t80) REVERT: B 99 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: C 72 GLU cc_start: 0.7947 (pm20) cc_final: 0.7489 (pt0) REVERT: E 364 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7536 (mt-10) outliers start: 60 outliers final: 23 residues processed: 240 average time/residue: 0.2523 time to fit residues: 98.4390 Evaluate side-chains 216 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 48 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.094120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.083384 restraints weight = 22431.888| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.20 r_work: 0.2666 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 18358 Z= 0.247 Angle : 0.672 7.312 24947 Z= 0.323 Chirality : 0.050 0.242 2776 Planarity : 0.004 0.033 3156 Dihedral : 8.776 116.119 2621 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.60 % Favored : 94.13 % Rotamer: Outliers : 3.70 % Allowed : 25.21 % Favored : 71.09 % 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: 0.36 (0.18), residues: 2196 helix: 0.85 (0.18), residues: 942 sheet: -0.25 (0.28), residues: 366 loop : -0.03 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.006 0.001 HIS A 161 PHE 0.011 0.001 PHE D 200 TYR 0.013 0.001 TYR C 133 ARG 0.004 0.000 ARG F 290 Details of bonding type rmsd link_TRANS : bond 0.00255 ( 14) link_TRANS : angle 0.96745 ( 42) hydrogen bonds : bond 0.03822 ( 809) hydrogen bonds : angle 5.23960 ( 2154) covalent geometry : bond 0.00605 (18344) covalent geometry : angle 0.67141 (24905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7153 (t80) REVERT: B 99 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: C 72 GLU cc_start: 0.8436 (pm20) cc_final: 0.8141 (pt0) REVERT: C 82 MET cc_start: 0.8579 (mmm) cc_final: 0.8362 (tpt) REVERT: C 283 MET cc_start: 0.7783 (ttm) cc_final: 0.7483 (mmt) REVERT: D 179 ASP cc_start: 0.8387 (m-30) cc_final: 0.8175 (m-30) REVERT: E 115 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8319 (t0) outliers start: 70 outliers final: 40 residues processed: 246 average time/residue: 0.2495 time to fit residues: 99.6484 Evaluate side-chains 230 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 103 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136560 restraints weight = 19932.506| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.37 r_work: 0.3427 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18358 Z= 0.152 Angle : 0.588 6.543 24947 Z= 0.277 Chirality : 0.047 0.244 2776 Planarity : 0.004 0.032 3156 Dihedral : 8.628 118.511 2621 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.83 % Favored : 94.90 % Rotamer: Outliers : 3.49 % Allowed : 25.32 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2196 helix: 1.00 (0.18), residues: 942 sheet: -0.27 (0.28), residues: 366 loop : 0.02 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.009 0.001 TYR D 279 ARG 0.005 0.000 ARG F 372 Details of bonding type rmsd link_TRANS : bond 0.00180 ( 14) link_TRANS : angle 0.49234 ( 42) hydrogen bonds : bond 0.02969 ( 809) hydrogen bonds : angle 5.01907 ( 2154) covalent geometry : bond 0.00366 (18344) covalent geometry : angle 0.58862 (24905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 124 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7026 (t80) REVERT: B 99 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: D 132 MET cc_start: 0.8947 (tmm) cc_final: 0.8447 (ttp) REVERT: F 123 MET cc_start: 0.8008 (tpp) cc_final: 0.7701 (mtp) outliers start: 66 outliers final: 42 residues processed: 245 average time/residue: 0.2575 time to fit residues: 102.9426 Evaluate side-chains 232 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 156 optimal weight: 1.9990 chunk 206 optimal weight: 0.1980 chunk 180 optimal weight: 0.0770 chunk 107 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 202 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.149230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137014 restraints weight = 20073.748| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.37 r_work: 0.3427 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18358 Z= 0.144 Angle : 0.581 6.532 24947 Z= 0.272 Chirality : 0.046 0.241 2776 Planarity : 0.004 0.032 3156 Dihedral : 8.478 117.334 2621 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.87 % Favored : 94.85 % Rotamer: Outliers : 3.33 % Allowed : 25.58 % Favored : 71.09 % 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: 0.53 (0.19), residues: 2196 helix: 1.07 (0.18), residues: 942 sheet: -0.38 (0.27), residues: 378 loop : 0.07 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 340 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.007 0.001 TYR E 279 ARG 0.005 0.000 ARG C 290 Details of bonding type rmsd link_TRANS : bond 0.00151 ( 14) link_TRANS : angle 0.50893 ( 42) hydrogen bonds : bond 0.02885 ( 809) hydrogen bonds : angle 4.91085 ( 2154) covalent geometry : bond 0.00346 (18344) covalent geometry : angle 0.58081 (24905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 196 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7796 (t80) REVERT: B 99 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: D 132 MET cc_start: 0.8958 (tmm) cc_final: 0.8469 (ttp) REVERT: E 115 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8393 (t0) outliers start: 63 outliers final: 43 residues processed: 240 average time/residue: 0.2466 time to fit residues: 97.7717 Evaluate side-chains 235 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 189 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.097109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.086241 restraints weight = 22282.887| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.21 r_work: 0.2701 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18358 Z= 0.135 Angle : 0.570 6.481 24947 Z= 0.266 Chirality : 0.046 0.242 2776 Planarity : 0.003 0.034 3156 Dihedral : 8.379 117.017 2621 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Rotamer: Outliers : 3.96 % Allowed : 24.84 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 2196 helix: 1.11 (0.18), residues: 942 sheet: -0.41 (0.26), residues: 378 loop : 0.13 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 340 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.007 0.001 TYR E 279 ARG 0.003 0.000 ARG C 290 Details of bonding type rmsd link_TRANS : bond 0.00148 ( 14) link_TRANS : angle 0.47024 ( 42) hydrogen bonds : bond 0.02763 ( 809) hydrogen bonds : angle 4.82741 ( 2154) covalent geometry : bond 0.00324 (18344) covalent geometry : angle 0.57015 (24905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 200 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.6884 (t80) REVERT: B 99 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8261 (pm20) REVERT: D 30 VAL cc_start: 0.9373 (t) cc_final: 0.9170 (p) REVERT: D 283 MET cc_start: 0.7630 (ttm) cc_final: 0.7234 (mtp) outliers start: 75 outliers final: 48 residues processed: 258 average time/residue: 0.2648 time to fit residues: 111.6505 Evaluate side-chains 239 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 157 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 14 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138007 restraints weight = 19959.772| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.39 r_work: 0.2701 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18358 Z= 0.126 Angle : 0.562 6.446 24947 Z= 0.263 Chirality : 0.046 0.241 2776 Planarity : 0.003 0.035 3156 Dihedral : 8.300 116.294 2621 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.87 % Favored : 94.85 % Rotamer: Outliers : 3.54 % Allowed : 24.89 % Favored : 71.56 % 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: 0.61 (0.19), residues: 2196 helix: 1.16 (0.18), residues: 942 sheet: -0.44 (0.26), residues: 378 loop : 0.15 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.007 0.001 TYR E 279 ARG 0.002 0.000 ARG E 95 Details of bonding type rmsd link_TRANS : bond 0.00133 ( 14) link_TRANS : angle 0.44272 ( 42) hydrogen bonds : bond 0.02707 ( 809) hydrogen bonds : angle 4.78796 ( 2154) covalent geometry : bond 0.00302 (18344) covalent geometry : angle 0.56260 (24905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 198 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.6887 (t80) REVERT: B 99 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: D 132 MET cc_start: 0.8966 (tmm) cc_final: 0.8413 (ttp) REVERT: D 283 MET cc_start: 0.7745 (ttm) cc_final: 0.7289 (mtp) REVERT: E 95 ARG cc_start: 0.8653 (ttm110) cc_final: 0.8306 (ttm110) REVERT: E 115 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8338 (t0) REVERT: E 132 MET cc_start: 0.8848 (ttp) cc_final: 0.8194 (tmm) REVERT: F 344 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8637 (p) outliers start: 67 outliers final: 52 residues processed: 250 average time/residue: 0.2532 time to fit residues: 104.6662 Evaluate side-chains 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.1980 chunk 186 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.0270 chunk 168 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 158 optimal weight: 0.2980 overall best weight: 0.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139729 restraints weight = 19885.713| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.39 r_work: 0.2731 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18358 Z= 0.107 Angle : 0.548 6.426 24947 Z= 0.255 Chirality : 0.045 0.238 2776 Planarity : 0.003 0.035 3156 Dihedral : 8.175 115.117 2621 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.69 % Favored : 95.04 % Rotamer: Outliers : 3.17 % Allowed : 25.11 % Favored : 71.72 % 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: 0.73 (0.19), residues: 2196 helix: 1.26 (0.18), residues: 942 sheet: -0.41 (0.26), residues: 378 loop : 0.21 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE E 255 TYR 0.008 0.001 TYR D 143 ARG 0.002 0.000 ARG F 290 Details of bonding type rmsd link_TRANS : bond 0.00100 ( 14) link_TRANS : angle 0.37166 ( 42) hydrogen bonds : bond 0.02557 ( 809) hydrogen bonds : angle 4.71778 ( 2154) covalent geometry : bond 0.00251 (18344) covalent geometry : angle 0.54844 (24905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.6669 (t80) REVERT: B 99 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: D 132 MET cc_start: 0.8952 (tmm) cc_final: 0.8375 (ttp) REVERT: E 95 ARG cc_start: 0.8603 (ttm110) cc_final: 0.8333 (ttm110) REVERT: E 115 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8247 (t0) REVERT: E 132 MET cc_start: 0.8834 (ttp) cc_final: 0.8105 (tmm) REVERT: E 346 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8167 (tp) outliers start: 60 outliers final: 47 residues processed: 254 average time/residue: 0.3907 time to fit residues: 165.6270 Evaluate side-chains 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.092876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.081422 restraints weight = 22869.974| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 1.31 r_work: 0.2620 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 18358 Z= 0.269 Angle : 0.674 7.571 24947 Z= 0.322 Chirality : 0.051 0.253 2776 Planarity : 0.004 0.038 3156 Dihedral : 8.453 112.940 2621 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.74 % Favored : 93.99 % Rotamer: Outliers : 3.44 % Allowed : 24.89 % Favored : 71.67 % 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: 0.21 (0.18), residues: 2196 helix: 0.84 (0.18), residues: 942 sheet: -0.71 (0.25), residues: 378 loop : -0.05 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.005 0.001 HIS A 161 PHE 0.010 0.001 PHE E 255 TYR 0.011 0.002 TYR C 133 ARG 0.006 0.000 ARG F 290 Details of bonding type rmsd link_TRANS : bond 0.00298 ( 14) link_TRANS : angle 0.77239 ( 42) hydrogen bonds : bond 0.03579 ( 809) hydrogen bonds : angle 4.97168 ( 2154) covalent geometry : bond 0.00660 (18344) covalent geometry : angle 0.67390 (24905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.7083 (t80) REVERT: B 99 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: D 132 MET cc_start: 0.9046 (tmm) cc_final: 0.8556 (ttp) REVERT: D 283 MET cc_start: 0.8261 (ttm) cc_final: 0.7871 (mmt) REVERT: E 115 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8408 (t0) REVERT: E 132 MET cc_start: 0.8916 (ttp) cc_final: 0.8208 (tmm) outliers start: 65 outliers final: 49 residues processed: 246 average time/residue: 0.4042 time to fit residues: 165.6503 Evaluate side-chains 242 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 4.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 200 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.096228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.086098 restraints weight = 22153.853| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 1.13 r_work: 0.2704 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18358 Z= 0.126 Angle : 0.577 6.613 24947 Z= 0.270 Chirality : 0.046 0.246 2776 Planarity : 0.004 0.035 3156 Dihedral : 8.352 115.448 2621 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.69 % Favored : 95.04 % Rotamer: Outliers : 2.85 % Allowed : 25.37 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2196 helix: 1.08 (0.18), residues: 942 sheet: -0.56 (0.26), residues: 378 loop : 0.04 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE E 255 TYR 0.007 0.001 TYR E 279 ARG 0.002 0.000 ARG E 95 Details of bonding type rmsd link_TRANS : bond 0.00142 ( 14) link_TRANS : angle 0.42052 ( 42) hydrogen bonds : bond 0.02754 ( 809) hydrogen bonds : angle 4.80342 ( 2154) covalent geometry : bond 0.00300 (18344) covalent geometry : angle 0.57684 (24905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.6907 (t80) REVERT: B 99 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: D 132 MET cc_start: 0.8938 (tmm) cc_final: 0.8377 (ttp) REVERT: D 283 MET cc_start: 0.7780 (ttm) cc_final: 0.7527 (mmt) REVERT: E 115 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8252 (t0) REVERT: E 132 MET cc_start: 0.8885 (ttp) cc_final: 0.8106 (tmm) outliers start: 54 outliers final: 45 residues processed: 238 average time/residue: 0.2941 time to fit residues: 115.5309 Evaluate side-chains 243 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 137 optimal weight: 0.0070 chunk 208 optimal weight: 0.0670 chunk 124 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 110 optimal weight: 0.0070 chunk 203 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 59 GLN C 12 ASN D 59 GLN D 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.099020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.088805 restraints weight = 22090.634| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.13 r_work: 0.2749 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18358 Z= 0.097 Angle : 0.547 6.550 24947 Z= 0.254 Chirality : 0.045 0.237 2776 Planarity : 0.003 0.035 3156 Dihedral : 8.089 112.120 2621 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.60 % Favored : 95.13 % Rotamer: Outliers : 2.70 % Allowed : 25.58 % Favored : 71.72 % 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: 0.78 (0.19), residues: 2196 helix: 1.31 (0.18), residues: 942 sheet: -0.40 (0.26), residues: 378 loop : 0.23 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 340 HIS 0.003 0.001 HIS C 161 PHE 0.008 0.001 PHE E 255 TYR 0.007 0.001 TYR E 279 ARG 0.003 0.000 ARG E 95 Details of bonding type rmsd link_TRANS : bond 0.00095 ( 14) link_TRANS : angle 0.32634 ( 42) hydrogen bonds : bond 0.02450 ( 809) hydrogen bonds : angle 4.65159 ( 2154) covalent geometry : bond 0.00222 (18344) covalent geometry : angle 0.54735 (24905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8330.62 seconds wall clock time: 149 minutes 0.88 seconds (8940.88 seconds total)