Starting phenix.real_space_refine on Wed Jan 22 04:56:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9duu_47179/01_2025/9duu_47179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9duu_47179/01_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_47179/01_2025/9duu_47179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9duu_47179/01_2025/9duu_47179.map" model { file = "/net/cci-nas-00/data/ceres_data/9duu_47179/01_2025/9duu_47179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9duu_47179/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 10.76, per 1000 atoms: 0.60 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: 4.87 Conformation dependent library (CDL) restraints added in 2.1 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: 2.44 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: 6.79 Time building geometry restraints manager: 5.48 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 42.020 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.470 ------------------------------------------------------------------------------- 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 18344 Z= 0.340 Angle : 0.756 10.576 24905 Z= 0.382 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 *********************** 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 : 2.089 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: 0.2580 time to fit residues: 90.2530 Evaluate side-chains 210 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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 = 0.2990 r_free = 0.2990 target = 0.101179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.090701 restraints weight = 22192.472| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.19 r_work: 0.2776 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18344 Z= 0.199 Angle : 0.584 6.450 24905 Z= 0.276 Chirality : 0.045 0.175 2776 Planarity : 0.004 0.032 3156 Dihedral : 9.299 118.865 2636 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Rotamer: Outliers : 3.12 % Allowed : 26.37 % Favored : 70.51 % 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: 0.76 (0.19), residues: 2196 helix: 1.13 (0.18), residues: 948 sheet: 0.14 (0.29), residues: 354 loop : 0.15 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 1 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE D 255 TYR 0.008 0.001 TYR A 198 ARG 0.002 0.000 ARG C 290 *********************** 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 257 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.6531 (t80) REVERT: B 99 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: C 72 GLU cc_start: 0.7963 (pm20) cc_final: 0.7520 (pt0) outliers start: 59 outliers final: 24 residues processed: 242 average time/residue: 0.2565 time to fit residues: 101.0562 Evaluate side-chains 218 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 85 ILE 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: 0.8980 chunk 131 optimal weight: 0.8980 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: 1.9990 chunk 163 optimal weight: 2.9990 chunk 158 optimal weight: 0.1980 chunk 111 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.2949 r_free = 0.2949 target = 0.097823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.086998 restraints weight = 22107.353| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.20 r_work: 0.2718 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18344 Z= 0.279 Angle : 0.603 6.775 24905 Z= 0.285 Chirality : 0.047 0.233 2776 Planarity : 0.004 0.033 3156 Dihedral : 8.623 115.938 2621 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.96 % Favored : 94.76 % Rotamer: Outliers : 3.33 % Allowed : 25.53 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 2196 helix: 1.02 (0.18), residues: 948 sheet: -0.09 (0.29), residues: 354 loop : 0.09 (0.21), residues: 894 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 C 255 TYR 0.009 0.001 TYR A 198 ARG 0.003 0.000 ARG F 290 *********************** 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 259 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 196 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8200 (mp) REVERT: A 124 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7018 (t80) REVERT: B 99 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8221 (pm20) REVERT: C 72 GLU cc_start: 0.8237 (pm20) cc_final: 0.7963 (pt0) REVERT: C 82 MET cc_start: 0.8502 (mmm) cc_final: 0.8269 (tpt) REVERT: C 132 MET cc_start: 0.8621 (ttp) cc_final: 0.8066 (ttt) REVERT: C 283 MET cc_start: 0.7684 (ttm) cc_final: 0.7347 (mmt) REVERT: C 305 MET cc_start: 0.9015 (mmm) cc_final: 0.8686 (mmm) REVERT: E 115 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8235 (t0) outliers start: 63 outliers final: 34 residues processed: 245 average time/residue: 0.2578 time to fit residues: 102.1522 Evaluate side-chains 228 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 99 GLU Chi-restraints excluded: chain B residue 115 ASN 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 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 271 SER 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 201 VAL Chi-restraints excluded: chain E residue 247 VAL 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 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: 1.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.2907 r_free = 0.2907 target = 0.094860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.084103 restraints weight = 22401.364| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.20 r_work: 0.2672 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18344 Z= 0.338 Angle : 0.629 7.473 24905 Z= 0.299 Chirality : 0.049 0.245 2776 Planarity : 0.004 0.041 3156 Dihedral : 8.616 116.548 2621 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.24 % Favored : 94.49 % Rotamer: Outliers : 4.12 % Allowed : 24.58 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2196 helix: 0.93 (0.18), residues: 942 sheet: -0.36 (0.27), residues: 366 loop : 0.01 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.005 0.001 HIS A 161 PHE 0.008 0.001 PHE C 255 TYR 0.014 0.001 TYR D 279 ARG 0.006 0.000 ARG F 372 *********************** 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 273 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7025 (t80) REVERT: B 99 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: C 82 MET cc_start: 0.8642 (mmm) cc_final: 0.8441 (tpt) REVERT: C 283 MET cc_start: 0.7779 (ttm) cc_final: 0.7579 (mmt) REVERT: C 335 ARG cc_start: 0.8856 (mtm-85) cc_final: 0.8565 (mtm-85) REVERT: E 115 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8294 (t0) outliers start: 78 outliers final: 50 residues processed: 255 average time/residue: 0.2600 time to fit residues: 107.0234 Evaluate side-chains 241 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 354 GLN Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU 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 56 ASP 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 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 350 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 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR 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: 0.9990 chunk 206 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 202 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.2931 r_free = 0.2931 target = 0.096782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.085924 restraints weight = 22332.341| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.21 r_work: 0.2703 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18344 Z= 0.214 Angle : 0.577 6.547 24905 Z= 0.271 Chirality : 0.046 0.243 2776 Planarity : 0.003 0.033 3156 Dihedral : 8.507 117.942 2621 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.37 % Favored : 95.36 % Rotamer: Outliers : 3.59 % Allowed : 25.05 % Favored : 71.35 % 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: 0.55 (0.19), residues: 2196 helix: 1.09 (0.18), residues: 942 sheet: -0.38 (0.27), residues: 366 loop : 0.09 (0.21), residues: 888 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 A 255 TYR 0.006 0.001 TYR A 133 ARG 0.002 0.000 ARG F 28 *********************** 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 271 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 99 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: D 132 MET cc_start: 0.8941 (tmm) cc_final: 0.8425 (ttp) REVERT: E 346 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8268 (tp) outliers start: 68 outliers final: 47 residues processed: 253 average time/residue: 0.2544 time to fit residues: 104.5649 Evaluate side-chains 238 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 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 151 ILE 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 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 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 346 LEU Chi-restraints excluded: chain E residue 350 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 189 optimal weight: 0.0870 chunk 144 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 84 optimal weight: 0.0000 chunk 49 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.5362 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.098116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.087208 restraints weight = 22177.588| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.21 r_work: 0.2722 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18344 Z= 0.183 Angle : 0.560 6.425 24905 Z= 0.261 Chirality : 0.045 0.240 2776 Planarity : 0.003 0.034 3156 Dihedral : 8.356 116.698 2621 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.96 % Favored : 94.76 % Rotamer: Outliers : 3.75 % Allowed : 24.89 % Favored : 71.35 % 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: 0.63 (0.19), residues: 2196 helix: 1.18 (0.18), residues: 942 sheet: -0.42 (0.26), residues: 378 loop : 0.15 (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 0.007 0.001 PHE A 255 TYR 0.010 0.001 TYR A 133 ARG 0.003 0.000 ARG C 290 *********************** 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 271 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 200 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.6864 (t80) REVERT: B 99 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: D 132 MET cc_start: 0.8947 (tmm) cc_final: 0.8405 (ttp) REVERT: D 283 MET cc_start: 0.7581 (ttm) cc_final: 0.7159 (mtp) REVERT: E 346 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8258 (tp) REVERT: F 344 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8613 (p) outliers start: 71 outliers final: 52 residues processed: 256 average time/residue: 0.2524 time to fit residues: 105.9656 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 : 1.791 ------------------------------------------------------------------------------- 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 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 16 LEU 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 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 LEU 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 67 LEU 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 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 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 346 LEU 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 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU 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: 0.5980 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.2912 r_free = 0.2912 target = 0.095437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.084612 restraints weight = 22408.129| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.21 r_work: 0.2668 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18344 Z= 0.293 Angle : 0.604 7.125 24905 Z= 0.284 Chirality : 0.048 0.246 2776 Planarity : 0.004 0.037 3156 Dihedral : 8.388 114.284 2621 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.15 % Favored : 94.58 % Rotamer: Outliers : 3.81 % Allowed : 24.63 % 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: 0.48 (0.19), residues: 2196 helix: 1.03 (0.18), residues: 942 sheet: -0.51 (0.26), residues: 366 loop : 0.09 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.004 0.001 HIS A 161 PHE 0.008 0.001 PHE A 255 TYR 0.008 0.001 TYR C 133 ARG 0.004 0.000 ARG C 290 *********************** 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 264 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 192 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7007 (t80) REVERT: B 99 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: D 132 MET cc_start: 0.9033 (tmm) cc_final: 0.8606 (ttp) REVERT: E 95 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8285 (ttm110) REVERT: E 115 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8351 (t0) REVERT: E 132 MET cc_start: 0.8970 (tmm) cc_final: 0.8666 (ttp) outliers start: 72 outliers final: 52 residues processed: 249 average time/residue: 0.2535 time to fit residues: 104.3103 Evaluate side-chains 244 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 1.964 ------------------------------------------------------------------------------- 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 16 LEU 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 199 SER 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 123 MET Chi-restraints excluded: chain D residue 148 THR 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 34 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.0970 chunk 186 optimal weight: 0.0670 chunk 187 optimal weight: 0.9990 chunk 218 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 73 optimal weight: 0.0070 chunk 158 optimal weight: 0.5980 overall best weight: 0.2334 ------------------------------------------------------------------------------- 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 = 0.2957 r_free = 0.2957 target = 0.098925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.088721 restraints weight = 22021.486| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.13 r_work: 0.2742 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 18344 Z= 0.137 Angle : 0.548 6.498 24905 Z= 0.255 Chirality : 0.044 0.237 2776 Planarity : 0.003 0.035 3156 Dihedral : 8.234 115.910 2621 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.28 % Favored : 95.45 % Rotamer: Outliers : 2.64 % Allowed : 25.53 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 2196 helix: 1.30 (0.18), residues: 942 sheet: -0.44 (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 173 PHE 0.007 0.001 PHE E 255 TYR 0.007 0.001 TYR E 279 ARG 0.002 0.000 ARG C 290 *********************** 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 257 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.6730 (t80) REVERT: B 99 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: C 179 ASP cc_start: 0.8210 (m-30) cc_final: 0.7983 (m-30) REVERT: D 132 MET cc_start: 0.8942 (tmm) cc_final: 0.8449 (ttp) REVERT: D 283 MET cc_start: 0.7506 (ttm) cc_final: 0.7168 (mtt) REVERT: E 95 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8365 (mtm-85) REVERT: E 132 MET cc_start: 0.8864 (tmm) cc_final: 0.8456 (ttp) outliers start: 50 outliers final: 37 residues processed: 246 average time/residue: 0.2490 time to fit residues: 100.6170 Evaluate side-chains 242 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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 124 PHE Chi-restraints excluded: chain A residue 149 THR 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 106 THR Chi-restraints excluded: chain C residue 148 THR 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 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 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 370 VAL 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 180 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 164 optimal weight: 0.0770 chunk 128 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.148658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136355 restraints weight = 20127.825| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 1.39 r_work: 0.2694 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18344 Z= 0.257 Angle : 0.589 6.700 24905 Z= 0.276 Chirality : 0.047 0.243 2776 Planarity : 0.004 0.037 3156 Dihedral : 8.233 112.980 2621 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.96 % Favored : 94.76 % Rotamer: Outliers : 3.07 % Allowed : 25.37 % 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: 0.60 (0.19), residues: 2196 helix: 1.16 (0.18), residues: 942 sheet: -0.51 (0.26), residues: 378 loop : 0.16 (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 0.008 0.001 PHE A 255 TYR 0.007 0.001 TYR E 279 ARG 0.003 0.000 ARG F 290 *********************** 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 254 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.6854 (t80) REVERT: B 99 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: C 361 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7479 (mt-10) REVERT: D 132 MET cc_start: 0.9035 (tmm) cc_final: 0.8615 (ttp) REVERT: D 283 MET cc_start: 0.7960 (ttm) cc_final: 0.7647 (mmt) REVERT: E 115 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8359 (t0) REVERT: E 132 MET cc_start: 0.8979 (tmm) cc_final: 0.8625 (ttp) outliers start: 58 outliers final: 45 residues processed: 242 average time/residue: 0.2529 time to fit residues: 100.4079 Evaluate side-chains 242 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 199 SER 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 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 67 LEU 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 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 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 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 200 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 chunk 205 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2944 r_free = 0.2944 target = 0.097728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.086883 restraints weight = 22030.687| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.20 r_work: 0.2716 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18344 Z= 0.199 Angle : 0.568 6.438 24905 Z= 0.265 Chirality : 0.046 0.242 2776 Planarity : 0.003 0.036 3156 Dihedral : 8.197 113.393 2621 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.74 % Favored : 94.99 % Rotamer: Outliers : 2.59 % Allowed : 25.74 % 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: 0.65 (0.19), residues: 2196 helix: 1.21 (0.18), residues: 942 sheet: -0.48 (0.26), residues: 378 loop : 0.17 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.007 0.001 TYR A 133 ARG 0.003 0.000 ARG E 95 ********************** 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 252 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.6802 (t80) REVERT: B 41 GLN cc_start: 0.8242 (tt0) cc_final: 0.7919 (tt0) REVERT: B 99 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: C 361 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7477 (mt-10) REVERT: D 132 MET cc_start: 0.9024 (tmm) cc_final: 0.8586 (ttp) REVERT: D 283 MET cc_start: 0.7830 (ttm) cc_final: 0.7611 (mmt) REVERT: E 95 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8402 (mtm-85) REVERT: E 115 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8307 (t0) REVERT: E 132 MET cc_start: 0.8945 (tmm) cc_final: 0.8576 (ttp) REVERT: E 346 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8291 (tp) outliers start: 49 outliers final: 41 residues processed: 240 average time/residue: 0.2512 time to fit residues: 98.6351 Evaluate side-chains 245 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 124 PHE Chi-restraints excluded: chain A residue 149 THR 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 199 SER 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 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 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 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 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 346 LEU 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: 0.8980 chunk 7 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 203 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.149711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137406 restraints weight = 19956.032| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.39 r_work: 0.2689 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18344 Z= 0.216 Angle : 0.573 6.428 24905 Z= 0.267 Chirality : 0.046 0.242 2776 Planarity : 0.003 0.036 3156 Dihedral : 8.163 112.147 2621 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.01 % Favored : 94.72 % 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: 0.63 (0.19), residues: 2196 helix: 1.19 (0.18), residues: 942 sheet: -0.49 (0.26), residues: 378 loop : 0.17 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 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 F 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6905.18 seconds wall clock time: 124 minutes 27.08 seconds (7467.08 seconds total)