Starting phenix.real_space_refine on Sun Nov 17 03:55:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/11_2024/8tup_41628.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/11_2024/8tup_41628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/11_2024/8tup_41628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/11_2024/8tup_41628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/11_2024/8tup_41628.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/11_2024/8tup_41628.cif" } resolution = 3.3 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= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 3 5.21 5 S 65 5.16 5 C 8210 2.51 5 N 2155 2.21 5 O 2436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12869 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2560 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 309} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Restraints were copied for chains: B, C, D, E Time building chain proxies: 6.25, per 1000 atoms: 0.49 Number of scatterers: 12869 At special positions: 0 Unit cell: (107.07, 108.73, 140.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Mg 3 11.99 O 2436 8.00 N 2155 7.00 C 8210 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 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 69.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.953A pdb=" N ARG A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE A 120 " --> pdb=" O ASP A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 120' Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 183 through 219 Proline residue: A 209 - end of helix removed outlier: 3.755A pdb=" N ALA A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 261 removed outlier: 3.606A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.528A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.168A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 399 removed outlier: 3.610A pdb=" N GLY A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.954A pdb=" N ARG B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE B 120 " --> pdb=" O ASP B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 120' Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 183 through 219 Proline residue: B 209 - end of helix removed outlier: 3.755A pdb=" N ALA B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 261 removed outlier: 3.605A pdb=" N LEU B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.528A pdb=" N LEU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.168A pdb=" N LYS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET B 292 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.611A pdb=" N GLY B 386 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.954A pdb=" N ARG C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE C 120 " --> pdb=" O ASP C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 120' Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 183 through 219 Proline residue: C 209 - end of helix removed outlier: 3.754A pdb=" N ALA C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 261 removed outlier: 3.606A pdb=" N LEU C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 268 removed outlier: 3.528A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.168A pdb=" N LYS C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET C 292 " --> pdb=" O HIS C 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 329 " --> pdb=" O PHE C 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 332 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 335 " --> pdb=" O HIS C 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 399 removed outlier: 3.610A pdb=" N GLY C 386 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.953A pdb=" N ARG D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE D 120 " --> pdb=" O ASP D 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 120' Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 183 through 219 Proline residue: D 209 - end of helix removed outlier: 3.755A pdb=" N ALA D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 261 removed outlier: 3.606A pdb=" N LEU D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 268 removed outlier: 3.529A pdb=" N LEU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 Processing helix chain 'D' and resid 277 through 282 removed outlier: 4.168A pdb=" N LYS D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP D 329 " --> pdb=" O PHE D 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET D 335 " --> pdb=" O HIS D 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY D 356 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 399 removed outlier: 3.610A pdb=" N GLY D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.953A pdb=" N ARG E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE E 120 " --> pdb=" O ASP E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 116 through 120' Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 166 through 172 Processing helix chain 'E' and resid 183 through 219 Proline residue: E 209 - end of helix removed outlier: 3.755A pdb=" N ALA E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 218 " --> pdb=" O THR E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 261 removed outlier: 3.605A pdb=" N LEU E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 268 removed outlier: 3.528A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.167A pdb=" N LYS E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP E 329 " --> pdb=" O PHE E 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 334 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET E 335 " --> pdb=" O HIS E 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY E 356 " --> pdb=" O PHE E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 399 removed outlier: 3.611A pdb=" N GLY E 386 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 396 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL A 88 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 102 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL B 88 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 102 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL C 88 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 102 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL D 88 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 102 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL E 88 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG E 102 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4230 1.34 - 1.46: 2607 1.46 - 1.58: 6068 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13025 Sorted by residual: bond pdb=" CB PRO A 221 " pdb=" CG PRO A 221 " ideal model delta sigma weight residual 1.492 1.533 -0.041 5.00e-02 4.00e+02 6.67e-01 bond pdb=" CB PRO D 221 " pdb=" CG PRO D 221 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.55e-01 bond pdb=" CB PRO E 221 " pdb=" CG PRO E 221 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.50e-01 bond pdb=" CB PRO C 221 " pdb=" CG PRO C 221 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.46e-01 bond pdb=" CB PRO B 221 " pdb=" CG PRO B 221 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.33e-01 ... (remaining 13020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 17270 1.10 - 2.21: 261 2.21 - 3.31: 44 3.31 - 4.41: 5 4.41 - 5.51: 15 Bond angle restraints: 17595 Sorted by residual: angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 118.23 -4.13 2.00e+00 2.50e-01 4.27e+00 angle pdb=" CA GLU B 101 " pdb=" CB GLU B 101 " pdb=" CG GLU B 101 " ideal model delta sigma weight residual 114.10 118.23 -4.13 2.00e+00 2.50e-01 4.26e+00 angle pdb=" CA GLU C 101 " pdb=" CB GLU C 101 " pdb=" CG GLU C 101 " ideal model delta sigma weight residual 114.10 118.23 -4.13 2.00e+00 2.50e-01 4.26e+00 angle pdb=" CA GLU A 101 " pdb=" CB GLU A 101 " pdb=" CG GLU A 101 " ideal model delta sigma weight residual 114.10 118.19 -4.09 2.00e+00 2.50e-01 4.18e+00 angle pdb=" CA GLU E 101 " pdb=" CB GLU E 101 " pdb=" CG GLU E 101 " ideal model delta sigma weight residual 114.10 118.18 -4.08 2.00e+00 2.50e-01 4.17e+00 ... (remaining 17590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 6905 16.14 - 32.27: 721 32.27 - 48.41: 229 48.41 - 64.54: 50 64.54 - 80.68: 10 Dihedral angle restraints: 7915 sinusoidal: 3270 harmonic: 4645 Sorted by residual: dihedral pdb=" CB MET D 381 " pdb=" CG MET D 381 " pdb=" SD MET D 381 " pdb=" CE MET D 381 " ideal model delta sinusoidal sigma weight residual 60.00 2.99 57.01 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CB MET C 381 " pdb=" CG MET C 381 " pdb=" SD MET C 381 " pdb=" CE MET C 381 " ideal model delta sinusoidal sigma weight residual 60.00 3.00 57.00 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CB MET E 381 " pdb=" CG MET E 381 " pdb=" SD MET E 381 " pdb=" CE MET E 381 " ideal model delta sinusoidal sigma weight residual 60.00 3.01 56.99 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 7912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1224 0.026 - 0.052: 545 0.052 - 0.078: 150 0.078 - 0.104: 77 0.104 - 0.130: 29 Chirality restraints: 2025 Sorted by residual: chirality pdb=" CA ILE A 126 " pdb=" N ILE A 126 " pdb=" C ILE A 126 " pdb=" CB ILE A 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE C 126 " pdb=" N ILE C 126 " pdb=" C ILE C 126 " pdb=" CB ILE C 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE E 126 " pdb=" N ILE E 126 " pdb=" C ILE E 126 " pdb=" CB ILE E 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 2022 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 145 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO B 146 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 145 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO D 146 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 145 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO C 146 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.030 5.00e-02 4.00e+02 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3065 2.80 - 3.33: 12153 3.33 - 3.85: 21004 3.85 - 4.38: 24334 4.38 - 4.90: 43627 Nonbonded interactions: 104183 Sorted by model distance: nonbonded pdb=" OG SER D 125 " pdb=" O HOH D 501 " model vdw 2.277 3.040 nonbonded pdb=" OG SER E 125 " pdb=" O HOH E 501 " model vdw 2.278 3.040 nonbonded pdb=" OG SER C 125 " pdb=" O HOH C 501 " model vdw 2.278 3.040 nonbonded pdb=" OG SER B 125 " pdb=" O HOH B 601 " model vdw 2.278 3.040 nonbonded pdb=" OG SER A 125 " pdb=" O HOH A 601 " model vdw 2.278 3.040 ... (remaining 104178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 83 through 400) selection = (chain 'B' and resid 83 through 400) selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.130 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.002 0.041 13025 Z= 0.129 Angle : 0.406 5.513 17595 Z= 0.235 Chirality : 0.036 0.130 2025 Planarity : 0.003 0.054 2240 Dihedral : 14.814 80.680 4885 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 15.66 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.22), residues: 1580 helix: 2.00 (0.16), residues: 1025 sheet: 1.87 (0.43), residues: 135 loop : -0.50 (0.36), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 196 HIS 0.003 0.001 HIS C 288 PHE 0.012 0.001 PHE A 352 TYR 0.006 0.001 TYR C 299 ARG 0.003 0.000 ARG B 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.478 Fit side-chains REVERT: A 336 MET cc_start: 0.8142 (mmt) cc_final: 0.7517 (mmt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2329 time to fit residues: 26.3632 Evaluate side-chains 70 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN B 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN C 131 ASN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN D 131 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN E 131 ASN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13025 Z= 0.268 Angle : 0.515 5.791 17595 Z= 0.272 Chirality : 0.041 0.140 2025 Planarity : 0.003 0.034 2240 Dihedral : 3.542 15.026 1710 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.28 % Allowed : 13.59 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.22), residues: 1580 helix: 1.93 (0.15), residues: 1030 sheet: 2.21 (0.43), residues: 145 loop : -0.14 (0.38), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.015 0.002 PHE A 352 TYR 0.019 0.002 TYR A 299 ARG 0.003 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.467 Fit side-chains REVERT: B 130 ASN cc_start: 0.8864 (t0) cc_final: 0.8585 (t0) REVERT: D 130 ASN cc_start: 0.8878 (t0) cc_final: 0.8565 (t0) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.2929 time to fit residues: 55.2467 Evaluate side-chains 107 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 152 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13025 Z= 0.243 Angle : 0.486 6.489 17595 Z= 0.256 Chirality : 0.039 0.140 2025 Planarity : 0.003 0.037 2240 Dihedral : 3.504 12.875 1710 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.14 % Allowed : 13.67 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.22), residues: 1580 helix: 1.96 (0.15), residues: 1035 sheet: 2.13 (0.44), residues: 145 loop : -0.26 (0.38), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.015 0.001 PHE A 352 TYR 0.016 0.002 TYR E 299 ARG 0.006 0.000 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: B 130 ASN cc_start: 0.8888 (t0) cc_final: 0.8582 (t0) REVERT: D 130 ASN cc_start: 0.8897 (t0) cc_final: 0.8529 (t0) outliers start: 30 outliers final: 22 residues processed: 118 average time/residue: 0.2234 time to fit residues: 40.5927 Evaluate side-chains 108 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS D 122 HIS ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13025 Z= 0.355 Angle : 0.561 7.902 17595 Z= 0.291 Chirality : 0.042 0.149 2025 Planarity : 0.003 0.038 2240 Dihedral : 3.732 13.105 1710 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.78 % Allowed : 13.81 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.22), residues: 1580 helix: 1.74 (0.15), residues: 1030 sheet: 1.78 (0.47), residues: 135 loop : -0.04 (0.37), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.017 0.002 PHE B 352 TYR 0.020 0.002 TYR B 299 ARG 0.006 0.000 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 83 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.8600 (tpt) cc_final: 0.8312 (tpt) REVERT: D 228 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7468 (mtm-85) outliers start: 39 outliers final: 36 residues processed: 116 average time/residue: 0.2238 time to fit residues: 40.1543 Evaluate side-chains 119 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 0.1980 chunk 134 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13025 Z= 0.164 Angle : 0.444 6.836 17595 Z= 0.234 Chirality : 0.038 0.137 2025 Planarity : 0.003 0.038 2240 Dihedral : 3.400 12.760 1710 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.20 % Allowed : 13.59 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.22), residues: 1580 helix: 2.18 (0.15), residues: 1030 sheet: 1.61 (0.46), residues: 135 loop : -0.12 (0.36), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.012 0.001 PHE B 352 TYR 0.011 0.001 TYR A 299 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 91 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.8548 (tpt) cc_final: 0.8223 (tpt) REVERT: B 130 ASN cc_start: 0.8823 (t0) cc_final: 0.8560 (t0) REVERT: B 292 MET cc_start: 0.7081 (mtt) cc_final: 0.6819 (mtt) REVERT: D 130 ASN cc_start: 0.8877 (t0) cc_final: 0.8533 (t0) outliers start: 45 outliers final: 37 residues processed: 130 average time/residue: 0.2184 time to fit residues: 44.6228 Evaluate side-chains 125 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13025 Z= 0.185 Angle : 0.471 7.858 17595 Z= 0.244 Chirality : 0.038 0.141 2025 Planarity : 0.003 0.036 2240 Dihedral : 3.385 12.599 1710 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.70 % Allowed : 13.31 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.22), residues: 1580 helix: 2.27 (0.15), residues: 1030 sheet: 1.64 (0.46), residues: 135 loop : -0.11 (0.36), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS C 331 PHE 0.012 0.001 PHE A 352 TYR 0.014 0.001 TYR E 299 ARG 0.006 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 90 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 108 TYR cc_start: 0.8008 (m-10) cc_final: 0.7745 (m-10) REVERT: A 124 MET cc_start: 0.8592 (tpt) cc_final: 0.8227 (tpt) REVERT: B 130 ASN cc_start: 0.8811 (t0) cc_final: 0.8541 (t0) REVERT: B 292 MET cc_start: 0.7130 (mtt) cc_final: 0.6823 (mtt) REVERT: D 130 ASN cc_start: 0.8867 (t0) cc_final: 0.8612 (t0) outliers start: 52 outliers final: 43 residues processed: 135 average time/residue: 0.2229 time to fit residues: 47.4592 Evaluate side-chains 133 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13025 Z= 0.201 Angle : 0.482 7.234 17595 Z= 0.250 Chirality : 0.039 0.142 2025 Planarity : 0.003 0.036 2240 Dihedral : 3.430 14.479 1710 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.13 % Allowed : 14.02 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.22), residues: 1580 helix: 2.26 (0.15), residues: 1030 sheet: 1.64 (0.46), residues: 135 loop : -0.09 (0.36), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS E 331 PHE 0.013 0.001 PHE A 352 TYR 0.015 0.001 TYR A 299 ARG 0.006 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 85 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.8600 (tpt) cc_final: 0.8214 (tpt) REVERT: B 292 MET cc_start: 0.7171 (mtt) cc_final: 0.6845 (mtt) REVERT: D 130 ASN cc_start: 0.8872 (t0) cc_final: 0.8594 (t0) outliers start: 44 outliers final: 42 residues processed: 124 average time/residue: 0.2156 time to fit residues: 41.9173 Evaluate side-chains 127 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13025 Z= 0.290 Angle : 0.541 6.722 17595 Z= 0.280 Chirality : 0.041 0.147 2025 Planarity : 0.003 0.037 2240 Dihedral : 3.616 14.188 1710 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.42 % Allowed : 13.95 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.22), residues: 1580 helix: 2.02 (0.15), residues: 1030 sheet: 2.05 (0.44), residues: 145 loop : -0.19 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS E 331 PHE 0.015 0.002 PHE A 352 TYR 0.019 0.002 TYR B 299 ARG 0.005 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 84 time to evaluate : 1.592 Fit side-chains REVERT: B 292 MET cc_start: 0.7189 (mtt) cc_final: 0.6847 (mtt) REVERT: E 228 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7512 (mtm180) outliers start: 48 outliers final: 46 residues processed: 127 average time/residue: 0.2367 time to fit residues: 47.1589 Evaluate side-chains 126 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 399 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13025 Z= 0.293 Angle : 0.545 8.611 17595 Z= 0.281 Chirality : 0.041 0.146 2025 Planarity : 0.003 0.037 2240 Dihedral : 3.678 14.260 1710 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.27 % Allowed : 14.38 % Favored : 82.35 % 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: 2.11 (0.21), residues: 1580 helix: 1.94 (0.15), residues: 1030 sheet: 2.02 (0.45), residues: 145 loop : -0.21 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.015 0.002 PHE A 352 TYR 0.018 0.002 TYR E 299 ARG 0.006 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 78 time to evaluate : 1.351 Fit side-chains REVERT: B 292 MET cc_start: 0.7192 (mtt) cc_final: 0.6851 (mtt) REVERT: E 228 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7518 (mtm180) outliers start: 46 outliers final: 43 residues processed: 119 average time/residue: 0.2150 time to fit residues: 40.2364 Evaluate side-chains 118 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 75 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 50.0000 chunk 154 optimal weight: 0.8980 chunk 142 optimal weight: 0.0770 chunk 122 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13025 Z= 0.190 Angle : 0.488 6.754 17595 Z= 0.253 Chirality : 0.039 0.139 2025 Planarity : 0.003 0.036 2240 Dihedral : 3.509 14.307 1710 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.06 % Allowed : 14.88 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.22), residues: 1580 helix: 2.22 (0.15), residues: 1030 sheet: 1.96 (0.44), residues: 145 loop : -0.21 (0.36), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 196 HIS 0.003 0.001 HIS B 331 PHE 0.013 0.001 PHE D 352 TYR 0.013 0.001 TYR E 299 ARG 0.005 0.000 ARG B 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 79 time to evaluate : 1.490 Fit side-chains REVERT: A 124 MET cc_start: 0.8580 (tpt) cc_final: 0.8173 (tpt) REVERT: B 135 MET cc_start: 0.8987 (ptm) cc_final: 0.8772 (ptm) REVERT: B 292 MET cc_start: 0.7133 (mtt) cc_final: 0.6813 (mtt) REVERT: B 336 MET cc_start: 0.8087 (mmt) cc_final: 0.7570 (mmt) REVERT: E 228 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7513 (mtm180) outliers start: 43 outliers final: 40 residues processed: 118 average time/residue: 0.2239 time to fit residues: 41.7544 Evaluate side-chains 116 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 327 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 399 GLN B 122 HIS E 399 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.196342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.134141 restraints weight = 12057.918| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.21 r_work: 0.2992 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13025 Z= 0.371 Angle : 0.601 9.516 17595 Z= 0.308 Chirality : 0.042 0.151 2025 Planarity : 0.003 0.038 2240 Dihedral : 3.802 15.829 1710 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.20 % Allowed : 14.73 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1580 helix: 1.82 (0.15), residues: 1030 sheet: 1.98 (0.45), residues: 145 loop : -0.17 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS E 331 PHE 0.017 0.002 PHE D 352 TYR 0.023 0.002 TYR B 299 ARG 0.006 0.000 ARG B 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2349.19 seconds wall clock time: 44 minutes 11.37 seconds (2651.37 seconds total)