Starting phenix.real_space_refine on Sun Dec 10 00:50:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/12_2023/8tup_41628.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/12_2023/8tup_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_41628/12_2023/8tup_41628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/12_2023/8tup_41628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/12_2023/8tup_41628.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/12_2023/8tup_41628.pdb" } 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 Residue "A GLU 101": "OE1" <-> "OE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12869 Number of models: 1 Model: "" Number of chains: 12 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: "B" 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: "C" 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: "D" 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: "E" 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} Time building chain proxies: 7.01, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.08 Conformation dependent library (CDL) restraints added in 2.2 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: 1.29 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: 3.62 Time building geometry restraints manager: 5.49 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: 98.35 - 105.49: 180 105.49 - 112.63: 6933 112.63 - 119.76: 4341 119.76 - 126.90: 6010 126.90 - 134.04: 131 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 2.440 nonbonded pdb=" OG SER E 125 " pdb=" O HOH E 501 " model vdw 2.278 2.440 nonbonded pdb=" OG SER C 125 " pdb=" O HOH C 501 " model vdw 2.278 2.440 nonbonded pdb=" OG SER B 125 " pdb=" O HOH B 601 " model vdw 2.278 2.440 nonbonded pdb=" OG SER A 125 " pdb=" O HOH A 601 " model vdw 2.278 2.440 ... (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 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: 2.080 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: 7.240 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.440 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.630 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.495 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2386 time to fit residues: 26.7698 Evaluate side-chains 70 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0581 ------------------------------------------------------------------------------- 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: 0.6980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 0.0470 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 140 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN B 339 ASN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13025 Z= 0.236 Angle : 0.482 5.991 17595 Z= 0.255 Chirality : 0.039 0.141 2025 Planarity : 0.003 0.033 2240 Dihedral : 3.408 14.273 1710 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.57 % Allowed : 15.02 % 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: 2.33 (0.22), residues: 1580 helix: 2.10 (0.16), residues: 1030 sheet: 1.98 (0.42), residues: 145 loop : -0.03 (0.39), 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 0.014 0.002 PHE A 352 TYR 0.018 0.002 TYR A 299 ARG 0.002 0.000 ARG C 228 *********************** 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 105 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 1.284 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 105 average time/residue: 0.2641 time to fit residues: 40.4830 Evaluate side-chains 82 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1141 time to fit residues: 4.1183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 152 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS B 122 HIS C 122 HIS D 122 HIS E 122 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13025 Z= 0.340 Angle : 0.549 6.570 17595 Z= 0.286 Chirality : 0.042 0.149 2025 Planarity : 0.003 0.038 2240 Dihedral : 3.706 13.228 1710 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.06 % Allowed : 15.02 % Favored : 82.92 % 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: 2.00 (0.22), residues: 1580 helix: 1.82 (0.15), residues: 1030 sheet: 1.54 (0.46), residues: 135 loop : 0.13 (0.38), 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 0.016 0.002 PHE A 352 TYR 0.019 0.002 TYR A 299 ARG 0.006 0.000 ARG B 102 *********************** 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 113 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 84 time to evaluate : 1.344 Fit side-chains outliers start: 29 outliers final: 15 residues processed: 111 average time/residue: 0.2418 time to fit residues: 40.6844 Evaluate side-chains 96 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1814 time to fit residues: 6.3400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 0.0670 chunk 141 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1689 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= 0.229 Angle : 0.468 6.588 17595 Z= 0.246 Chirality : 0.039 0.140 2025 Planarity : 0.003 0.038 2240 Dihedral : 3.499 12.703 1710 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.78 % Allowed : 15.37 % Favored : 83.84 % 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: 2.23 (0.22), residues: 1580 helix: 2.06 (0.15), residues: 1030 sheet: 1.44 (0.46), residues: 135 loop : 0.07 (0.38), 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 0.013 0.001 PHE D 352 TYR 0.016 0.002 TYR E 299 ARG 0.004 0.000 ARG B 102 *********************** 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 98 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.563 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 96 average time/residue: 0.2350 time to fit residues: 35.4351 Evaluate side-chains 89 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1295 time to fit residues: 4.6721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7607 moved from start: 0.1835 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= 0.263 Angle : 0.495 7.092 17595 Z= 0.258 Chirality : 0.039 0.142 2025 Planarity : 0.003 0.038 2240 Dihedral : 3.531 12.948 1710 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.49 % Allowed : 15.09 % 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: 2.24 (0.22), residues: 1580 helix: 2.06 (0.15), residues: 1030 sheet: 1.46 (0.46), residues: 135 loop : 0.12 (0.38), residues: 415 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 0.014 0.002 PHE B 352 TYR 0.017 0.002 TYR E 299 ARG 0.004 0.000 ARG B 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 105 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 1.335 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 0.2336 time to fit residues: 38.2295 Evaluate side-chains 94 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1438 time to fit residues: 5.5068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7654 moved from start: 0.2125 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= 0.393 Angle : 0.592 7.066 17595 Z= 0.303 Chirality : 0.042 0.150 2025 Planarity : 0.003 0.039 2240 Dihedral : 3.822 13.380 1710 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.49 % Allowed : 15.16 % Favored : 83.35 % 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: 1.89 (0.22), residues: 1580 helix: 1.72 (0.15), residues: 1030 sheet: 1.40 (0.47), residues: 135 loop : 0.15 (0.38), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 196 HIS 0.004 0.001 HIS B 331 PHE 0.018 0.002 PHE A 86 TYR 0.021 0.002 TYR B 299 ARG 0.003 0.000 ARG E 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 108 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.513 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 104 average time/residue: 0.2401 time to fit residues: 38.1870 Evaluate side-chains 99 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1185 time to fit residues: 5.6671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 109 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.1889 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= 0.174 Angle : 0.463 6.938 17595 Z= 0.239 Chirality : 0.038 0.137 2025 Planarity : 0.003 0.036 2240 Dihedral : 3.470 12.986 1710 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.43 % Allowed : 15.44 % 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: 2.44 (0.22), residues: 1580 helix: 2.22 (0.15), residues: 1030 sheet: 1.69 (0.45), residues: 145 loop : 0.06 (0.38), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 E 299 ARG 0.003 0.000 ARG D 228 *********************** 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 92 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.349 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 90 average time/residue: 0.2338 time to fit residues: 32.7114 Evaluate side-chains 80 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1186 time to fit residues: 2.6466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.0370 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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: 0.7602 moved from start: 0.1983 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= 0.246 Angle : 0.501 6.953 17595 Z= 0.258 Chirality : 0.039 0.144 2025 Planarity : 0.003 0.036 2240 Dihedral : 3.536 12.915 1710 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.50 % Allowed : 16.30 % 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: 2.41 (0.22), residues: 1580 helix: 2.16 (0.15), residues: 1030 sheet: 1.74 (0.45), residues: 145 loop : 0.14 (0.38), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 196 HIS 0.003 0.001 HIS B 331 PHE 0.014 0.002 PHE C 352 TYR 0.017 0.002 TYR E 299 ARG 0.003 0.000 ARG D 228 *********************** 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 86 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.524 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 85 average time/residue: 0.2986 time to fit residues: 39.3760 Evaluate side-chains 82 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.489 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1200 time to fit residues: 2.5747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7594 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13025 Z= 0.229 Angle : 0.493 6.934 17595 Z= 0.254 Chirality : 0.039 0.143 2025 Planarity : 0.003 0.036 2240 Dihedral : 3.527 14.367 1710 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.36 % Allowed : 16.65 % 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: 2.46 (0.22), residues: 1580 helix: 2.21 (0.15), residues: 1030 sheet: 1.73 (0.45), residues: 145 loop : 0.13 (0.38), 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 0.014 0.001 PHE C 352 TYR 0.016 0.001 TYR E 299 ARG 0.003 0.000 ARG D 228 *********************** 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 85 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.450 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.2459 time to fit residues: 30.9762 Evaluate side-chains 83 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1679 time to fit residues: 3.5299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 102 optimal weight: 0.1980 chunk 154 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.1935 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= 0.176 Angle : 0.465 6.909 17595 Z= 0.240 Chirality : 0.038 0.137 2025 Planarity : 0.003 0.035 2240 Dihedral : 3.425 13.930 1710 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 16.87 % Favored : 83.13 % 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: 2.64 (0.22), residues: 1580 helix: 2.38 (0.15), residues: 1030 sheet: 1.70 (0.45), residues: 145 loop : 0.12 (0.38), residues: 405 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 C 352 TYR 0.012 0.001 TYR E 299 ARG 0.004 0.000 ARG D 228 ********************** 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 77 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.472 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2412 time to fit residues: 29.0150 Evaluate side-chains 76 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.207323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141479 restraints weight = 11680.670| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.18 r_work: 0.3176 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1960 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= 0.181 Angle : 0.469 7.050 17595 Z= 0.241 Chirality : 0.038 0.140 2025 Planarity : 0.003 0.035 2240 Dihedral : 3.406 13.364 1710 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.14 % Allowed : 17.01 % 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: 2.69 (0.22), residues: 1580 helix: 2.41 (0.15), residues: 1030 sheet: 1.73 (0.45), residues: 145 loop : 0.15 (0.38), 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 0.012 0.001 PHE D 352 TYR 0.013 0.001 TYR E 299 ARG 0.004 0.000 ARG D 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2227.30 seconds wall clock time: 41 minutes 37.81 seconds (2497.81 seconds total)