Starting phenix.real_space_refine on Fri Jul 3 20:40:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eki_31168/07_2026/7eki_31168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eki_31168/07_2026/7eki_31168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eki_31168/07_2026/7eki_31168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eki_31168/07_2026/7eki_31168.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7eki_31168/07_2026/7eki_31168.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eki_31168/07_2026/7eki_31168.cif" model { file = "/net/cci-nas-00/data/ceres_data/7eki_31168/07_2026/7eki_31168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eki_31168/07_2026/7eki_31168.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.010 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10480 2.51 5 N 2555 2.21 5 O 2855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16005 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 3200 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.86, per 1000 atoms: 0.18 Number of scatterers: 16005 At special positions: 0 Unit cell: (92.92, 93.93, 164.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 2855 8.00 N 2555 7.00 C 10480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 46 " " NAG B 601 " - " ASN B 46 " " NAG C 601 " - " ASN C 46 " " NAG D 601 " - " ASN D 46 " " NAG E 601 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 43.1% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.912A pdb=" N LYS A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 removed outlier: 3.541A pdb=" N GLY A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 removed outlier: 3.873A pdb=" N LEU A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.736A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 319 removed outlier: 3.640A pdb=" N VAL A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.925A pdb=" N ILE A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.618A pdb=" N LEU A 343 " --> pdb=" O CYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 490 removed outlier: 3.536A pdb=" N TYR A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.912A pdb=" N LYS B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 removed outlier: 3.542A pdb=" N GLY B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 removed outlier: 3.873A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 260 through 283 removed outlier: 3.736A pdb=" N THR B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 319 removed outlier: 3.640A pdb=" N VAL B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 removed outlier: 3.926A pdb=" N ILE B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.618A pdb=" N LEU B 343 " --> pdb=" O CYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 490 removed outlier: 3.537A pdb=" N TYR B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 461 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.911A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 237 removed outlier: 3.542A pdb=" N GLY C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 249 removed outlier: 3.873A pdb=" N LEU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 260 through 283 removed outlier: 3.736A pdb=" N THR C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU C 278 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 removed outlier: 3.639A pdb=" N VAL C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 removed outlier: 3.925A pdb=" N ILE C 334 " --> pdb=" O TRP C 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 335 " --> pdb=" O THR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.617A pdb=" N LEU C 343 " --> pdb=" O CYS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 490 removed outlier: 3.536A pdb=" N TYR C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 461 " --> pdb=" O CYS C 457 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.911A pdb=" N LYS D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 237 removed outlier: 3.542A pdb=" N GLY D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.873A pdb=" N LEU D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 260 through 283 removed outlier: 3.737A pdb=" N THR D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D 277 " --> pdb=" O THR D 273 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU D 278 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 319 removed outlier: 3.640A pdb=" N VAL D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 336 removed outlier: 3.925A pdb=" N ILE D 334 " --> pdb=" O TRP D 330 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 335 " --> pdb=" O THR D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.618A pdb=" N LEU D 343 " --> pdb=" O CYS D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 490 removed outlier: 3.537A pdb=" N TYR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 461 " --> pdb=" O CYS D 457 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.911A pdb=" N LYS E 28 " --> pdb=" O GLU E 24 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 237 removed outlier: 3.541A pdb=" N GLY E 234 " --> pdb=" O THR E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 249 removed outlier: 3.873A pdb=" N LEU E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 260 through 283 removed outlier: 3.736A pdb=" N THR E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU E 277 " --> pdb=" O THR E 273 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU E 278 " --> pdb=" O VAL E 274 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 319 removed outlier: 3.640A pdb=" N VAL E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 336 removed outlier: 3.925A pdb=" N ILE E 334 " --> pdb=" O TRP E 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 335 " --> pdb=" O THR E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.618A pdb=" N LEU E 343 " --> pdb=" O CYS E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 490 removed outlier: 3.537A pdb=" N TYR E 442 " --> pdb=" O GLU E 438 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 461 " --> pdb=" O CYS E 457 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 487 " --> pdb=" O THR E 483 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA E 490 " --> pdb=" O ILE E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 removed outlier: 5.017A pdb=" N GLY A 136 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 5.017A pdb=" N GLY A 136 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 71 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP A 64 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN A 75 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 79 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A 83 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR A 52 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 53 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.526A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.526A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 208 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 removed outlier: 5.018A pdb=" N GLY B 136 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 5.018A pdb=" N GLY B 136 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 71 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 64 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR B 73 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN B 75 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 79 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR B 83 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR B 52 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.527A pdb=" N GLY B 169 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.527A pdb=" N GLY B 169 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 208 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 removed outlier: 5.017A pdb=" N GLY C 136 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 5.017A pdb=" N GLY C 136 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL C 71 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP C 64 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 79 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR C 83 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR C 52 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 53 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.526A pdb=" N GLY C 169 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.526A pdb=" N GLY C 169 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 208 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 102 removed outlier: 5.017A pdb=" N GLY D 136 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 102 removed outlier: 5.017A pdb=" N GLY D 136 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL D 71 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN D 75 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D 79 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU D 51 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLN D 181 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 53 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 3.527A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 3.527A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 208 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102 removed outlier: 5.018A pdb=" N GLY E 136 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 5.018A pdb=" N GLY E 136 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL E 71 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP E 64 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN E 75 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN E 79 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR E 83 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR E 52 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 3.526A pdb=" N GLY E 169 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 3.526A pdb=" N GLY E 169 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 208 " --> pdb=" O TYR E 217 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2463 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: 2.59 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4890 1.35 - 1.47: 4220 1.47 - 1.59: 7155 1.59 - 1.71: 20 1.71 - 1.83: 170 Bond restraints: 16455 Sorted by residual: bond pdb=" C3 CLR E 602 " pdb=" O1 CLR E 602 " ideal model delta sigma weight residual 1.413 1.511 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C3 CLR B 602 " pdb=" O1 CLR B 602 " ideal model delta sigma weight residual 1.413 1.510 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C3 CLR C 602 " pdb=" O1 CLR C 602 " ideal model delta sigma weight residual 1.413 1.510 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C3 CLR D 602 " pdb=" O1 CLR D 602 " ideal model delta sigma weight residual 1.413 1.510 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C3 CLR A 602 " pdb=" O1 CLR A 602 " ideal model delta sigma weight residual 1.413 1.510 -0.097 2.00e-02 2.50e+03 2.33e+01 ... (remaining 16450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 22054 1.99 - 3.98: 352 3.98 - 5.98: 59 5.98 - 7.97: 15 7.97 - 9.96: 10 Bond angle restraints: 22490 Sorted by residual: angle pdb=" CB GLU B 452 " pdb=" CG GLU B 452 " pdb=" CD GLU B 452 " ideal model delta sigma weight residual 112.60 120.00 -7.40 1.70e+00 3.46e-01 1.89e+01 angle pdb=" CB GLU E 452 " pdb=" CG GLU E 452 " pdb=" CD GLU E 452 " ideal model delta sigma weight residual 112.60 119.98 -7.38 1.70e+00 3.46e-01 1.88e+01 angle pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " pdb=" CD GLU A 452 " ideal model delta sigma weight residual 112.60 119.97 -7.37 1.70e+00 3.46e-01 1.88e+01 angle pdb=" CB GLU C 452 " pdb=" CG GLU C 452 " pdb=" CD GLU C 452 " ideal model delta sigma weight residual 112.60 119.96 -7.36 1.70e+00 3.46e-01 1.88e+01 angle pdb=" CB GLU D 452 " pdb=" CG GLU D 452 " pdb=" CD GLU D 452 " ideal model delta sigma weight residual 112.60 119.95 -7.35 1.70e+00 3.46e-01 1.87e+01 ... (remaining 22485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 8643 15.88 - 31.76: 662 31.76 - 47.65: 185 47.65 - 63.53: 15 63.53 - 79.41: 10 Dihedral angle restraints: 9515 sinusoidal: 3685 harmonic: 5830 Sorted by residual: dihedral pdb=" CA CYS C 212 " pdb=" C CYS C 212 " pdb=" N CYS C 213 " pdb=" CA CYS C 213 " ideal model delta harmonic sigma weight residual 180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA CYS D 212 " pdb=" C CYS D 212 " pdb=" N CYS D 213 " pdb=" CA CYS D 213 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS E 212 " pdb=" C CYS E 212 " pdb=" N CYS E 213 " pdb=" CA CYS E 213 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 9512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2531 0.114 - 0.227: 64 0.227 - 0.341: 0 0.341 - 0.454: 10 0.454 - 0.568: 15 Chirality restraints: 2620 Sorted by residual: chirality pdb=" C3 CLR E 602 " pdb=" C2 CLR E 602 " pdb=" C4 CLR E 602 " pdb=" O1 CLR E 602 " both_signs ideal model delta sigma weight residual False -2.46 -3.02 0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" C14 CLR E 602 " pdb=" C13 CLR E 602 " pdb=" C15 CLR E 602 " pdb=" C8 CLR E 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.88 0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" C3 CLR D 602 " pdb=" C2 CLR D 602 " pdb=" C4 CLR D 602 " pdb=" O1 CLR D 602 " both_signs ideal model delta sigma weight residual False -2.46 -3.02 0.57 2.00e-01 2.50e+01 8.03e+00 ... (remaining 2617 not shown) Planarity restraints: 2765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 490 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO D 491 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 491 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 491 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 490 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO E 491 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 491 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 491 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 490 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 491 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.018 5.00e-02 4.00e+02 ... (remaining 2762 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2631 2.76 - 3.30: 14288 3.30 - 3.83: 24877 3.83 - 4.37: 28492 4.37 - 4.90: 51551 Nonbonded interactions: 121839 Sorted by model distance: nonbonded pdb=" OD1 ASP B 123 " pdb=" OG1 THR B 125 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP A 123 " pdb=" OG1 THR A 125 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP E 123 " pdb=" OG1 THR E 125 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP D 123 " pdb=" OG1 THR D 125 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP C 123 " pdb=" OG1 THR C 125 " model vdw 2.231 3.040 ... (remaining 121834 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.260 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 16480 Z= 0.249 Angle : 0.659 10.682 22555 Z= 0.310 Chirality : 0.063 0.568 2620 Planarity : 0.003 0.033 2755 Dihedral : 12.315 79.410 5715 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.88 % Allowed : 0.88 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 1960 helix: -0.98 (0.18), residues: 760 sheet: -0.88 (0.23), residues: 445 loop : -1.56 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 441 TYR 0.012 0.001 TYR C 190 PHE 0.005 0.001 PHE C 157 TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.25 (16455) covalent geometry : angle 0.62668 / 0.30 (22490) SS BOND : bond 0.00566 / 0.36 ( 10) SS BOND : angle 0.87818 / 0.60 ( 20) hydrogen bonds : bond 0.27039 / 17.22 ( 746) hydrogen bonds : angle 8.59569 / 6.03 ( 2463) link_BETA1-4 : bond 0.00820 / 0.52 ( 5) link_BETA1-4 : angle 1.38842 / 0.79 ( 15) link_NAG-ASN : bond 0.00531 / 0.34 ( 10) link_NAG-ASN : angle 5.50593 / 3.18 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.579 Fit side-chains REVERT: C 332 ARG cc_start: 0.7269 (tmm-80) cc_final: 0.6894 (ptm-80) REVERT: E 301 MET cc_start: 0.7686 (ttt) cc_final: 0.7379 (ttp) REVERT: E 452 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8078 (tt0) outliers start: 15 outliers final: 1 residues processed: 209 average time/residue: 0.1064 time to fit residues: 33.9505 Evaluate side-chains 162 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain E residue 452 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101135 restraints weight = 36486.602| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.03 r_work: 0.3119 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16480 Z= 0.139 Angle : 0.601 10.123 22555 Z= 0.303 Chirality : 0.042 0.143 2620 Planarity : 0.004 0.028 2755 Dihedral : 5.100 47.530 2186 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.52 % Allowed : 3.33 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.18), residues: 1960 helix: 0.35 (0.18), residues: 760 sheet: -0.53 (0.24), residues: 445 loop : -1.82 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 332 TYR 0.020 0.001 TYR C 190 PHE 0.009 0.001 PHE A 297 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS E 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (16455) covalent geometry : angle 0.57684 / 0.30 (22490) SS BOND : bond 0.00791 / 0.51 ( 10) SS BOND : angle 1.45578 / 0.99 ( 20) hydrogen bonds : bond 0.06511 / 4.23 ( 746) hydrogen bonds : angle 4.90220 / 3.43 ( 2463) link_BETA1-4 : bond 0.00438 / 0.27 ( 5) link_BETA1-4 : angle 1.88686 / 1.07 ( 15) link_NAG-ASN : bond 0.00571 / 0.36 ( 10) link_NAG-ASN : angle 4.30849 / 2.52 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: B 190 TYR cc_start: 0.7798 (t80) cc_final: 0.7411 (t80) REVERT: D 190 TYR cc_start: 0.7949 (t80) cc_final: 0.7566 (t80) REVERT: D 332 ARG cc_start: 0.6910 (ptm-80) cc_final: 0.6418 (tmm-80) REVERT: E 276 MET cc_start: 0.7180 (mtm) cc_final: 0.6700 (mmt) REVERT: E 332 ARG cc_start: 0.6906 (ptm-80) cc_final: 0.6402 (tmm-80) REVERT: E 452 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7874 (tm-30) outliers start: 26 outliers final: 22 residues processed: 202 average time/residue: 0.1137 time to fit residues: 34.9764 Evaluate side-chains 185 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 452 GLU Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 484 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 82 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.097965 restraints weight = 48031.070| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.50 r_work: 0.3040 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16480 Z= 0.145 Angle : 0.561 10.087 22555 Z= 0.282 Chirality : 0.041 0.136 2620 Planarity : 0.004 0.030 2755 Dihedral : 4.804 41.497 2186 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.88 % Allowed : 6.67 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 1960 helix: 0.98 (0.19), residues: 760 sheet: -0.46 (0.24), residues: 445 loop : -1.88 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 332 TYR 0.024 0.001 TYR E 190 PHE 0.014 0.001 PHE E 275 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (16455) covalent geometry : angle 0.54001 / 0.28 (22490) SS BOND : bond 0.00807 / 0.52 ( 10) SS BOND : angle 1.62614 / 1.15 ( 20) hydrogen bonds : bond 0.05658 / 3.67 ( 746) hydrogen bonds : angle 4.40378 / 3.09 ( 2463) link_BETA1-4 : bond 0.00380 / 0.24 ( 5) link_BETA1-4 : angle 1.26321 / 0.73 ( 15) link_NAG-ASN : bond 0.00537 / 0.34 ( 10) link_NAG-ASN : angle 3.91336 / 2.30 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 TYR cc_start: 0.8159 (t80) cc_final: 0.7830 (t80) REVERT: A 452 GLU cc_start: 0.8224 (tm-30) cc_final: 0.8024 (tm-30) REVERT: B 332 ARG cc_start: 0.7266 (ptm-80) cc_final: 0.6649 (tmm-80) REVERT: D 190 TYR cc_start: 0.8199 (t80) cc_final: 0.7816 (t80) REVERT: D 332 ARG cc_start: 0.6882 (ptm-80) cc_final: 0.6557 (tmm-80) REVERT: E 332 ARG cc_start: 0.6830 (ptm-80) cc_final: 0.6397 (tmm-80) REVERT: E 452 GLU cc_start: 0.8232 (tm-30) cc_final: 0.8003 (tm-30) outliers start: 15 outliers final: 14 residues processed: 187 average time/residue: 0.0983 time to fit residues: 27.7111 Evaluate side-chains 191 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 257 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 190 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.132109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099090 restraints weight = 44971.860| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.39 r_work: 0.3053 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16480 Z= 0.128 Angle : 0.538 9.871 22555 Z= 0.269 Chirality : 0.040 0.138 2620 Planarity : 0.003 0.029 2755 Dihedral : 4.462 34.527 2180 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.23 % Allowed : 7.60 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1960 helix: 1.13 (0.19), residues: 760 sheet: -0.31 (0.24), residues: 445 loop : -1.97 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.022 0.001 TYR B 190 PHE 0.027 0.001 PHE C 275 TRP 0.016 0.001 TRP D 460 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16455) covalent geometry : angle 0.52000 / 0.26 (22490) SS BOND : bond 0.00838 / 0.54 ( 10) SS BOND : angle 1.67597 / 1.19 ( 20) hydrogen bonds : bond 0.04837 / 3.14 ( 746) hydrogen bonds : angle 4.15407 / 2.92 ( 2463) link_BETA1-4 : bond 0.00507 / 0.33 ( 5) link_BETA1-4 : angle 1.05939 / 0.61 ( 15) link_NAG-ASN : bond 0.00449 / 0.29 ( 10) link_NAG-ASN : angle 3.51711 / 2.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8396 (t70) cc_final: 0.7696 (t0) REVERT: A 190 TYR cc_start: 0.8114 (t80) cc_final: 0.7770 (t80) REVERT: A 450 GLN cc_start: 0.7678 (tt0) cc_final: 0.7215 (mt0) REVERT: A 452 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8068 (tm-30) REVERT: D 190 TYR cc_start: 0.8079 (t80) cc_final: 0.7710 (t80) REVERT: D 332 ARG cc_start: 0.7003 (ptm-80) cc_final: 0.6449 (tmm-80) REVERT: E 297 PHE cc_start: 0.7207 (m-10) cc_final: 0.6957 (t80) REVERT: E 332 ARG cc_start: 0.6951 (ptm-80) cc_final: 0.6527 (tmm-80) REVERT: E 450 GLN cc_start: 0.7648 (tt0) cc_final: 0.7371 (mt0) REVERT: E 452 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8045 (tm-30) outliers start: 21 outliers final: 17 residues processed: 193 average time/residue: 0.1110 time to fit residues: 32.3729 Evaluate side-chains 190 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 226 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 6 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 133 optimal weight: 0.0020 chunk 185 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 236 ASN E 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099690 restraints weight = 50291.774| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.58 r_work: 0.3057 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16480 Z= 0.117 Angle : 0.528 9.379 22555 Z= 0.262 Chirality : 0.040 0.137 2620 Planarity : 0.003 0.028 2755 Dihedral : 4.361 32.343 2180 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.17 % Allowed : 8.30 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1960 helix: 1.17 (0.19), residues: 785 sheet: -0.16 (0.25), residues: 445 loop : -1.96 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 332 TYR 0.019 0.001 TYR E 190 PHE 0.025 0.001 PHE B 275 TRP 0.011 0.001 TRP D 460 HIS 0.002 0.001 HIS D 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16455) covalent geometry : angle 0.51185 / 0.26 (22490) SS BOND : bond 0.00850 / 0.54 ( 10) SS BOND : angle 1.69231 / 1.19 ( 20) hydrogen bonds : bond 0.04509 / 2.92 ( 746) hydrogen bonds : angle 4.01680 / 2.83 ( 2463) link_BETA1-4 : bond 0.00453 / 0.29 ( 5) link_BETA1-4 : angle 0.98704 / 0.57 ( 15) link_NAG-ASN : bond 0.00418 / 0.27 ( 10) link_NAG-ASN : angle 3.32323 / 1.97 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8357 (t70) cc_final: 0.7679 (t0) REVERT: A 190 TYR cc_start: 0.8091 (t80) cc_final: 0.7762 (t80) REVERT: A 450 GLN cc_start: 0.7634 (tt0) cc_final: 0.7202 (mt0) REVERT: A 452 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 190 TYR cc_start: 0.8033 (t80) cc_final: 0.7664 (t80) REVERT: E 297 PHE cc_start: 0.7232 (m-10) cc_final: 0.6926 (t80) REVERT: E 332 ARG cc_start: 0.6980 (ptm-80) cc_final: 0.6560 (tmm-80) REVERT: E 450 GLN cc_start: 0.7655 (tt0) cc_final: 0.7418 (mt0) REVERT: E 452 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8034 (tm-30) outliers start: 20 outliers final: 17 residues processed: 187 average time/residue: 0.1176 time to fit residues: 33.2193 Evaluate side-chains 191 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 257 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 40 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098264 restraints weight = 49925.187| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.55 r_work: 0.3039 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16480 Z= 0.140 Angle : 0.545 9.254 22555 Z= 0.270 Chirality : 0.041 0.140 2620 Planarity : 0.003 0.029 2755 Dihedral : 4.396 29.775 2180 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.40 % Allowed : 9.06 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1960 helix: 1.20 (0.18), residues: 780 sheet: -0.15 (0.25), residues: 455 loop : -1.95 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.022 0.001 TYR B 190 PHE 0.025 0.001 PHE A 275 TRP 0.011 0.001 TRP D 460 HIS 0.009 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (16455) covalent geometry : angle 0.52806 / 0.27 (22490) SS BOND : bond 0.00827 / 0.53 ( 10) SS BOND : angle 1.64201 / 1.16 ( 20) hydrogen bonds : bond 0.04636 / 3.01 ( 746) hydrogen bonds : angle 4.06460 / 2.86 ( 2463) link_BETA1-4 : bond 0.00400 / 0.26 ( 5) link_BETA1-4 : angle 1.00787 / 0.59 ( 15) link_NAG-ASN : bond 0.00441 / 0.28 ( 10) link_NAG-ASN : angle 3.47873 / 2.05 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8379 (t70) cc_final: 0.7814 (t0) REVERT: A 190 TYR cc_start: 0.8160 (t80) cc_final: 0.7882 (t80) REVERT: A 450 GLN cc_start: 0.7644 (tt0) cc_final: 0.7221 (mt0) REVERT: A 452 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 66 ASP cc_start: 0.8514 (t70) cc_final: 0.7995 (t0) REVERT: E 332 ARG cc_start: 0.7039 (ptm-80) cc_final: 0.6637 (tmm-80) REVERT: E 450 GLN cc_start: 0.7682 (tt0) cc_final: 0.7460 (mt0) REVERT: E 452 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8051 (tm-30) outliers start: 24 outliers final: 22 residues processed: 188 average time/residue: 0.1142 time to fit residues: 32.4360 Evaluate side-chains 198 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 257 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098365 restraints weight = 44938.557| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.81 r_work: 0.2984 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16480 Z= 0.194 Angle : 0.595 10.253 22555 Z= 0.294 Chirality : 0.042 0.144 2620 Planarity : 0.004 0.030 2755 Dihedral : 4.551 27.863 2180 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.64 % Allowed : 9.36 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1960 helix: 1.09 (0.18), residues: 780 sheet: -0.23 (0.25), residues: 445 loop : -2.07 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.025 0.001 TYR B 190 PHE 0.023 0.002 PHE A 275 TRP 0.008 0.001 TRP E 82 HIS 0.006 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (16455) covalent geometry : angle 0.57603 / 0.29 (22490) SS BOND : bond 0.00826 / 0.53 ( 10) SS BOND : angle 1.69557 / 1.19 ( 20) hydrogen bonds : bond 0.05088 / 3.29 ( 746) hydrogen bonds : angle 4.20424 / 2.96 ( 2463) link_BETA1-4 : bond 0.00311 / 0.20 ( 5) link_BETA1-4 : angle 1.08875 / 0.63 ( 15) link_NAG-ASN : bond 0.00565 / 0.36 ( 10) link_NAG-ASN : angle 3.89877 / 2.29 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.7718 (tt0) cc_final: 0.7295 (mt0) REVERT: A 452 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 489 SER cc_start: 0.8080 (t) cc_final: 0.7696 (p) REVERT: B 489 SER cc_start: 0.8038 (t) cc_final: 0.7666 (p) REVERT: C 489 SER cc_start: 0.7931 (t) cc_final: 0.7603 (p) REVERT: D 66 ASP cc_start: 0.8609 (t70) cc_final: 0.8016 (t0) REVERT: D 489 SER cc_start: 0.7950 (t) cc_final: 0.7571 (p) REVERT: E 332 ARG cc_start: 0.7090 (ptm-80) cc_final: 0.6717 (tmm-80) REVERT: E 450 GLN cc_start: 0.7778 (tt0) cc_final: 0.7551 (mt0) REVERT: E 452 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8198 (tm-30) REVERT: E 489 SER cc_start: 0.7790 (t) cc_final: 0.7241 (p) outliers start: 28 outliers final: 24 residues processed: 198 average time/residue: 0.1233 time to fit residues: 37.1374 Evaluate side-chains 205 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 257 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101408 restraints weight = 45598.401| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.75 r_work: 0.3040 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16480 Z= 0.116 Angle : 0.538 9.135 22555 Z= 0.264 Chirality : 0.040 0.145 2620 Planarity : 0.003 0.029 2755 Dihedral : 4.414 28.546 2180 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.17 % Allowed : 10.82 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1960 helix: 1.20 (0.18), residues: 780 sheet: -0.16 (0.24), residues: 455 loop : -2.02 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 332 TYR 0.015 0.001 TYR E 190 PHE 0.023 0.001 PHE A 275 TRP 0.013 0.001 TRP D 460 HIS 0.006 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (16455) covalent geometry : angle 0.52153 / 0.26 (22490) SS BOND : bond 0.00850 / 0.54 ( 10) SS BOND : angle 1.70672 / 1.20 ( 20) hydrogen bonds : bond 0.04394 / 2.84 ( 746) hydrogen bonds : angle 3.94815 / 2.78 ( 2463) link_BETA1-4 : bond 0.00485 / 0.31 ( 5) link_BETA1-4 : angle 0.99014 / 0.57 ( 15) link_NAG-ASN : bond 0.00429 / 0.27 ( 10) link_NAG-ASN : angle 3.34621 / 1.98 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.7716 (tt0) cc_final: 0.7338 (mt0) REVERT: A 452 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 489 SER cc_start: 0.8045 (t) cc_final: 0.7670 (p) REVERT: B 489 SER cc_start: 0.7957 (t) cc_final: 0.7594 (p) REVERT: C 489 SER cc_start: 0.7897 (t) cc_final: 0.7564 (p) REVERT: D 66 ASP cc_start: 0.8544 (t70) cc_final: 0.8038 (t0) REVERT: D 68 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8153 (mmmm) REVERT: D 489 SER cc_start: 0.7905 (t) cc_final: 0.7538 (p) REVERT: E 332 ARG cc_start: 0.7112 (ptm-80) cc_final: 0.6703 (tmm-80) REVERT: E 452 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8206 (tm-30) REVERT: E 489 SER cc_start: 0.7751 (t) cc_final: 0.7225 (p) outliers start: 20 outliers final: 17 residues processed: 186 average time/residue: 0.1268 time to fit residues: 35.7897 Evaluate side-chains 190 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 187 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 8.9990 chunk 114 optimal weight: 0.5980 chunk 179 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 188 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098608 restraints weight = 48176.527| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.51 r_work: 0.3051 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16480 Z= 0.127 Angle : 0.540 8.939 22555 Z= 0.266 Chirality : 0.040 0.145 2620 Planarity : 0.003 0.029 2755 Dihedral : 4.362 27.677 2180 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.23 % Allowed : 10.99 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 1960 helix: 1.18 (0.18), residues: 785 sheet: -0.16 (0.24), residues: 455 loop : -2.04 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 332 TYR 0.018 0.001 TYR B 190 PHE 0.026 0.001 PHE C 275 TRP 0.013 0.001 TRP D 460 HIS 0.005 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16455) covalent geometry : angle 0.52404 / 0.26 (22490) SS BOND : bond 0.00846 / 0.54 ( 10) SS BOND : angle 1.67026 / 1.17 ( 20) hydrogen bonds : bond 0.04403 / 2.85 ( 746) hydrogen bonds : angle 3.93098 / 2.77 ( 2463) link_BETA1-4 : bond 0.00392 / 0.25 ( 5) link_BETA1-4 : angle 0.95876 / 0.56 ( 15) link_NAG-ASN : bond 0.00414 / 0.26 ( 10) link_NAG-ASN : angle 3.38304 / 1.99 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.7632 (tt0) cc_final: 0.7253 (mt0) REVERT: A 452 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 489 SER cc_start: 0.8091 (t) cc_final: 0.7695 (p) REVERT: B 489 SER cc_start: 0.7921 (t) cc_final: 0.7544 (p) REVERT: C 489 SER cc_start: 0.7854 (t) cc_final: 0.7509 (p) REVERT: D 66 ASP cc_start: 0.8481 (t70) cc_final: 0.7935 (t0) REVERT: D 489 SER cc_start: 0.7862 (t) cc_final: 0.7483 (p) REVERT: E 452 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8145 (tm-30) REVERT: E 489 SER cc_start: 0.7714 (t) cc_final: 0.7165 (p) outliers start: 21 outliers final: 19 residues processed: 185 average time/residue: 0.1121 time to fit residues: 31.7742 Evaluate side-chains 190 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 226 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 49 optimal weight: 0.0470 chunk 185 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.0270 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103522 restraints weight = 41252.404| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.50 r_work: 0.3084 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16480 Z= 0.104 Angle : 0.515 8.642 22555 Z= 0.254 Chirality : 0.039 0.146 2620 Planarity : 0.003 0.028 2755 Dihedral : 4.237 28.074 2180 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.11 % Allowed : 11.11 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1960 helix: 1.28 (0.18), residues: 785 sheet: -0.04 (0.24), residues: 455 loop : -1.99 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 332 TYR 0.011 0.001 TYR A 140 PHE 0.027 0.001 PHE C 275 TRP 0.010 0.001 TRP D 460 HIS 0.005 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (16455) covalent geometry : angle 0.50055 / 0.25 (22490) SS BOND : bond 0.00862 / 0.55 ( 10) SS BOND : angle 1.70834 / 1.20 ( 20) hydrogen bonds : bond 0.03913 / 2.53 ( 746) hydrogen bonds : angle 3.74450 / 2.64 ( 2463) link_BETA1-4 : bond 0.00548 / 0.35 ( 5) link_BETA1-4 : angle 0.86407 / 0.50 ( 15) link_NAG-ASN : bond 0.00380 / 0.24 ( 10) link_NAG-ASN : angle 2.99777 / 1.78 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8347 (t70) cc_final: 0.7892 (t0) REVERT: A 450 GLN cc_start: 0.7674 (tt0) cc_final: 0.7353 (mt0) REVERT: A 452 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 489 SER cc_start: 0.8027 (t) cc_final: 0.7644 (p) REVERT: B 66 ASP cc_start: 0.8333 (t70) cc_final: 0.7916 (t0) REVERT: B 236 ASN cc_start: 0.8351 (m110) cc_final: 0.8110 (m-40) REVERT: B 489 SER cc_start: 0.7895 (t) cc_final: 0.7536 (p) REVERT: C 66 ASP cc_start: 0.8322 (t70) cc_final: 0.7830 (t0) REVERT: C 489 SER cc_start: 0.7824 (t) cc_final: 0.7485 (p) REVERT: D 66 ASP cc_start: 0.8437 (t70) cc_final: 0.7995 (t0) REVERT: D 68 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8122 (mmmm) REVERT: D 489 SER cc_start: 0.7882 (t) cc_final: 0.7522 (p) REVERT: E 66 ASP cc_start: 0.8375 (t70) cc_final: 0.7674 (t0) REVERT: E 68 LYS cc_start: 0.8420 (mmmm) cc_final: 0.8042 (mmmt) REVERT: E 452 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8194 (tm-30) outliers start: 19 outliers final: 14 residues processed: 190 average time/residue: 0.1190 time to fit residues: 34.4109 Evaluate side-chains 191 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain E residue 187 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 107 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.130303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099710 restraints weight = 46391.713| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.82 r_work: 0.3019 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16480 Z= 0.169 Angle : 0.573 9.123 22555 Z= 0.283 Chirality : 0.042 0.139 2620 Planarity : 0.004 0.029 2755 Dihedral : 4.371 26.328 2180 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.88 % Allowed : 11.58 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 1960 helix: 1.24 (0.18), residues: 780 sheet: -0.18 (0.24), residues: 455 loop : -2.03 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 332 TYR 0.025 0.001 TYR B 190 PHE 0.028 0.002 PHE C 275 TRP 0.011 0.001 TRP D 460 HIS 0.004 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (16455) covalent geometry : angle 0.55530 / 0.28 (22490) SS BOND : bond 0.00825 / 0.53 ( 10) SS BOND : angle 1.64528 / 1.15 ( 20) hydrogen bonds : bond 0.04662 / 3.02 ( 746) hydrogen bonds : angle 4.00758 / 2.82 ( 2463) link_BETA1-4 : bond 0.00285 / 0.18 ( 5) link_BETA1-4 : angle 1.01596 / 0.59 ( 15) link_NAG-ASN : bond 0.00490 / 0.31 ( 10) link_NAG-ASN : angle 3.64683 / 2.14 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.74 seconds wall clock time: 57 minutes 47.84 seconds (3467.84 seconds total)