Starting phenix.real_space_refine on Tue Dec 31 16:06:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eki_31168/12_2024/7eki_31168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eki_31168/12_2024/7eki_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_31168/12_2024/7eki_31168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eki_31168/12_2024/7eki_31168.map" model { file = "/net/cci-nas-00/data/ceres_data/7eki_31168/12_2024/7eki_31168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eki_31168/12_2024/7eki_31168.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} 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: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 3200 Chain: "G" 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: F, I, H, J, C, B, E, D Time building chain proxies: 8.35, per 1000 atoms: 0.52 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=2, 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 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: 4.63 Conformation dependent library (CDL) restraints added in 4.1 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: 1.68 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: 5.05 Time building geometry restraints manager: 5.25 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: 9170 15.88 - 31.76: 681 31.76 - 47.65: 210 47.65 - 63.53: 15 63.53 - 79.41: 10 Dihedral angle restraints: 10086 sinusoidal: 4256 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 10083 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: 2.03 - 2.61: 113 2.61 - 3.18: 13089 3.18 - 3.75: 22916 3.75 - 4.33: 31571 4.33 - 4.90: 54174 Nonbonded interactions: 121863 Sorted by model distance: nonbonded pdb=" SG CYS C 150 " pdb=" SG CYS C 164 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS E 150 " pdb=" SG CYS E 164 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS B 150 " pdb=" SG CYS B 164 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS D 150 " pdb=" SG CYS D 164 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS B 212 " pdb=" SG CYS B 213 " model vdw 2.039 3.760 ... (remaining 121858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 39.140 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 16455 Z= 0.321 Angle : 0.627 9.959 22490 Z= 0.302 Chirality : 0.063 0.568 2620 Planarity : 0.003 0.033 2755 Dihedral : 12.209 79.410 6310 Min Nonbonded Distance : 2.033 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (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 TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS B 320 PHE 0.005 0.001 PHE C 157 TYR 0.012 0.001 TYR C 190 ARG 0.007 0.000 ARG B 441 *********************** 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 : 1.767 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: 0.2977 time to fit residues: 93.2805 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 : 2.160 ------------------------------------------------------------------------------- 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 164 optimal weight: 0.0670 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 0.1980 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16455 Z= 0.288 Angle : 0.616 10.525 22490 Z= 0.319 Chirality : 0.044 0.152 2620 Planarity : 0.004 0.030 2755 Dihedral : 6.046 42.090 2781 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.75 % Allowed : 3.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 1960 helix: 0.26 (0.18), residues: 760 sheet: -0.64 (0.24), residues: 445 loop : -1.97 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.002 HIS A 163 PHE 0.011 0.002 PHE B 126 TYR 0.029 0.002 TYR C 190 ARG 0.005 0.000 ARG D 332 *********************** 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 230 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: B 332 ARG cc_start: 0.7379 (tmm-80) cc_final: 0.7147 (ptm-80) REVERT: C 489 SER cc_start: 0.7778 (t) cc_final: 0.7397 (p) REVERT: D 332 ARG cc_start: 0.6958 (ptm-80) cc_final: 0.6539 (tmm-80) REVERT: E 301 MET cc_start: 0.7582 (ttt) cc_final: 0.7246 (ttp) REVERT: E 332 ARG cc_start: 0.7093 (ptm-80) cc_final: 0.6613 (tmm-80) REVERT: E 452 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: E 489 SER cc_start: 0.7847 (t) cc_final: 0.7371 (p) outliers start: 30 outliers final: 27 residues processed: 206 average time/residue: 0.2799 time to fit residues: 87.5851 Evaluate side-chains 195 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 452 GLU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 483 THR 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 483 THR 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 483 THR Chi-restraints excluded: chain C residue 484 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 D residue 483 THR 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 257 ASP Chi-restraints excluded: chain E residue 452 GLU Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 483 THR 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 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16455 Z= 0.167 Angle : 0.531 10.174 22490 Z= 0.270 Chirality : 0.041 0.138 2620 Planarity : 0.004 0.029 2755 Dihedral : 5.491 42.003 2781 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.58 % Allowed : 7.25 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1960 helix: 0.83 (0.19), residues: 770 sheet: -0.37 (0.24), residues: 445 loop : -2.00 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 460 HIS 0.003 0.001 HIS A 163 PHE 0.011 0.001 PHE A 297 TYR 0.015 0.001 TYR C 190 ARG 0.005 0.000 ARG C 332 *********************** 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 194 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 184 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 332 ARG cc_start: 0.7353 (tmm-80) cc_final: 0.6942 (ptm-80) REVERT: D 190 TYR cc_start: 0.7911 (t80) cc_final: 0.7660 (t80) REVERT: D 332 ARG cc_start: 0.6964 (ptm-80) cc_final: 0.6555 (tmm-80) REVERT: E 332 ARG cc_start: 0.6894 (ptm-80) cc_final: 0.6510 (tmm-80) REVERT: E 452 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8048 (tm-30) outliers start: 10 outliers final: 9 residues processed: 188 average time/residue: 0.2986 time to fit residues: 83.9138 Evaluate side-chains 186 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 B residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 187 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 16455 Z= 0.311 Angle : 0.579 10.091 22490 Z= 0.295 Chirality : 0.043 0.145 2620 Planarity : 0.004 0.029 2755 Dihedral : 5.362 30.411 2775 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.11 % Allowed : 7.95 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1960 helix: 1.05 (0.19), residues: 755 sheet: -0.45 (0.24), residues: 445 loop : -2.08 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.010 0.001 HIS D 320 PHE 0.027 0.002 PHE C 275 TYR 0.027 0.002 TYR E 190 ARG 0.003 0.000 ARG A 332 *********************** 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 218 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 TYR cc_start: 0.8034 (t80) cc_final: 0.7761 (t80) REVERT: A 450 GLN cc_start: 0.7833 (tt0) cc_final: 0.7329 (mt0) REVERT: B 332 ARG cc_start: 0.7472 (tmm-80) cc_final: 0.7032 (ptm-80) REVERT: B 489 SER cc_start: 0.8001 (t) cc_final: 0.7632 (p) REVERT: C 489 SER cc_start: 0.7852 (t) cc_final: 0.7464 (p) REVERT: D 66 ASP cc_start: 0.8466 (t70) cc_final: 0.7968 (t0) REVERT: D 332 ARG cc_start: 0.7112 (ptm-80) cc_final: 0.6623 (tmm-80) REVERT: D 489 SER cc_start: 0.7864 (t) cc_final: 0.7485 (p) REVERT: E 332 ARG cc_start: 0.7127 (ptm-80) cc_final: 0.6712 (tmm-80) REVERT: E 450 GLN cc_start: 0.7884 (tt0) cc_final: 0.7532 (mt0) REVERT: E 452 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8183 (tm-30) REVERT: E 489 SER cc_start: 0.7950 (t) cc_final: 0.7395 (p) outliers start: 19 outliers final: 16 residues processed: 203 average time/residue: 0.3094 time to fit residues: 94.6603 Evaluate side-chains 207 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 A residue 484 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 C residue 238 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 481 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16455 Z= 0.151 Angle : 0.509 9.778 22490 Z= 0.258 Chirality : 0.039 0.138 2620 Planarity : 0.003 0.028 2755 Dihedral : 5.075 29.991 2775 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.47 % Allowed : 9.42 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 1960 helix: 1.14 (0.19), residues: 785 sheet: -0.12 (0.25), residues: 445 loop : -2.06 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.005 0.001 HIS D 320 PHE 0.025 0.001 PHE C 275 TYR 0.015 0.001 TYR B 190 ARG 0.004 0.000 ARG C 332 *********************** 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 190 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8273 (t70) cc_final: 0.7813 (t0) REVERT: A 450 GLN cc_start: 0.7708 (tt0) cc_final: 0.7249 (mt0) REVERT: B 332 ARG cc_start: 0.7476 (tmm-80) cc_final: 0.7045 (ptm-80) REVERT: B 450 GLN cc_start: 0.8032 (tt0) cc_final: 0.7697 (mt0) REVERT: D 66 ASP cc_start: 0.8309 (t70) cc_final: 0.7931 (t0) REVERT: D 332 ARG cc_start: 0.7084 (ptm-80) cc_final: 0.6633 (tmm-80) REVERT: D 489 SER cc_start: 0.7765 (t) cc_final: 0.7423 (p) REVERT: E 332 ARG cc_start: 0.7092 (ptm-80) cc_final: 0.6715 (tmm-80) REVERT: E 450 GLN cc_start: 0.7832 (tt0) cc_final: 0.7586 (mt0) REVERT: E 452 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8122 (tm-30) outliers start: 8 outliers final: 6 residues processed: 185 average time/residue: 0.3059 time to fit residues: 84.6827 Evaluate side-chains 178 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain E residue 187 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 16455 Z= 0.322 Angle : 0.590 9.692 22490 Z= 0.298 Chirality : 0.043 0.145 2620 Planarity : 0.004 0.031 2755 Dihedral : 5.238 31.097 2775 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.52 % Allowed : 10.00 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1960 helix: 1.03 (0.19), residues: 780 sheet: -0.28 (0.24), residues: 445 loop : -2.11 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS D 320 PHE 0.026 0.002 PHE A 275 TYR 0.031 0.002 TYR E 190 ARG 0.004 0.001 ARG A 332 *********************** 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 216 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 SER cc_start: 0.8135 (t) cc_final: 0.7759 (p) REVERT: B 332 ARG cc_start: 0.7451 (tmm-80) cc_final: 0.7067 (ptm-80) REVERT: B 450 GLN cc_start: 0.8153 (tt0) cc_final: 0.7797 (mt0) REVERT: B 489 SER cc_start: 0.7999 (t) cc_final: 0.7655 (p) REVERT: C 489 SER cc_start: 0.7901 (t) cc_final: 0.7540 (p) REVERT: D 66 ASP cc_start: 0.8444 (t70) cc_final: 0.7958 (t0) REVERT: D 332 ARG cc_start: 0.7202 (ptm-80) cc_final: 0.6664 (tmm-80) REVERT: D 489 SER cc_start: 0.7995 (t) cc_final: 0.7627 (p) REVERT: E 450 GLN cc_start: 0.7878 (tt0) cc_final: 0.7605 (mt0) REVERT: E 452 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8131 (tm-30) REVERT: E 489 SER cc_start: 0.7948 (t) cc_final: 0.7390 (p) outliers start: 26 outliers final: 23 residues processed: 195 average time/residue: 0.3047 time to fit residues: 89.2046 Evaluate side-chains 209 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 481 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 187 ILE 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 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 187 ILE Chi-restraints excluded: chain D residue 235 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 226 MET Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 484 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16455 Z= 0.153 Angle : 0.520 9.321 22490 Z= 0.260 Chirality : 0.039 0.146 2620 Planarity : 0.003 0.029 2755 Dihedral : 4.977 31.562 2775 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.70 % Allowed : 11.64 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 1960 helix: 1.16 (0.19), residues: 780 sheet: -0.13 (0.24), residues: 455 loop : -2.08 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 156 HIS 0.003 0.001 HIS D 320 PHE 0.024 0.001 PHE A 275 TYR 0.012 0.001 TYR A 140 ARG 0.005 0.000 ARG C 332 *********************** 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 193 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 2.015 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: 0.7297 (mt0) REVERT: A 489 SER cc_start: 0.8069 (t) cc_final: 0.7686 (p) REVERT: B 332 ARG cc_start: 0.7499 (tmm-80) cc_final: 0.7271 (ptm-80) REVERT: B 489 SER cc_start: 0.7945 (t) cc_final: 0.7598 (p) REVERT: C 489 SER cc_start: 0.7793 (t) cc_final: 0.7446 (p) REVERT: D 66 ASP cc_start: 0.8297 (t70) cc_final: 0.7925 (t0) REVERT: D 489 SER cc_start: 0.7938 (t) cc_final: 0.7578 (p) REVERT: E 332 ARG cc_start: 0.7215 (ptm-80) cc_final: 0.6851 (tmm-80) REVERT: E 450 GLN cc_start: 0.7864 (tt0) cc_final: 0.7655 (mt0) REVERT: E 452 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8146 (tm-30) REVERT: E 489 SER cc_start: 0.7875 (t) cc_final: 0.7344 (p) outliers start: 12 outliers final: 10 residues processed: 188 average time/residue: 0.3077 time to fit residues: 86.5772 Evaluate side-chains 187 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 B residue 187 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 226 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16455 Z= 0.152 Angle : 0.507 8.886 22490 Z= 0.254 Chirality : 0.039 0.146 2620 Planarity : 0.003 0.028 2755 Dihedral : 4.749 27.641 2775 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.64 % Allowed : 12.28 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1960 helix: 1.25 (0.19), residues: 780 sheet: -0.06 (0.24), residues: 455 loop : -2.00 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 156 HIS 0.003 0.001 HIS D 320 PHE 0.023 0.001 PHE A 275 TYR 0.015 0.001 TYR B 190 ARG 0.004 0.000 ARG C 332 *********************** 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 196 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8226 (t70) cc_final: 0.7794 (t0) REVERT: A 450 GLN cc_start: 0.7700 (tt0) cc_final: 0.7342 (mt0) REVERT: A 489 SER cc_start: 0.8121 (t) cc_final: 0.7710 (p) REVERT: B 66 ASP cc_start: 0.8236 (t70) cc_final: 0.7815 (t0) REVERT: B 332 ARG cc_start: 0.7486 (tmm-80) cc_final: 0.7268 (ptm-80) REVERT: B 489 SER cc_start: 0.7896 (t) cc_final: 0.7549 (p) REVERT: C 66 ASP cc_start: 0.8113 (t70) cc_final: 0.7646 (t0) REVERT: C 489 SER cc_start: 0.7829 (t) cc_final: 0.7499 (p) REVERT: D 66 ASP cc_start: 0.8272 (t70) cc_final: 0.7926 (t0) REVERT: D 68 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8099 (mmmm) REVERT: D 489 SER cc_start: 0.7916 (t) cc_final: 0.7560 (p) REVERT: E 66 ASP cc_start: 0.8187 (t70) cc_final: 0.7521 (t0) REVERT: E 68 LYS cc_start: 0.8349 (mmmt) cc_final: 0.7927 (mmmt) REVERT: E 332 ARG cc_start: 0.7346 (ptm-80) cc_final: 0.6945 (tmm-80) REVERT: E 452 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8167 (tm-30) outliers start: 11 outliers final: 10 residues processed: 193 average time/residue: 0.2957 time to fit residues: 86.1822 Evaluate side-chains 190 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 1.889 ------------------------------------------------------------------------------- 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 B residue 187 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 226 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16455 Z= 0.200 Angle : 0.528 9.679 22490 Z= 0.264 Chirality : 0.040 0.143 2620 Planarity : 0.003 0.028 2755 Dihedral : 4.739 27.612 2775 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.82 % Allowed : 12.51 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1960 helix: 1.22 (0.18), residues: 780 sheet: -0.13 (0.24), residues: 455 loop : -2.04 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 156 HIS 0.003 0.001 HIS D 320 PHE 0.025 0.001 PHE A 275 TYR 0.018 0.001 TYR E 190 ARG 0.004 0.000 ARG C 332 *********************** 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 196 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.7713 (tt0) cc_final: 0.7349 (mt0) REVERT: A 489 SER cc_start: 0.8102 (t) cc_final: 0.7714 (p) REVERT: B 332 ARG cc_start: 0.7492 (tmm-80) cc_final: 0.7283 (ptm-80) REVERT: B 489 SER cc_start: 0.7864 (t) cc_final: 0.7516 (p) REVERT: C 66 ASP cc_start: 0.8153 (t70) cc_final: 0.7661 (t0) REVERT: C 276 MET cc_start: 0.6726 (mmp) cc_final: 0.6068 (mtm) REVERT: C 489 SER cc_start: 0.7864 (t) cc_final: 0.7526 (p) REVERT: D 66 ASP cc_start: 0.8286 (t70) cc_final: 0.7809 (t0) REVERT: D 489 SER cc_start: 0.7993 (t) cc_final: 0.7603 (p) REVERT: E 452 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8191 (tm-30) REVERT: E 489 SER cc_start: 0.7806 (t) cc_final: 0.7400 (p) outliers start: 14 outliers final: 12 residues processed: 190 average time/residue: 0.2989 time to fit residues: 86.0944 Evaluate side-chains 192 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 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 187 ILE Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 235 LEU 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 185 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 194 optimal weight: 0.2980 chunk 178 optimal weight: 0.0020 chunk 154 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 49 GLN C 49 GLN E 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16455 Z= 0.140 Angle : 0.496 8.831 22490 Z= 0.249 Chirality : 0.039 0.149 2620 Planarity : 0.003 0.028 2755 Dihedral : 4.482 27.874 2775 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.58 % Allowed : 12.69 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1960 helix: 1.21 (0.18), residues: 795 sheet: 0.10 (0.24), residues: 455 loop : -1.99 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 156 HIS 0.003 0.001 HIS D 320 PHE 0.026 0.001 PHE C 275 TYR 0.011 0.001 TYR A 140 ARG 0.004 0.000 ARG C 332 ********************** 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 192 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8145 (t70) cc_final: 0.7639 (t0) REVERT: A 450 GLN cc_start: 0.7691 (tt0) cc_final: 0.7397 (mt0) REVERT: A 489 SER cc_start: 0.8037 (t) cc_final: 0.7634 (p) REVERT: B 66 ASP cc_start: 0.8120 (t70) cc_final: 0.7759 (t0) REVERT: B 332 ARG cc_start: 0.7466 (tmm-80) cc_final: 0.7264 (ptm-80) REVERT: B 489 SER cc_start: 0.7782 (t) cc_final: 0.7434 (p) REVERT: C 66 ASP cc_start: 0.8071 (t70) cc_final: 0.7648 (t0) REVERT: C 276 MET cc_start: 0.6907 (mmp) cc_final: 0.6252 (mtm) REVERT: D 66 ASP cc_start: 0.8152 (t70) cc_final: 0.7787 (t0) REVERT: D 68 LYS cc_start: 0.8380 (mmmm) cc_final: 0.8070 (mmmm) REVERT: D 283 MET cc_start: 0.8271 (mmm) cc_final: 0.7959 (mmm) REVERT: D 489 SER cc_start: 0.7981 (t) cc_final: 0.7599 (p) REVERT: E 66 ASP cc_start: 0.8133 (t70) cc_final: 0.7519 (t0) REVERT: E 68 LYS cc_start: 0.8317 (mmmt) cc_final: 0.8005 (mmmm) REVERT: E 452 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8171 (tm-30) outliers start: 10 outliers final: 9 residues processed: 189 average time/residue: 0.2929 time to fit residues: 83.4482 Evaluate side-chains 186 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 235 LEU 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 164 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100681 restraints weight = 35320.615| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.00 r_work: 0.3107 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16455 Z= 0.176 Angle : 0.509 8.790 22490 Z= 0.255 Chirality : 0.040 0.145 2620 Planarity : 0.003 0.028 2755 Dihedral : 4.471 28.592 2775 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.64 % Allowed : 12.92 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1960 helix: 1.23 (0.18), residues: 795 sheet: 0.06 (0.24), residues: 455 loop : -1.99 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.002 0.001 HIS D 320 PHE 0.028 0.001 PHE E 275 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG C 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3160.19 seconds wall clock time: 58 minutes 59.65 seconds (3539.65 seconds total)