Starting phenix.real_space_refine on Sun May 11 04:15:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j15_61068/05_2025/9j15_61068.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j15_61068/05_2025/9j15_61068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j15_61068/05_2025/9j15_61068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j15_61068/05_2025/9j15_61068.map" model { file = "/net/cci-nas-00/data/ceres_data/9j15_61068/05_2025/9j15_61068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j15_61068/05_2025/9j15_61068.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.052 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 56 5.16 5 C 4836 2.51 5 N 1202 2.21 5 O 1364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7458 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3718 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 487} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B Time building chain proxies: 6.75, per 1000 atoms: 0.91 Number of scatterers: 7458 At special positions: 0 Unit cell: (111.1, 95.7, 88, 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 56 16.00 O 1364 8.00 N 1202 7.00 C 4836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 101 " distance=2.04 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 101 " distance=2.04 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 242 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 59.9% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 6 through 24 removed outlier: 4.150A pdb=" N MET A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 15 " --> pdb=" O TRP A 11 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.727A pdb=" N PHE A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 53 removed outlier: 3.650A pdb=" N THR A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.330A pdb=" N CYS A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 106 through 129 removed outlier: 4.215A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.662A pdb=" N ILE A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 175 removed outlier: 3.522A pdb=" N ALA A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.910A pdb=" N ARG A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 209 removed outlier: 4.176A pdb=" N ALA A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 3.746A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.563A pdb=" N ILE A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 4.070A pdb=" N SER A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.656A pdb=" N TRP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.706A pdb=" N ILE A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 removed outlier: 4.491A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.531A pdb=" N GLY A 402 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 422 removed outlier: 3.519A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.636A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.661A pdb=" N ILE A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 477 removed outlier: 3.684A pdb=" N ALA A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix Processing helix chain 'A' and resid 480 through 494 removed outlier: 3.961A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 507 Processing helix chain 'B' and resid 6 through 24 removed outlier: 4.150A pdb=" N MET B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 15 " --> pdb=" O TRP B 11 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 removed outlier: 3.727A pdb=" N PHE B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.650A pdb=" N THR B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.329A pdb=" N CYS B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 91' Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 106 through 129 removed outlier: 4.215A pdb=" N VAL B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.661A pdb=" N ILE B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.522A pdb=" N ALA B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 167 " --> pdb=" O MET B 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.909A pdb=" N ARG B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 removed outlier: 4.176A pdb=" N ALA B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 removed outlier: 3.745A pdb=" N ALA B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.563A pdb=" N ILE B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 4.070A pdb=" N SER B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 352 removed outlier: 4.656A pdb=" N TRP B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.705A pdb=" N ILE B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 387 removed outlier: 4.490A pdb=" N SER B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 387 " --> pdb=" O VAL B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.531A pdb=" N GLY B 402 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 422 removed outlier: 3.520A pdb=" N ILE B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 438 through 451 removed outlier: 3.635A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.662A pdb=" N ILE B 456 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 477 removed outlier: 3.684A pdb=" N ALA B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) Proline residue: B 475 - end of helix Processing helix chain 'B' and resid 480 through 494 removed outlier: 3.962A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 507 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 136 removed outlier: 4.070A pdb=" N ALA A 135 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 removed outlier: 7.307A pdb=" N GLU A 234 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 136 removed outlier: 4.071A pdb=" N ALA B 135 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 235 removed outlier: 7.308A pdb=" N GLU B 234 " --> pdb=" O LEU B 243 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 846 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: 1.90 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1296 1.33 - 1.45: 2008 1.45 - 1.58: 4210 1.58 - 1.70: 0 1.70 - 1.83: 94 Bond restraints: 7608 Sorted by residual: bond pdb=" CA VAL A 397 " pdb=" CB VAL A 397 " ideal model delta sigma weight residual 1.540 1.503 0.037 1.15e-02 7.56e+03 1.06e+01 bond pdb=" CA VAL B 397 " pdb=" CB VAL B 397 " ideal model delta sigma weight residual 1.540 1.504 0.036 1.15e-02 7.56e+03 9.94e+00 bond pdb=" C PHE A 396 " pdb=" O PHE A 396 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.23e-02 6.61e+03 7.61e+00 bond pdb=" C PHE B 396 " pdb=" O PHE B 396 " ideal model delta sigma weight residual 1.234 1.201 0.034 1.23e-02 6.61e+03 7.52e+00 bond pdb=" N PHE B 396 " pdb=" CA PHE B 396 " ideal model delta sigma weight residual 1.455 1.422 0.033 1.30e-02 5.92e+03 6.38e+00 ... (remaining 7603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 9648 1.68 - 3.36: 551 3.36 - 5.04: 85 5.04 - 6.71: 42 6.71 - 8.39: 16 Bond angle restraints: 10342 Sorted by residual: angle pdb=" N VAL A 227 " pdb=" CA VAL A 227 " pdb=" CB VAL A 227 " ideal model delta sigma weight residual 111.19 118.82 -7.63 1.35e+00 5.49e-01 3.19e+01 angle pdb=" N VAL B 227 " pdb=" CA VAL B 227 " pdb=" CB VAL B 227 " ideal model delta sigma weight residual 111.19 118.78 -7.59 1.35e+00 5.49e-01 3.16e+01 angle pdb=" N PHE A 396 " pdb=" CA PHE A 396 " pdb=" CB PHE A 396 " ideal model delta sigma weight residual 110.06 102.22 7.84 1.51e+00 4.39e-01 2.69e+01 angle pdb=" N PHE B 396 " pdb=" CA PHE B 396 " pdb=" CB PHE B 396 " ideal model delta sigma weight residual 110.06 102.32 7.74 1.51e+00 4.39e-01 2.63e+01 angle pdb=" N PHE B 396 " pdb=" CA PHE B 396 " pdb=" C PHE B 396 " ideal model delta sigma weight residual 110.20 118.06 -7.86 1.58e+00 4.01e-01 2.47e+01 ... (remaining 10337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.49: 3804 9.49 - 18.98: 452 18.98 - 28.47: 126 28.47 - 37.96: 36 37.96 - 47.45: 8 Dihedral angle restraints: 4426 sinusoidal: 1588 harmonic: 2838 Sorted by residual: dihedral pdb=" CA ARG A 36 " pdb=" C ARG A 36 " pdb=" N LYS A 37 " pdb=" CA LYS A 37 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ARG B 36 " pdb=" C ARG B 36 " pdb=" N LYS B 37 " pdb=" CA LYS B 37 " ideal model delta harmonic sigma weight residual 180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA PHE B 362 " pdb=" C PHE B 362 " pdb=" N VAL B 363 " pdb=" CA VAL B 363 " ideal model delta harmonic sigma weight residual 180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 4423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1142 0.091 - 0.182: 96 0.182 - 0.272: 10 0.272 - 0.363: 0 0.363 - 0.454: 2 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CB ILE A 57 " pdb=" CA ILE A 57 " pdb=" CG1 ILE A 57 " pdb=" CG2 ILE A 57 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CB ILE B 57 " pdb=" CA ILE B 57 " pdb=" CG1 ILE B 57 " pdb=" CG2 ILE B 57 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CA ASN B 432 " pdb=" N ASN B 432 " pdb=" C ASN B 432 " pdb=" CB ASN B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1247 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 430 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C VAL B 430 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL B 430 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 431 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 430 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C VAL A 430 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL A 430 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 431 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 135 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO A 136 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.027 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2548 2.85 - 3.37: 6790 3.37 - 3.88: 11256 3.88 - 4.39: 13228 4.39 - 4.90: 23079 Nonbonded interactions: 56901 Sorted by model distance: nonbonded pdb=" OG1 THR B 192 " pdb=" OE1 GLU B 463 " model vdw 2.342 3.040 nonbonded pdb=" OG1 THR A 192 " pdb=" OE1 GLU A 463 " model vdw 2.343 3.040 nonbonded pdb=" OE1 GLU B 43 " pdb=" OG1 THR B 412 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLU A 43 " pdb=" OG1 THR A 412 " model vdw 2.371 3.040 nonbonded pdb=" OG SER A 73 " pdb=" OD1 ASN A 75 " model vdw 2.435 3.040 ... (remaining 56896 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.007 0.070 7614 Z= 0.312 Angle : 0.965 8.393 10354 Z= 0.529 Chirality : 0.059 0.454 1250 Planarity : 0.006 0.049 1272 Dihedral : 9.605 47.445 2608 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -6.55 (0.15), residues: 1004 helix: -4.72 (0.07), residues: 558 sheet: None (None), residues: 0 loop : -3.72 (0.22), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 253 HIS 0.003 0.001 HIS B 315 PHE 0.022 0.002 PHE A 207 TYR 0.018 0.002 TYR A 146 ARG 0.005 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.35879 ( 294) hydrogen bonds : angle 11.18167 ( 846) SS BOND : bond 0.00652 ( 6) SS BOND : angle 1.53956 ( 12) covalent geometry : bond 0.00681 ( 7608) covalent geometry : angle 0.96440 (10342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7896 (mtm180) REVERT: A 108 ASP cc_start: 0.8623 (m-30) cc_final: 0.8307 (m-30) REVERT: A 187 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7550 (mtm180) REVERT: A 228 THR cc_start: 0.8693 (t) cc_final: 0.8338 (m) REVERT: A 353 LEU cc_start: 0.8542 (tp) cc_final: 0.8319 (tp) REVERT: A 354 TYR cc_start: 0.8125 (t80) cc_final: 0.7705 (t80) REVERT: A 378 ASP cc_start: 0.8031 (t0) cc_final: 0.7711 (t0) REVERT: A 404 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8119 (mtpp) REVERT: A 482 ASN cc_start: 0.8347 (m-40) cc_final: 0.7997 (m110) REVERT: A 496 MET cc_start: 0.6570 (ttp) cc_final: 0.6188 (ttm) REVERT: B 104 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7814 (mtm-85) REVERT: B 108 ASP cc_start: 0.8689 (m-30) cc_final: 0.8299 (m-30) REVERT: B 187 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7660 (mtm180) REVERT: B 228 THR cc_start: 0.8707 (t) cc_final: 0.8322 (m) REVERT: B 353 LEU cc_start: 0.8532 (tp) cc_final: 0.8307 (tp) REVERT: B 354 TYR cc_start: 0.8085 (t80) cc_final: 0.7632 (t80) REVERT: B 378 ASP cc_start: 0.8078 (t0) cc_final: 0.7740 (t0) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2158 time to fit residues: 64.0974 Evaluate side-chains 138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 147 ASN A 160 HIS B 95 ASN B 147 ASN B 160 HIS B 432 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118185 restraints weight = 9042.745| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.87 r_work: 0.3001 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7614 Z= 0.113 Angle : 0.581 5.218 10354 Z= 0.309 Chirality : 0.041 0.135 1250 Planarity : 0.005 0.032 1272 Dihedral : 5.458 18.826 1062 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.66 % Allowed : 11.42 % Favored : 85.91 % 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: -4.65 (0.20), residues: 1004 helix: -2.96 (0.16), residues: 554 sheet: None (None), residues: 0 loop : -3.17 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 297 PHE 0.017 0.001 PHE B 280 TYR 0.018 0.002 TYR B 419 ARG 0.003 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 294) hydrogen bonds : angle 5.03752 ( 846) SS BOND : bond 0.00325 ( 6) SS BOND : angle 0.77399 ( 12) covalent geometry : bond 0.00248 ( 7608) covalent geometry : angle 0.58064 (10342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8939 (m-30) cc_final: 0.8667 (m-30) REVERT: A 132 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7971 (p90) REVERT: A 187 ARG cc_start: 0.8131 (mtm110) cc_final: 0.7722 (mtm180) REVERT: A 228 THR cc_start: 0.8722 (t) cc_final: 0.8408 (m) REVERT: A 378 ASP cc_start: 0.7953 (t0) cc_final: 0.7569 (t0) REVERT: A 404 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8365 (mtpp) REVERT: A 482 ASN cc_start: 0.8642 (m-40) cc_final: 0.8188 (m110) REVERT: A 496 MET cc_start: 0.6748 (ttp) cc_final: 0.6263 (ttm) REVERT: B 108 ASP cc_start: 0.8887 (m-30) cc_final: 0.8628 (m-30) REVERT: B 132 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7974 (p90) REVERT: B 187 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7757 (mtm180) REVERT: B 228 THR cc_start: 0.8784 (t) cc_final: 0.8467 (m) REVERT: B 268 LYS cc_start: 0.7951 (mttm) cc_final: 0.7725 (mtmt) REVERT: B 311 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8587 (mt) REVERT: B 378 ASP cc_start: 0.7831 (t0) cc_final: 0.7499 (t0) REVERT: B 482 ASN cc_start: 0.8681 (m-40) cc_final: 0.8240 (m110) outliers start: 21 outliers final: 6 residues processed: 156 average time/residue: 0.1693 time to fit residues: 36.5375 Evaluate side-chains 133 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 0.0770 chunk 59 optimal weight: 0.0020 chunk 7 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 315 HIS A 432 ASN B 147 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.138065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.107551 restraints weight = 9198.568| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.86 r_work: 0.3004 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7614 Z= 0.087 Angle : 0.505 5.119 10354 Z= 0.269 Chirality : 0.040 0.152 1250 Planarity : 0.004 0.028 1272 Dihedral : 4.780 16.469 1062 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.30 % Allowed : 12.56 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.23), residues: 1004 helix: -1.72 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -2.88 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 11 HIS 0.001 0.000 HIS A 315 PHE 0.013 0.001 PHE B 280 TYR 0.014 0.001 TYR A 343 ARG 0.003 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 294) hydrogen bonds : angle 4.22442 ( 846) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.68002 ( 12) covalent geometry : bond 0.00185 ( 7608) covalent geometry : angle 0.50467 (10342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.823 Fit side-chains REVERT: A 108 ASP cc_start: 0.8891 (m-30) cc_final: 0.8608 (m-30) REVERT: A 122 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 187 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7635 (mtm180) REVERT: A 378 ASP cc_start: 0.7965 (t0) cc_final: 0.7660 (t0) REVERT: A 482 ASN cc_start: 0.8661 (m-40) cc_final: 0.8253 (m110) REVERT: A 496 MET cc_start: 0.6653 (ttp) cc_final: 0.6150 (ttm) REVERT: B 108 ASP cc_start: 0.8940 (m-30) cc_final: 0.8638 (m-30) REVERT: B 122 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8701 (mp) REVERT: B 187 ARG cc_start: 0.8064 (mtm110) cc_final: 0.7689 (mtm180) REVERT: B 378 ASP cc_start: 0.7935 (t0) cc_final: 0.7618 (t0) REVERT: B 482 ASN cc_start: 0.8680 (m-40) cc_final: 0.8293 (m110) outliers start: 26 outliers final: 7 residues processed: 152 average time/residue: 0.2012 time to fit residues: 41.4522 Evaluate side-chains 126 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 211 GLN B 147 ASN B 211 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.101709 restraints weight = 9361.728| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.89 r_work: 0.2905 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7614 Z= 0.139 Angle : 0.554 6.188 10354 Z= 0.289 Chirality : 0.042 0.149 1250 Planarity : 0.004 0.030 1272 Dihedral : 4.838 18.686 1062 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.66 % Allowed : 14.72 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.25), residues: 1004 helix: -1.01 (0.21), residues: 580 sheet: -3.07 (1.10), residues: 20 loop : -2.61 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 335 HIS 0.002 0.001 HIS A 160 PHE 0.014 0.002 PHE A 132 TYR 0.009 0.001 TYR B 343 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 294) hydrogen bonds : angle 4.22271 ( 846) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.75827 ( 12) covalent geometry : bond 0.00332 ( 7608) covalent geometry : angle 0.55363 (10342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9086 (tt) cc_final: 0.8835 (tt) REVERT: A 108 ASP cc_start: 0.8867 (m-30) cc_final: 0.8582 (m-30) REVERT: A 187 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7706 (mtm180) REVERT: A 378 ASP cc_start: 0.7852 (t0) cc_final: 0.7489 (t0) REVERT: A 496 MET cc_start: 0.6733 (ttp) cc_final: 0.6237 (ttm) REVERT: B 102 ILE cc_start: 0.9089 (tt) cc_final: 0.8837 (tt) REVERT: B 108 ASP cc_start: 0.8896 (m-30) cc_final: 0.8552 (m-30) REVERT: B 182 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7773 (ttm110) REVERT: B 187 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7579 (mtm180) REVERT: B 212 MET cc_start: 0.7344 (ppp) cc_final: 0.7122 (ppp) REVERT: B 332 SER cc_start: 0.8829 (m) cc_final: 0.8607 (t) REVERT: B 378 ASP cc_start: 0.7831 (t0) cc_final: 0.7470 (t0) outliers start: 21 outliers final: 16 residues processed: 140 average time/residue: 0.1795 time to fit residues: 34.4353 Evaluate side-chains 145 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 496 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 0.0370 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 0.0020 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.135394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.104533 restraints weight = 9142.728| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.84 r_work: 0.2958 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7614 Z= 0.085 Angle : 0.495 6.951 10354 Z= 0.259 Chirality : 0.039 0.149 1250 Planarity : 0.003 0.033 1272 Dihedral : 4.457 16.005 1062 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.41 % Allowed : 15.23 % Favored : 82.36 % 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: -1.83 (0.26), residues: 1004 helix: -0.35 (0.22), residues: 570 sheet: -3.13 (1.05), residues: 20 loop : -2.34 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 335 HIS 0.001 0.001 HIS B 160 PHE 0.010 0.001 PHE B 280 TYR 0.016 0.001 TYR A 343 ARG 0.002 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.02739 ( 294) hydrogen bonds : angle 3.87147 ( 846) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.60962 ( 12) covalent geometry : bond 0.00191 ( 7608) covalent geometry : angle 0.49533 (10342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.761 Fit side-chains REVERT: A 15 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6642 (mtmm) REVERT: A 102 ILE cc_start: 0.9011 (tt) cc_final: 0.8769 (tt) REVERT: A 108 ASP cc_start: 0.8934 (m-30) cc_final: 0.8638 (m-30) REVERT: A 122 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8754 (mp) REVERT: A 187 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7644 (mtm180) REVERT: A 378 ASP cc_start: 0.7848 (t0) cc_final: 0.7447 (t0) REVERT: A 435 ARG cc_start: 0.8866 (ptp90) cc_final: 0.8664 (ttp80) REVERT: A 479 SER cc_start: 0.9208 (t) cc_final: 0.8824 (p) REVERT: A 496 MET cc_start: 0.6683 (ttp) cc_final: 0.6163 (ttm) REVERT: B 15 LYS cc_start: 0.6991 (mtmt) cc_final: 0.6567 (mtmm) REVERT: B 102 ILE cc_start: 0.9047 (tt) cc_final: 0.8807 (tt) REVERT: B 104 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.7953 (ttp-110) REVERT: B 108 ASP cc_start: 0.8856 (m-30) cc_final: 0.8512 (m-30) REVERT: B 182 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7755 (ttm110) REVERT: B 187 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7634 (mtm180) REVERT: B 332 SER cc_start: 0.8824 (m) cc_final: 0.8570 (t) REVERT: B 378 ASP cc_start: 0.7844 (t0) cc_final: 0.7442 (t0) REVERT: B 479 SER cc_start: 0.9190 (t) cc_final: 0.8823 (p) outliers start: 19 outliers final: 7 residues processed: 154 average time/residue: 0.2312 time to fit residues: 45.8680 Evaluate side-chains 145 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 0.0170 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.163589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131591 restraints weight = 9119.804| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.08 r_work: 0.2950 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7614 Z= 0.093 Angle : 0.499 7.334 10354 Z= 0.258 Chirality : 0.040 0.143 1250 Planarity : 0.003 0.033 1272 Dihedral : 4.348 15.758 1062 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.65 % Allowed : 17.77 % Favored : 80.58 % 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: -1.39 (0.27), residues: 1004 helix: 0.07 (0.23), residues: 570 sheet: -3.18 (1.01), residues: 20 loop : -2.22 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 335 HIS 0.001 0.001 HIS B 297 PHE 0.011 0.001 PHE A 132 TYR 0.010 0.001 TYR A 343 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 294) hydrogen bonds : angle 3.79854 ( 846) SS BOND : bond 0.00227 ( 6) SS BOND : angle 0.58639 ( 12) covalent geometry : bond 0.00216 ( 7608) covalent geometry : angle 0.49843 (10342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.875 Fit side-chains REVERT: A 32 LYS cc_start: 0.8212 (mtmp) cc_final: 0.7975 (mtmm) REVERT: A 102 ILE cc_start: 0.9088 (tt) cc_final: 0.8848 (tt) REVERT: A 108 ASP cc_start: 0.8938 (m-30) cc_final: 0.8643 (m-30) REVERT: A 187 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7638 (mtm180) REVERT: A 378 ASP cc_start: 0.7853 (t0) cc_final: 0.7419 (t0) REVERT: A 479 SER cc_start: 0.9214 (t) cc_final: 0.8935 (p) REVERT: A 496 MET cc_start: 0.6752 (ttp) cc_final: 0.6242 (ttm) REVERT: B 15 LYS cc_start: 0.6895 (mtmt) cc_final: 0.6448 (mtmm) REVERT: B 102 ILE cc_start: 0.9097 (tt) cc_final: 0.8867 (tt) REVERT: B 108 ASP cc_start: 0.8927 (m-30) cc_final: 0.8620 (m-30) REVERT: B 187 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7640 (mtm180) REVERT: B 332 SER cc_start: 0.8884 (m) cc_final: 0.8646 (t) REVERT: B 378 ASP cc_start: 0.7774 (t0) cc_final: 0.7387 (t0) REVERT: B 479 SER cc_start: 0.9222 (t) cc_final: 0.8926 (p) outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 0.2080 time to fit residues: 39.3670 Evaluate side-chains 138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 54 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.101256 restraints weight = 9288.843| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.96 r_work: 0.2897 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7614 Z= 0.121 Angle : 0.529 7.993 10354 Z= 0.271 Chirality : 0.041 0.148 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.497 17.335 1062 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.90 % Allowed : 17.64 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.27), residues: 1004 helix: 0.21 (0.23), residues: 572 sheet: -3.45 (0.99), residues: 20 loop : -2.14 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 335 HIS 0.002 0.001 HIS B 297 PHE 0.011 0.001 PHE A 368 TYR 0.009 0.001 TYR B 375 ARG 0.002 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 294) hydrogen bonds : angle 3.88488 ( 846) SS BOND : bond 0.00270 ( 6) SS BOND : angle 0.69021 ( 12) covalent geometry : bond 0.00290 ( 7608) covalent geometry : angle 0.52838 (10342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9109 (tt) cc_final: 0.8861 (tt) REVERT: A 108 ASP cc_start: 0.8968 (m-30) cc_final: 0.8694 (m-30) REVERT: A 187 ARG cc_start: 0.8159 (mtm110) cc_final: 0.7891 (mtm180) REVERT: A 378 ASP cc_start: 0.7778 (t0) cc_final: 0.7374 (t0) REVERT: A 496 MET cc_start: 0.6674 (ttp) cc_final: 0.6426 (ttp) REVERT: B 102 ILE cc_start: 0.9108 (tt) cc_final: 0.8862 (tt) REVERT: B 108 ASP cc_start: 0.8964 (m-30) cc_final: 0.8667 (m-30) REVERT: B 187 ARG cc_start: 0.8083 (mtm110) cc_final: 0.7609 (mtm180) REVERT: B 332 SER cc_start: 0.8909 (m) cc_final: 0.8661 (t) REVERT: B 378 ASP cc_start: 0.7774 (t0) cc_final: 0.7380 (t0) outliers start: 15 outliers final: 9 residues processed: 138 average time/residue: 0.2177 time to fit residues: 40.6600 Evaluate side-chains 138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 496 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.134284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.102670 restraints weight = 9349.775| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.92 r_work: 0.2897 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7614 Z= 0.119 Angle : 0.532 8.454 10354 Z= 0.272 Chirality : 0.041 0.147 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.493 17.344 1062 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.65 % Allowed : 17.64 % Favored : 80.71 % 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: -1.06 (0.27), residues: 1004 helix: 0.33 (0.23), residues: 572 sheet: -3.43 (1.00), residues: 20 loop : -2.06 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS A 160 PHE 0.011 0.001 PHE A 368 TYR 0.010 0.001 TYR B 375 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 294) hydrogen bonds : angle 3.81087 ( 846) SS BOND : bond 0.00228 ( 6) SS BOND : angle 1.10388 ( 12) covalent geometry : bond 0.00287 ( 7608) covalent geometry : angle 0.53109 (10342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9076 (tt) cc_final: 0.8819 (tt) REVERT: A 108 ASP cc_start: 0.8957 (m-30) cc_final: 0.8687 (m-30) REVERT: A 122 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8786 (mp) REVERT: A 187 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7852 (mtm180) REVERT: A 378 ASP cc_start: 0.7741 (t0) cc_final: 0.7326 (t0) REVERT: A 496 MET cc_start: 0.6699 (ttp) cc_final: 0.6148 (ttm) REVERT: B 102 ILE cc_start: 0.9129 (tt) cc_final: 0.8895 (tt) REVERT: B 108 ASP cc_start: 0.8956 (m-30) cc_final: 0.8668 (m-30) REVERT: B 187 ARG cc_start: 0.8184 (mtm110) cc_final: 0.7919 (mtm180) REVERT: B 332 SER cc_start: 0.8863 (m) cc_final: 0.8612 (t) REVERT: B 378 ASP cc_start: 0.7734 (t0) cc_final: 0.7331 (t0) outliers start: 13 outliers final: 9 residues processed: 137 average time/residue: 0.2091 time to fit residues: 37.9667 Evaluate side-chains 140 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 496 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.0270 chunk 9 optimal weight: 0.0020 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 31 optimal weight: 0.0020 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106714 restraints weight = 9255.404| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.96 r_work: 0.2969 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7614 Z= 0.077 Angle : 0.494 8.505 10354 Z= 0.253 Chirality : 0.039 0.141 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.191 15.080 1062 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.51 % Allowed : 18.78 % Favored : 80.71 % 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: -0.73 (0.27), residues: 1004 helix: 0.58 (0.23), residues: 584 sheet: -3.18 (1.05), residues: 20 loop : -1.97 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 335 HIS 0.001 0.000 HIS A 297 PHE 0.009 0.001 PHE B 280 TYR 0.011 0.001 TYR B 343 ARG 0.001 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.02281 ( 294) hydrogen bonds : angle 3.57562 ( 846) SS BOND : bond 0.00406 ( 6) SS BOND : angle 1.16478 ( 12) covalent geometry : bond 0.00165 ( 7608) covalent geometry : angle 0.49242 (10342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.843 Fit side-chains REVERT: A 32 LYS cc_start: 0.8149 (mtmp) cc_final: 0.7888 (mtmm) REVERT: A 102 ILE cc_start: 0.9061 (tt) cc_final: 0.8829 (tt) REVERT: A 108 ASP cc_start: 0.8955 (m-30) cc_final: 0.8720 (m-30) REVERT: A 378 ASP cc_start: 0.7850 (t0) cc_final: 0.7548 (t0) REVERT: A 479 SER cc_start: 0.9176 (t) cc_final: 0.8904 (p) REVERT: A 496 MET cc_start: 0.6701 (ttp) cc_final: 0.6124 (ttm) REVERT: B 102 ILE cc_start: 0.9047 (tt) cc_final: 0.8813 (tt) REVERT: B 108 ASP cc_start: 0.8940 (m-30) cc_final: 0.8669 (m-30) REVERT: B 187 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7906 (mtm180) REVERT: B 332 SER cc_start: 0.8833 (m) cc_final: 0.8570 (t) REVERT: B 378 ASP cc_start: 0.7848 (t0) cc_final: 0.7533 (t0) REVERT: B 479 SER cc_start: 0.9195 (t) cc_final: 0.8925 (p) outliers start: 4 outliers final: 3 residues processed: 137 average time/residue: 0.1914 time to fit residues: 35.5517 Evaluate side-chains 132 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 6 optimal weight: 0.0270 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.136029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.104283 restraints weight = 9381.438| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.93 r_work: 0.2941 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7614 Z= 0.103 Angle : 0.510 8.266 10354 Z= 0.261 Chirality : 0.041 0.145 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.257 16.136 1062 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.63 % Allowed : 19.54 % Favored : 79.82 % 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: -0.52 (0.27), residues: 1004 helix: 0.84 (0.23), residues: 572 sheet: -3.22 (1.02), residues: 20 loop : -1.94 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS A 160 PHE 0.009 0.001 PHE B 368 TYR 0.007 0.001 TYR A 343 ARG 0.002 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 294) hydrogen bonds : angle 3.65118 ( 846) SS BOND : bond 0.00239 ( 6) SS BOND : angle 1.25548 ( 12) covalent geometry : bond 0.00244 ( 7608) covalent geometry : angle 0.50841 (10342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.779 Fit side-chains REVERT: A 102 ILE cc_start: 0.9133 (tt) cc_final: 0.8891 (tt) REVERT: A 108 ASP cc_start: 0.8948 (m-30) cc_final: 0.8689 (m-30) REVERT: A 378 ASP cc_start: 0.7873 (t0) cc_final: 0.7284 (t0) REVERT: A 496 MET cc_start: 0.6719 (ttp) cc_final: 0.6177 (ttm) REVERT: B 102 ILE cc_start: 0.9134 (tt) cc_final: 0.8896 (tt) REVERT: B 108 ASP cc_start: 0.8969 (m-30) cc_final: 0.8684 (m-30) REVERT: B 187 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7943 (mtm180) REVERT: B 332 SER cc_start: 0.8835 (m) cc_final: 0.8620 (t) REVERT: B 378 ASP cc_start: 0.7869 (t0) cc_final: 0.7287 (t0) outliers start: 5 outliers final: 4 residues processed: 124 average time/residue: 0.1881 time to fit residues: 31.5447 Evaluate side-chains 125 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 0.0020 chunk 83 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.103512 restraints weight = 9277.631| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.96 r_work: 0.2935 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7614 Z= 0.097 Angle : 0.505 8.168 10354 Z= 0.259 Chirality : 0.040 0.145 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.248 16.174 1062 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.76 % Allowed : 19.42 % Favored : 79.82 % 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: -0.37 (0.27), residues: 1004 helix: 0.99 (0.23), residues: 572 sheet: -3.26 (1.00), residues: 20 loop : -1.92 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS B 160 PHE 0.009 0.001 PHE A 368 TYR 0.009 0.001 TYR A 375 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 294) hydrogen bonds : angle 3.65984 ( 846) SS BOND : bond 0.00221 ( 6) SS BOND : angle 1.13371 ( 12) covalent geometry : bond 0.00229 ( 7608) covalent geometry : angle 0.50423 (10342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3851.56 seconds wall clock time: 67 minutes 18.19 seconds (4038.19 seconds total)