Starting phenix.real_space_refine on Thu Jul 2 07:06:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j15_61068/07_2026/9j15_61068.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j15_61068/07_2026/9j15_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j15_61068/07_2026/9j15_61068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j15_61068/07_2026/9j15_61068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j15_61068/07_2026/9j15_61068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j15_61068/07_2026/9j15_61068.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'TRP:plan': 1, 'ASN:plan1': 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: 2.39, per 1000 atoms: 0.32 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: 0.64 Conformation dependent library (CDL) restraints added in 490.5 milliseconds 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: 0.18 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: 0.92 Time building geometry restraints manager: 0.89 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: 0.02 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: 1.160 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.380 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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= 0.317 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 : 1.26 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.001 ARG A 36 TYR 0.018 0.002 TYR A 146 PHE 0.022 0.002 PHE A 207 TRP 0.012 0.002 TRP A 253 HIS 0.003 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.32 ( 7608) covalent geometry : angle 0.96445 / 0.53 (10342) SS BOND : bond 0.00652 / 0.37 ( 6) SS BOND : angle 1.53956 / 0.93 ( 12) hydrogen bonds : bond 0.35879 / 23.45 ( 294) hydrogen bonds : angle 11.18167 / 7.69 ( 846) *********************** 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 : 0.182 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: 0.0743 time to fit residues: 22.5530 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 : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 147 ASN A 160 HIS B 95 ASN B 147 ASN B 160 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105517 restraints weight = 9359.419| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.89 r_work: 0.2975 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7614 Z= 0.150 Angle : 0.661 6.691 10354 Z= 0.352 Chirality : 0.043 0.140 1250 Planarity : 0.005 0.034 1272 Dihedral : 5.833 20.156 1062 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.81 % Allowed : 10.66 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.71 (0.20), residues: 1004 helix: -2.96 (0.16), residues: 562 sheet: None (None), residues: 0 loop : -3.27 (0.24), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 36 TYR 0.016 0.002 TYR B 354 PHE 0.016 0.002 PHE A 40 TRP 0.012 0.001 TRP B 253 HIS 0.002 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7608) covalent geometry : angle 0.66055 / 0.35 (10342) SS BOND : bond 0.00487 / 0.29 ( 6) SS BOND : angle 0.86403 / 0.54 ( 12) hydrogen bonds : bond 0.05986 / 3.83 ( 294) hydrogen bonds : angle 5.60309 / 3.76 ( 846) *********************** 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 158 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8002 (t0) REVERT: A 108 ASP cc_start: 0.8863 (m-30) cc_final: 0.8597 (m-30) REVERT: A 187 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7723 (mtm180) REVERT: A 228 THR cc_start: 0.8773 (t) cc_final: 0.8440 (m) REVERT: A 378 ASP cc_start: 0.8119 (t0) cc_final: 0.7711 (t0) REVERT: A 404 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8304 (mtpp) REVERT: A 482 ASN cc_start: 0.8675 (m-40) cc_final: 0.8201 (m110) REVERT: A 496 MET cc_start: 0.6851 (ttp) cc_final: 0.6398 (ttm) REVERT: B 108 ASP cc_start: 0.8910 (m-30) cc_final: 0.8622 (m-30) REVERT: B 228 THR cc_start: 0.8831 (t) cc_final: 0.8490 (m) REVERT: B 311 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8561 (mt) REVERT: B 378 ASP cc_start: 0.7972 (t0) cc_final: 0.7608 (t0) REVERT: B 482 ASN cc_start: 0.8754 (m-40) cc_final: 0.8299 (m110) outliers start: 30 outliers final: 16 residues processed: 145 average time/residue: 0.0559 time to fit residues: 11.5629 Evaluate side-chains 144 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 188 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 20 ASP Chi-restraints excluded: chain B residue 22 VAL 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 147 ASN Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 239 THR 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 31 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN B 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.135310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.105163 restraints weight = 9156.721| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.86 r_work: 0.2963 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7614 Z= 0.112 Angle : 0.566 7.873 10354 Z= 0.302 Chirality : 0.041 0.139 1250 Planarity : 0.004 0.033 1272 Dihedral : 5.375 19.162 1062 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.68 % Allowed : 10.03 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.23), residues: 1004 helix: -1.91 (0.19), residues: 562 sheet: None (None), residues: 0 loop : -2.93 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.010 0.001 TYR A 343 PHE 0.013 0.001 PHE B 280 TRP 0.008 0.001 TRP A 11 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7608) covalent geometry : angle 0.56397 / 0.30 (10342) SS BOND : bond 0.00359 / 0.21 ( 6) SS BOND : angle 1.45708 / 1.07 ( 12) hydrogen bonds : bond 0.04780 / 3.07 ( 294) hydrogen bonds : angle 4.88323 / 3.30 ( 846) *********************** 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 156 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8084 (t0) REVERT: A 108 ASP cc_start: 0.8915 (m-30) cc_final: 0.8633 (m-30) REVERT: A 187 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7708 (mtm180) REVERT: A 228 THR cc_start: 0.8756 (t) cc_final: 0.8455 (m) REVERT: A 311 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8596 (mt) REVERT: A 378 ASP cc_start: 0.7963 (t0) cc_final: 0.7669 (t0) REVERT: A 404 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8367 (mtpp) REVERT: A 479 SER cc_start: 0.9189 (t) cc_final: 0.8700 (p) REVERT: A 496 MET cc_start: 0.6806 (ttp) cc_final: 0.6308 (ttm) REVERT: B 108 ASP cc_start: 0.8890 (m-30) cc_final: 0.8587 (m-30) REVERT: B 187 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7517 (mtm180) REVERT: B 228 THR cc_start: 0.8828 (t) cc_final: 0.8514 (m) REVERT: B 268 LYS cc_start: 0.7986 (mttm) cc_final: 0.7761 (mtmt) REVERT: B 311 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8520 (mt) REVERT: B 378 ASP cc_start: 0.7870 (t0) cc_final: 0.7557 (t0) outliers start: 29 outliers final: 14 residues processed: 145 average time/residue: 0.0602 time to fit residues: 12.5408 Evaluate side-chains 139 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 147 ASN 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 A residue 311 ILE Chi-restraints excluded: chain B residue 20 ASP 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 147 ASN Chi-restraints excluded: chain B residue 223 LYS 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 78 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 50 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 432 ASN B 147 ASN B 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.104451 restraints weight = 9389.008| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.87 r_work: 0.2937 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7614 Z= 0.132 Angle : 0.555 5.213 10354 Z= 0.295 Chirality : 0.041 0.140 1250 Planarity : 0.004 0.034 1272 Dihedral : 5.159 18.444 1062 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.68 % Allowed : 11.17 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.24), residues: 1004 helix: -1.29 (0.21), residues: 562 sheet: -3.31 (1.06), residues: 20 loop : -2.66 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.017 0.001 TYR B 343 PHE 0.013 0.001 PHE B 132 TRP 0.007 0.001 TRP B 11 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 7608) covalent geometry : angle 0.55340 / 0.29 (10342) SS BOND : bond 0.00337 / 0.19 ( 6) SS BOND : angle 1.48454 / 1.07 ( 12) hydrogen bonds : bond 0.04298 / 2.77 ( 294) hydrogen bonds : angle 4.53292 / 3.06 ( 846) *********************** 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: 29 poor density : 122 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8917 (m-30) cc_final: 0.8629 (m-30) REVERT: A 168 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7514 (mp) REVERT: A 187 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7633 (mtm180) REVERT: A 228 THR cc_start: 0.8779 (t) cc_final: 0.8497 (m) REVERT: A 378 ASP cc_start: 0.7807 (t0) cc_final: 0.7497 (t0) REVERT: A 479 SER cc_start: 0.9215 (t) cc_final: 0.8813 (p) REVERT: A 496 MET cc_start: 0.6815 (ttp) cc_final: 0.6584 (ttp) REVERT: B 108 ASP cc_start: 0.8897 (m-30) cc_final: 0.8588 (m-30) REVERT: B 187 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7717 (mtm180) REVERT: B 228 THR cc_start: 0.8861 (t) cc_final: 0.8527 (m) REVERT: B 378 ASP cc_start: 0.7828 (t0) cc_final: 0.7483 (t0) outliers start: 29 outliers final: 20 residues processed: 141 average time/residue: 0.0626 time to fit residues: 12.5796 Evaluate side-chains 143 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 ILE 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 261 ILE Chi-restraints excluded: chain A residue 384 VAL 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 147 ASN Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN B 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.134513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.104542 restraints weight = 9294.340| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.83 r_work: 0.2949 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7614 Z= 0.110 Angle : 0.529 5.034 10354 Z= 0.281 Chirality : 0.041 0.139 1250 Planarity : 0.004 0.035 1272 Dihedral : 4.968 17.868 1062 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.17 % Allowed : 12.44 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.25), residues: 1004 helix: -0.82 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.75 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.019 0.001 TYR B 343 PHE 0.012 0.001 PHE B 132 TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 7608) covalent geometry : angle 0.52771 / 0.28 (10342) SS BOND : bond 0.00307 / 0.17 ( 6) SS BOND : angle 1.19286 / 0.84 ( 12) hydrogen bonds : bond 0.03776 / 2.43 ( 294) hydrogen bonds : angle 4.34008 / 2.92 ( 846) *********************** 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 156 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8246 (mtmp) cc_final: 0.8004 (mtmm) REVERT: A 108 ASP cc_start: 0.8989 (m-30) cc_final: 0.8661 (m-30) REVERT: A 122 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 168 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7581 (mp) REVERT: A 187 ARG cc_start: 0.8079 (mtm110) cc_final: 0.7631 (mtm180) REVERT: A 228 THR cc_start: 0.8791 (t) cc_final: 0.8506 (m) REVERT: A 378 ASP cc_start: 0.7863 (t0) cc_final: 0.7489 (t0) REVERT: A 479 SER cc_start: 0.9244 (t) cc_final: 0.8852 (p) REVERT: A 496 MET cc_start: 0.6783 (ttp) cc_final: 0.6552 (ttp) REVERT: B 108 ASP cc_start: 0.8967 (m-30) cc_final: 0.8637 (m-30) REVERT: B 122 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8650 (mp) REVERT: B 187 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7692 (mtm180) REVERT: B 228 THR cc_start: 0.8869 (t) cc_final: 0.8539 (m) REVERT: B 378 ASP cc_start: 0.7731 (t0) cc_final: 0.7369 (t0) REVERT: B 479 SER cc_start: 0.9247 (t) cc_final: 0.8821 (p) outliers start: 25 outliers final: 18 residues processed: 149 average time/residue: 0.0642 time to fit residues: 13.4251 Evaluate side-chains 145 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 216 ILE 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 261 ILE Chi-restraints excluded: chain A residue 384 VAL 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 147 ASN Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN B 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.135202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.104790 restraints weight = 9342.033| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.86 r_work: 0.2939 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7614 Z= 0.115 Angle : 0.534 6.496 10354 Z= 0.283 Chirality : 0.041 0.150 1250 Planarity : 0.004 0.036 1272 Dihedral : 4.856 17.363 1062 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.79 % Allowed : 14.21 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.26), residues: 1004 helix: -0.49 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.65 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.018 0.001 TYR B 343 PHE 0.012 0.001 PHE B 132 TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7608) covalent geometry : angle 0.53364 / 0.28 (10342) SS BOND : bond 0.00363 / 0.23 ( 6) SS BOND : angle 1.03704 / 0.70 ( 12) hydrogen bonds : bond 0.03669 / 2.37 ( 294) hydrogen bonds : angle 4.24985 / 2.86 ( 846) *********************** 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 152 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8256 (mtmp) cc_final: 0.8009 (mtmm) REVERT: A 108 ASP cc_start: 0.9005 (m-30) cc_final: 0.8677 (m-30) REVERT: A 122 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 168 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7515 (mp) REVERT: A 187 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7631 (mtm180) REVERT: A 203 MET cc_start: 0.9165 (mtp) cc_final: 0.8897 (mtp) REVERT: A 378 ASP cc_start: 0.7724 (t0) cc_final: 0.7370 (t0) REVERT: A 479 SER cc_start: 0.9234 (t) cc_final: 0.8858 (p) REVERT: A 496 MET cc_start: 0.6806 (ttp) cc_final: 0.6562 (ttp) REVERT: B 15 LYS cc_start: 0.7041 (mtmt) cc_final: 0.6588 (mtmm) REVERT: B 108 ASP cc_start: 0.9006 (m-30) cc_final: 0.8660 (m-30) REVERT: B 122 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 187 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7695 (mtm180) REVERT: B 203 MET cc_start: 0.9112 (mtp) cc_final: 0.8837 (mtp) REVERT: B 228 THR cc_start: 0.8865 (t) cc_final: 0.8544 (m) REVERT: B 332 SER cc_start: 0.8731 (m) cc_final: 0.8519 (t) REVERT: B 378 ASP cc_start: 0.7724 (t0) cc_final: 0.7361 (t0) REVERT: B 479 SER cc_start: 0.9241 (t) cc_final: 0.8828 (p) outliers start: 22 outliers final: 17 residues processed: 146 average time/residue: 0.0658 time to fit residues: 13.5408 Evaluate side-chains 143 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 216 ILE 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 353 LEU Chi-restraints excluded: chain A residue 384 VAL 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 147 ASN Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131024 restraints weight = 9209.077| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.06 r_work: 0.3313 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7614 Z= 0.119 Angle : 0.549 8.186 10354 Z= 0.287 Chirality : 0.041 0.150 1250 Planarity : 0.004 0.036 1272 Dihedral : 4.802 17.036 1062 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.66 % Allowed : 15.23 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.26), residues: 1004 helix: -0.24 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.57 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.017 0.001 TYR B 343 PHE 0.012 0.001 PHE B 132 TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7608) covalent geometry : angle 0.54608 / 0.29 (10342) SS BOND : bond 0.00390 / 0.22 ( 6) SS BOND : angle 1.77768 / 1.07 ( 12) hydrogen bonds : bond 0.03568 / 2.30 ( 294) hydrogen bonds : angle 4.14240 / 2.77 ( 846) *********************** 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 144 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8986 (m-30) cc_final: 0.8692 (m-30) REVERT: A 122 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8767 (mp) REVERT: A 168 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 187 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7741 (mtm180) REVERT: A 378 ASP cc_start: 0.7822 (t0) cc_final: 0.7390 (t0) REVERT: A 479 SER cc_start: 0.9252 (t) cc_final: 0.9001 (p) REVERT: A 496 MET cc_start: 0.6898 (ttp) cc_final: 0.6670 (ttp) REVERT: B 15 LYS cc_start: 0.7106 (mtmt) cc_final: 0.6644 (mtmm) REVERT: B 108 ASP cc_start: 0.9012 (m-30) cc_final: 0.8672 (m-30) REVERT: B 122 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8793 (mp) REVERT: B 187 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7797 (mtm180) REVERT: B 378 ASP cc_start: 0.7795 (t0) cc_final: 0.7329 (t0) REVERT: B 479 SER cc_start: 0.9263 (t) cc_final: 0.8989 (p) outliers start: 21 outliers final: 13 residues processed: 136 average time/residue: 0.0618 time to fit residues: 11.9967 Evaluate side-chains 132 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 353 LEU 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 353 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 39 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN B 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.163185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131192 restraints weight = 9208.056| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.07 r_work: 0.3316 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7614 Z= 0.102 Angle : 0.534 8.460 10354 Z= 0.279 Chirality : 0.041 0.149 1250 Planarity : 0.003 0.036 1272 Dihedral : 4.679 16.688 1062 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.16 % Allowed : 16.12 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.26), residues: 1004 helix: -0.08 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -2.61 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 187 TYR 0.018 0.001 TYR B 343 PHE 0.011 0.001 PHE B 132 TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 7608) covalent geometry : angle 0.53202 / 0.28 (10342) SS BOND : bond 0.00253 / 0.15 ( 6) SS BOND : angle 1.55271 / 0.92 ( 12) hydrogen bonds : bond 0.03321 / 2.13 ( 294) hydrogen bonds : angle 4.03244 / 2.69 ( 846) *********************** 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 141 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8964 (m-30) cc_final: 0.8641 (m-30) REVERT: A 122 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8805 (mp) REVERT: A 187 ARG cc_start: 0.8139 (mtm110) cc_final: 0.7721 (mtm180) REVERT: A 203 MET cc_start: 0.9102 (mtp) cc_final: 0.8856 (mtp) REVERT: A 378 ASP cc_start: 0.7796 (t0) cc_final: 0.7331 (t0) REVERT: A 479 SER cc_start: 0.9240 (t) cc_final: 0.8994 (p) REVERT: A 496 MET cc_start: 0.6865 (ttp) cc_final: 0.6638 (ttp) REVERT: B 15 LYS cc_start: 0.7234 (mtmt) cc_final: 0.6768 (mtmm) REVERT: B 102 ILE cc_start: 0.9148 (tt) cc_final: 0.8894 (tt) REVERT: B 108 ASP cc_start: 0.8982 (m-30) cc_final: 0.8630 (m-30) REVERT: B 122 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8864 (mp) REVERT: B 187 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7812 (mtm180) REVERT: B 203 MET cc_start: 0.9118 (mtp) cc_final: 0.8873 (mtp) REVERT: B 378 ASP cc_start: 0.7741 (t0) cc_final: 0.7345 (t0) outliers start: 17 outliers final: 13 residues processed: 134 average time/residue: 0.0653 time to fit residues: 12.5335 Evaluate side-chains 131 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 353 LEU 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 147 ASN Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 353 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 76 optimal weight: 0.0040 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS B 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132507 restraints weight = 9099.785| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.08 r_work: 0.3330 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3606 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= 0.095 Angle : 0.526 8.500 10354 Z= 0.275 Chirality : 0.040 0.147 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.603 16.498 1062 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.78 % Allowed : 16.37 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.27), residues: 1004 helix: 0.18 (0.23), residues: 576 sheet: None (None), residues: 0 loop : -2.44 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 187 TYR 0.018 0.001 TYR B 343 PHE 0.010 0.001 PHE B 132 TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 7608) covalent geometry : angle 0.52380 / 0.27 (10342) SS BOND : bond 0.00244 / 0.14 ( 6) SS BOND : angle 1.46206 / 0.88 ( 12) hydrogen bonds : bond 0.03068 / 1.97 ( 294) hydrogen bonds : angle 4.05319 / 2.72 ( 846) *********************** 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 135 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9109 (tt) cc_final: 0.8855 (tt) REVERT: A 108 ASP cc_start: 0.8958 (m-30) cc_final: 0.8633 (m-30) REVERT: A 122 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 187 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7730 (mtm180) REVERT: A 378 ASP cc_start: 0.7903 (t0) cc_final: 0.7432 (t0) REVERT: A 479 SER cc_start: 0.9231 (t) cc_final: 0.8980 (p) REVERT: A 496 MET cc_start: 0.6873 (ttp) cc_final: 0.6630 (ttp) REVERT: B 15 LYS cc_start: 0.7271 (mtmt) cc_final: 0.6794 (mtmm) REVERT: B 102 ILE cc_start: 0.9159 (tt) cc_final: 0.8909 (tt) REVERT: B 108 ASP cc_start: 0.8968 (m-30) cc_final: 0.8623 (m-30) REVERT: B 122 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8879 (mp) REVERT: B 187 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7815 (mtm180) REVERT: B 378 ASP cc_start: 0.7716 (t0) cc_final: 0.7334 (t0) REVERT: B 479 SER cc_start: 0.9197 (t) cc_final: 0.8872 (p) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.0619 time to fit residues: 11.1566 Evaluate side-chains 134 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 353 LEU 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 147 ASN Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.162544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130618 restraints weight = 9124.845| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.07 r_work: 0.2920 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3651 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= 0.126 Angle : 0.539 8.523 10354 Z= 0.280 Chirality : 0.041 0.144 1250 Planarity : 0.004 0.035 1272 Dihedral : 4.576 16.398 1062 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.52 % Allowed : 16.50 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.27), residues: 1004 helix: 0.27 (0.23), residues: 576 sheet: None (None), residues: 0 loop : -2.41 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.016 0.001 TYR B 343 PHE 0.012 0.001 PHE B 132 TRP 0.009 0.001 TRP A 11 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7608) covalent geometry : angle 0.53701 / 0.28 (10342) SS BOND : bond 0.00287 / 0.16 ( 6) SS BOND : angle 1.44749 / 0.88 ( 12) hydrogen bonds : bond 0.03344 / 2.14 ( 294) hydrogen bonds : angle 3.90409 / 2.60 ( 846) ********************** 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 134 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.9011 (m-30) cc_final: 0.8676 (m-30) REVERT: A 122 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8841 (mp) REVERT: A 187 ARG cc_start: 0.8123 (mtm110) cc_final: 0.7762 (mtm180) REVERT: A 378 ASP cc_start: 0.7782 (t0) cc_final: 0.7426 (t0) REVERT: A 496 MET cc_start: 0.6820 (ttp) cc_final: 0.6565 (ttp) REVERT: B 15 LYS cc_start: 0.7090 (mtmt) cc_final: 0.6632 (mtmm) REVERT: B 102 ILE cc_start: 0.9119 (tt) cc_final: 0.8864 (tt) REVERT: B 108 ASP cc_start: 0.9010 (m-30) cc_final: 0.8678 (m-30) REVERT: B 122 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8855 (mp) REVERT: B 187 ARG cc_start: 0.8044 (mtm110) cc_final: 0.7735 (mtm180) REVERT: B 378 ASP cc_start: 0.7718 (t0) cc_final: 0.7348 (t0) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.0767 time to fit residues: 13.2089 Evaluate side-chains 130 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 353 LEU 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 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN B 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132389 restraints weight = 8980.708| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.05 r_work: 0.2942 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3791 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= 0.093 Angle : 0.516 8.491 10354 Z= 0.269 Chirality : 0.040 0.144 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.455 15.902 1062 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.27 % Allowed : 16.88 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.27), residues: 1004 helix: 0.56 (0.23), residues: 576 sheet: None (None), residues: 0 loop : -2.33 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.017 0.001 TYR B 343 PHE 0.010 0.001 PHE B 132 TRP 0.006 0.001 TRP A 436 HIS 0.001 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 ( 7608) covalent geometry : angle 0.51444 / 0.27 (10342) SS BOND : bond 0.00234 / 0.13 ( 6) SS BOND : angle 1.29213 / 0.79 ( 12) hydrogen bonds : bond 0.02933 / 1.88 ( 294) hydrogen bonds : angle 3.82065 / 2.57 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.33 seconds wall clock time: 27 minutes 40.31 seconds (1660.31 seconds total)