Starting phenix.real_space_refine on Thu Jul 2 07:05:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j16_61069/07_2026/9j16_61069.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j16_61069/07_2026/9j16_61069.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/9j16_61069/07_2026/9j16_61069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j16_61069/07_2026/9j16_61069.map" model { file = "/net/cci-nas-00/data/ceres_data/9j16_61069/07_2026/9j16_61069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j16_61069/07_2026/9j16_61069.cif" } 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= 0.050 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: 2.38, per 1000 atoms: 0.32 Number of scatterers: 7458 At special positions: 0 Unit cell: (89.1, 118.8, 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=2.02 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: 0.47 Conformation dependent library (CDL) restraints added in 281.7 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: 0.20 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: 3.995A 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: 4.474A 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: 3.893A pdb=" N ALA A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.683A 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: 3.523A 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: 3.909A 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: 3.560A 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: 4.054A 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: 3.705A 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: 3.662A 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: 3.962A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 4.072A 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: 4.149A pdb=" N MET B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.647A 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: 3.726A pdb=" N PHE B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.651A 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: 4.330A 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: 3.769A 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: 3.560A pdb=" N GLY B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 removed outlier: 3.746A pdb=" N ALA B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.562A pdb=" N ILE B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 4.071A pdb=" N SER B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.771A 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: 4.491A 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: 3.626A 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: 3.636A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.576A 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: 3.961A 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: 7.307A 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: 0.90 Time building geometry restraints manager: 0.63 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: 1297 1.33 - 1.45: 2004 1.45 - 1.58: 4213 1.58 - 1.70: 0 1.70 - 1.82: 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 1.03e+01 bond pdb=" CA VAL B 397 " pdb=" CB VAL B 397 " ideal model delta sigma weight residual 1.540 1.504 0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" C PHE A 396 " pdb=" O PHE A 396 " ideal model delta sigma weight residual 1.234 1.201 0.034 1.23e-02 6.61e+03 7.58e+00 bond pdb=" C PHE B 396 " pdb=" O PHE B 396 " ideal model delta sigma weight residual 1.234 1.201 0.033 1.23e-02 6.61e+03 7.32e+00 bond pdb=" N PHE A 396 " pdb=" CA PHE A 396 " ideal model delta sigma weight residual 1.455 1.423 0.033 1.30e-02 5.92e+03 6.34e+00 ... (remaining 7603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 9642 1.68 - 3.35: 557 3.35 - 5.03: 85 5.03 - 6.70: 42 6.70 - 8.38: 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 111.19 118.80 -7.61 1.35e+00 5.49e-01 3.17e+01 angle pdb=" N VAL B 227 " pdb=" CA VAL B 227 " pdb=" CB VAL B 227 " ideal model delta sigma weight residual 111.19 118.79 -7.60 1.35e+00 5.49e-01 3.17e+01 angle pdb=" N PHE A 396 " pdb=" CA PHE A 396 " pdb=" CB PHE A 396 " ideal model delta sigma weight residual 110.06 102.25 7.81 1.51e+00 4.39e-01 2.68e+01 angle pdb=" N PHE B 396 " pdb=" CA PHE B 396 " pdb=" CB PHE B 396 " ideal model delta sigma weight residual 110.06 102.28 7.78 1.51e+00 4.39e-01 2.65e+01 angle pdb=" N PHE A 396 " pdb=" CA PHE A 396 " pdb=" C PHE A 396 " ideal model delta sigma weight residual 110.20 118.06 -7.86 1.58e+00 4.01e-01 2.48e+01 ... (remaining 10337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.49: 3804 9.49 - 18.98: 452 18.98 - 28.46: 126 28.46 - 37.95: 36 37.95 - 47.44: 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 -156.40 -23.60 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 -156.41 -23.59 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 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 4423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1145 0.091 - 0.182: 93 0.182 - 0.273: 10 0.273 - 0.363: 0 0.363 - 0.454: 2 Chirality restraints: 1250 Sorted by residual: 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 5.16e+00 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 5.13e+00 chirality pdb=" CA ASN A 432 " pdb=" N ASN A 432 " pdb=" C ASN A 432 " pdb=" CB ASN A 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 1.17e+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 1.16e+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 3.86e+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: 2546 2.85 - 3.37: 6791 3.37 - 3.88: 11254 3.88 - 4.39: 13224 4.39 - 4.90: 23088 Nonbonded interactions: 56903 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 2.370 3.040 nonbonded pdb=" OE1 GLU A 43 " pdb=" OG1 THR A 412 " model vdw 2.370 3.040 nonbonded pdb=" OG SER B 73 " pdb=" OD1 ASN B 75 " model vdw 2.435 3.040 ... (remaining 56898 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: 0.900 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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= 0.316 Angle : 0.965 8.377 10354 Z= 0.529 Chirality : 0.059 0.454 1250 Planarity : 0.006 0.049 1272 Dihedral : 9.605 47.438 2608 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % 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 B 36 TYR 0.018 0.002 TYR B 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 0.00680 / 0.32 ( 7608) covalent geometry : angle 0.96461 / 0.53 (10342) SS BOND : bond 0.00648 / 0.37 ( 6) SS BOND : angle 1.53442 / 0.93 ( 12) hydrogen bonds : bond 0.35878 / 23.45 ( 294) hydrogen bonds : angle 11.18073 / 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 203 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.260 Fit side-chains REVERT: A 15 LYS cc_start: 0.8137 (mptt) cc_final: 0.7824 (mtpt) REVERT: A 26 PHE cc_start: 0.7465 (t80) cc_final: 0.7069 (p90) REVERT: A 213 ASN cc_start: 0.7785 (m-40) cc_final: 0.7292 (p0) REVERT: A 378 ASP cc_start: 0.8454 (t0) cc_final: 0.8248 (t0) REVERT: A 479 SER cc_start: 0.9583 (t) cc_final: 0.8831 (p) REVERT: B 15 LYS cc_start: 0.7973 (mptt) cc_final: 0.7663 (ttpt) REVERT: B 26 PHE cc_start: 0.7450 (t80) cc_final: 0.6964 (p90) REVERT: B 203 MET cc_start: 0.9103 (mtp) cc_final: 0.8820 (mtm) REVERT: B 213 ASN cc_start: 0.7832 (m-40) cc_final: 0.7455 (p0) REVERT: B 324 ILE cc_start: 0.8526 (mm) cc_final: 0.8278 (mt) REVERT: B 479 SER cc_start: 0.9605 (t) cc_final: 0.8831 (p) REVERT: B 482 ASN cc_start: 0.8265 (m-40) cc_final: 0.8036 (m110) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0681 time to fit residues: 18.8561 Evaluate side-chains 117 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS B 95 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121727 restraints weight = 10148.527| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.36 r_work: 0.3126 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7614 Z= 0.140 Angle : 0.666 7.020 10354 Z= 0.352 Chirality : 0.044 0.198 1250 Planarity : 0.005 0.034 1272 Dihedral : 5.799 20.714 1062 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.16 % Allowed : 9.52 % Favored : 88.32 % 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: -4.80 (0.20), residues: 1004 helix: -3.02 (0.16), residues: 564 sheet: None (None), residues: 0 loop : -3.33 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 36 TYR 0.013 0.002 TYR A 343 PHE 0.017 0.002 PHE A 40 TRP 0.010 0.001 TRP B 253 HIS 0.002 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 7608) covalent geometry : angle 0.66582 / 0.35 (10342) SS BOND : bond 0.00486 / 0.30 ( 6) SS BOND : angle 0.83913 / 0.53 ( 12) hydrogen bonds : bond 0.06826 / 4.38 ( 294) hydrogen bonds : angle 5.69640 / 3.83 ( 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 141 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.161 Fit side-chains REVERT: A 15 LYS cc_start: 0.8313 (mptt) cc_final: 0.8003 (mtpt) REVERT: A 212 MET cc_start: 0.7732 (pmm) cc_final: 0.7297 (mtt) REVERT: A 213 ASN cc_start: 0.8086 (m-40) cc_final: 0.7427 (p0) REVERT: A 324 ILE cc_start: 0.8522 (mm) cc_final: 0.8165 (mt) REVERT: A 479 SER cc_start: 0.9287 (t) cc_final: 0.8962 (p) REVERT: B 15 LYS cc_start: 0.8208 (mptt) cc_final: 0.7998 (ttpt) REVERT: B 213 ASN cc_start: 0.8127 (m-40) cc_final: 0.7517 (p0) REVERT: B 324 ILE cc_start: 0.8556 (mm) cc_final: 0.8329 (mt) REVERT: B 479 SER cc_start: 0.9423 (t) cc_final: 0.8911 (p) REVERT: B 482 ASN cc_start: 0.8627 (m-40) cc_final: 0.8304 (m110) outliers start: 17 outliers final: 12 residues processed: 133 average time/residue: 0.0634 time to fit residues: 11.8145 Evaluate side-chains 121 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.148840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118446 restraints weight = 9877.179| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.27 r_work: 0.3141 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2543 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= 0.120 Angle : 0.578 5.283 10354 Z= 0.306 Chirality : 0.042 0.191 1250 Planarity : 0.004 0.032 1272 Dihedral : 5.296 19.454 1062 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.05 % Allowed : 9.64 % Favored : 87.31 % 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: -3.82 (0.22), residues: 1004 helix: -2.08 (0.19), residues: 566 sheet: None (None), residues: 0 loop : -3.11 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 182 TYR 0.016 0.001 TYR B 343 PHE 0.012 0.001 PHE A 132 TRP 0.009 0.001 TRP B 253 HIS 0.002 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7608) covalent geometry : angle 0.57799 / 0.31 (10342) SS BOND : bond 0.00349 / 0.21 ( 6) SS BOND : angle 0.81003 / 0.49 ( 12) hydrogen bonds : bond 0.04943 / 3.17 ( 294) hydrogen bonds : angle 4.86151 / 3.27 ( 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 136 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.243 Fit side-chains REVERT: A 15 LYS cc_start: 0.8180 (mptt) cc_final: 0.7822 (ttpt) REVERT: A 212 MET cc_start: 0.7806 (pmm) cc_final: 0.7337 (mtt) REVERT: A 213 ASN cc_start: 0.8079 (m-40) cc_final: 0.7445 (p0) REVERT: A 274 MET cc_start: 0.9037 (mtp) cc_final: 0.8773 (mtm) REVERT: A 324 ILE cc_start: 0.8427 (mm) cc_final: 0.8088 (mt) REVERT: A 479 SER cc_start: 0.9312 (t) cc_final: 0.8992 (p) REVERT: B 213 ASN cc_start: 0.8125 (m-40) cc_final: 0.7541 (p0) REVERT: B 479 SER cc_start: 0.9363 (t) cc_final: 0.8877 (p) REVERT: B 482 ASN cc_start: 0.8683 (m-40) cc_final: 0.8322 (m110) outliers start: 24 outliers final: 16 residues processed: 125 average time/residue: 0.0455 time to fit residues: 8.8710 Evaluate side-chains 115 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3706 r_free = 0.3706 target = 0.149524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118979 restraints weight = 10048.695| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.29 r_work: 0.3149 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7614 Z= 0.107 Angle : 0.551 5.147 10354 Z= 0.293 Chirality : 0.041 0.167 1250 Planarity : 0.003 0.033 1272 Dihedral : 5.053 18.919 1062 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.17 % Allowed : 10.03 % Favored : 86.80 % 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: -3.19 (0.24), residues: 1004 helix: -1.44 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -3.04 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.013 0.001 TYR B 343 PHE 0.012 0.001 PHE B 132 TRP 0.007 0.001 TRP B 253 HIS 0.002 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 7608) covalent geometry : angle 0.55068 / 0.29 (10342) SS BOND : bond 0.00335 / 0.20 ( 6) SS BOND : angle 0.81321 / 0.49 ( 12) hydrogen bonds : bond 0.04006 / 2.57 ( 294) hydrogen bonds : angle 4.43347 / 3.00 ( 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 132 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.263 Fit side-chains REVERT: A 15 LYS cc_start: 0.8094 (mptt) cc_final: 0.7798 (tttt) REVERT: A 213 ASN cc_start: 0.8043 (m-40) cc_final: 0.7342 (p0) REVERT: A 274 MET cc_start: 0.9027 (mtp) cc_final: 0.8796 (mtm) REVERT: A 324 ILE cc_start: 0.8360 (mm) cc_final: 0.8040 (mt) REVERT: A 479 SER cc_start: 0.9305 (t) cc_final: 0.9036 (p) REVERT: B 213 ASN cc_start: 0.8136 (m-40) cc_final: 0.7531 (p0) REVERT: B 479 SER cc_start: 0.9384 (t) cc_final: 0.8905 (p) REVERT: B 482 ASN cc_start: 0.8671 (m-40) cc_final: 0.8381 (m110) outliers start: 25 outliers final: 19 residues processed: 123 average time/residue: 0.0460 time to fit residues: 8.7649 Evaluate side-chains 121 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 0.0970 chunk 80 optimal weight: 0.4980 chunk 29 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 432 ASN A 482 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124187 restraints weight = 9971.605| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.32 r_work: 0.3210 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7614 Z= 0.090 Angle : 0.520 5.379 10354 Z= 0.278 Chirality : 0.040 0.163 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.741 17.915 1062 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.79 % Allowed : 11.17 % Favored : 86.04 % 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: -2.55 (0.25), residues: 1004 helix: -0.86 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.88 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.025 0.001 TYR A 343 PHE 0.010 0.001 PHE B 368 TRP 0.006 0.001 TRP B 253 HIS 0.001 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 ( 7608) covalent geometry : angle 0.51987 / 0.28 (10342) SS BOND : bond 0.00272 / 0.16 ( 6) SS BOND : angle 0.75034 / 0.45 ( 12) hydrogen bonds : bond 0.03245 / 2.07 ( 294) hydrogen bonds : angle 4.10087 / 2.76 ( 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 138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.186 Fit side-chains REVERT: A 15 LYS cc_start: 0.7995 (mptt) cc_final: 0.7745 (tttt) REVERT: A 102 ILE cc_start: 0.8962 (tt) cc_final: 0.8701 (tt) REVERT: A 213 ASN cc_start: 0.8080 (m-40) cc_final: 0.7351 (p0) REVERT: A 274 MET cc_start: 0.9007 (mtp) cc_final: 0.8764 (mtm) REVERT: B 102 ILE cc_start: 0.8919 (tt) cc_final: 0.8655 (tt) REVERT: B 212 MET cc_start: 0.7801 (pmm) cc_final: 0.7231 (mtt) REVERT: B 213 ASN cc_start: 0.8088 (m-40) cc_final: 0.7399 (p0) REVERT: B 479 SER cc_start: 0.9367 (t) cc_final: 0.8920 (p) REVERT: B 482 ASN cc_start: 0.8641 (m-40) cc_final: 0.8374 (m110) outliers start: 22 outliers final: 12 residues processed: 128 average time/residue: 0.0395 time to fit residues: 7.9682 Evaluate side-chains 116 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 353 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 0.0010 chunk 19 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119522 restraints weight = 10014.947| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.26 r_work: 0.3157 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3207 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= 0.098 Angle : 0.518 5.735 10354 Z= 0.274 Chirality : 0.040 0.158 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.606 17.293 1062 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.66 % Allowed : 11.55 % Favored : 85.79 % 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: -2.03 (0.26), residues: 1004 helix: -0.43 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -2.66 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.021 0.001 TYR B 343 PHE 0.011 0.001 PHE B 368 TRP 0.006 0.001 TRP A 335 HIS 0.001 0.000 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 7608) covalent geometry : angle 0.51739 / 0.27 (10342) SS BOND : bond 0.00278 / 0.16 ( 6) SS BOND : angle 0.72591 / 0.43 ( 12) hydrogen bonds : bond 0.03261 / 2.09 ( 294) hydrogen bonds : angle 4.05074 / 2.73 ( 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 130 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.165 Fit side-chains REVERT: A 102 ILE cc_start: 0.8953 (tt) cc_final: 0.8687 (tt) REVERT: A 213 ASN cc_start: 0.8074 (m-40) cc_final: 0.7354 (p0) REVERT: A 274 MET cc_start: 0.8999 (mtp) cc_final: 0.8750 (mtm) REVERT: B 102 ILE cc_start: 0.8945 (tt) cc_final: 0.8671 (tt) REVERT: B 213 ASN cc_start: 0.8164 (m-40) cc_final: 0.7457 (p0) REVERT: B 479 SER cc_start: 0.9397 (t) cc_final: 0.8969 (p) REVERT: B 482 ASN cc_start: 0.8639 (m-40) cc_final: 0.8324 (m110) outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 0.0458 time to fit residues: 8.7040 Evaluate side-chains 116 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 353 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 97 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112676 restraints weight = 9954.945| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.32 r_work: 0.3117 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3366 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= 0.110 Angle : 0.532 7.012 10354 Z= 0.279 Chirality : 0.041 0.152 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.549 16.883 1062 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.16 % Allowed : 12.94 % Favored : 84.90 % 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: -0.15 (0.22), residues: 574 sheet: -3.35 (1.05), residues: 20 loop : -2.36 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 29 TYR 0.017 0.001 TYR A 343 PHE 0.012 0.001 PHE A 368 TRP 0.007 0.001 TRP B 335 HIS 0.001 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 7608) covalent geometry : angle 0.53182 / 0.28 (10342) SS BOND : bond 0.00289 / 0.17 ( 6) SS BOND : angle 0.74084 / 0.44 ( 12) hydrogen bonds : bond 0.03322 / 2.14 ( 294) hydrogen bonds : angle 4.00633 / 2.70 ( 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 125 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.184 Fit side-chains REVERT: A 102 ILE cc_start: 0.9014 (tt) cc_final: 0.8772 (tt) REVERT: A 213 ASN cc_start: 0.8018 (m-40) cc_final: 0.7341 (p0) REVERT: A 324 ILE cc_start: 0.8334 (mm) cc_final: 0.8074 (mt) REVERT: B 102 ILE cc_start: 0.9003 (tt) cc_final: 0.8728 (tt) REVERT: B 212 MET cc_start: 0.7812 (pmm) cc_final: 0.7244 (mtt) REVERT: B 213 ASN cc_start: 0.8211 (m-40) cc_final: 0.7475 (p0) REVERT: B 479 SER cc_start: 0.9458 (t) cc_final: 0.9061 (p) REVERT: B 482 ASN cc_start: 0.8677 (m-40) cc_final: 0.8345 (m110) outliers start: 17 outliers final: 14 residues processed: 117 average time/residue: 0.0452 time to fit residues: 8.4149 Evaluate side-chains 118 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 ILE 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: 0.5980 chunk 64 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.0040 chunk 41 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113387 restraints weight = 9984.249| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.34 r_work: 0.3125 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7614 Z= 0.097 Angle : 0.519 6.665 10354 Z= 0.271 Chirality : 0.040 0.149 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.470 16.477 1062 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.16 % Allowed : 13.58 % Favored : 84.26 % 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: -1.31 (0.27), residues: 1004 helix: 0.16 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -2.35 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 36 TYR 0.016 0.001 TYR B 343 PHE 0.011 0.001 PHE A 368 TRP 0.007 0.001 TRP B 335 HIS 0.001 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 7608) covalent geometry : angle 0.51884 / 0.27 (10342) SS BOND : bond 0.00257 / 0.15 ( 6) SS BOND : angle 0.71168 / 0.42 ( 12) hydrogen bonds : bond 0.03101 / 2.00 ( 294) hydrogen bonds : angle 3.93986 / 2.66 ( 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 120 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.266 Fit side-chains REVERT: A 102 ILE cc_start: 0.9021 (tt) cc_final: 0.8782 (tt) REVERT: A 213 ASN cc_start: 0.8025 (m-40) cc_final: 0.7334 (p0) REVERT: B 102 ILE cc_start: 0.8988 (tt) cc_final: 0.8719 (tt) REVERT: B 212 MET cc_start: 0.7808 (pmm) cc_final: 0.7231 (mtt) REVERT: B 213 ASN cc_start: 0.8211 (m-40) cc_final: 0.7470 (p0) REVERT: B 324 ILE cc_start: 0.8259 (mm) cc_final: 0.7979 (mt) REVERT: B 479 SER cc_start: 0.9450 (t) cc_final: 0.9057 (p) REVERT: B 482 ASN cc_start: 0.8606 (m-40) cc_final: 0.8275 (m110) outliers start: 17 outliers final: 15 residues processed: 112 average time/residue: 0.0443 time to fit residues: 7.9777 Evaluate side-chains 115 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114665 restraints weight = 9844.962| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.31 r_work: 0.3143 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3596 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= 0.088 Angle : 0.509 6.992 10354 Z= 0.264 Chirality : 0.040 0.147 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.350 15.938 1062 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.78 % Allowed : 13.96 % Favored : 84.26 % 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: -0.87 (0.27), residues: 1004 helix: 0.54 (0.23), residues: 572 sheet: -3.32 (1.04), residues: 20 loop : -2.07 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 36 TYR 0.015 0.001 TYR B 343 PHE 0.010 0.001 PHE B 368 TRP 0.006 0.001 TRP B 253 HIS 0.001 0.000 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 7608) covalent geometry : angle 0.50896 / 0.26 (10342) SS BOND : bond 0.00232 / 0.13 ( 6) SS BOND : angle 0.66251 / 0.39 ( 12) hydrogen bonds : bond 0.02872 / 1.85 ( 294) hydrogen bonds : angle 3.85304 / 2.60 ( 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 121 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.167 Fit side-chains REVERT: A 102 ILE cc_start: 0.9034 (tt) cc_final: 0.8801 (tt) REVERT: A 213 ASN cc_start: 0.8010 (m-40) cc_final: 0.7334 (p0) REVERT: B 102 ILE cc_start: 0.9008 (tt) cc_final: 0.8748 (tt) REVERT: B 212 MET cc_start: 0.7783 (pmm) cc_final: 0.7206 (mtt) REVERT: B 213 ASN cc_start: 0.8173 (m-40) cc_final: 0.7438 (p0) REVERT: B 479 SER cc_start: 0.9442 (t) cc_final: 0.9088 (p) REVERT: B 482 ASN cc_start: 0.8604 (m-40) cc_final: 0.8281 (m110) outliers start: 14 outliers final: 13 residues processed: 115 average time/residue: 0.0435 time to fit residues: 7.9079 Evaluate side-chains 114 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 ILE 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: 0.7980 chunk 31 optimal weight: 0.0570 chunk 74 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114747 restraints weight = 9891.981| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.32 r_work: 0.3143 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3681 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= 0.089 Angle : 0.511 6.972 10354 Z= 0.263 Chirality : 0.040 0.146 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.307 15.979 1062 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.52 % Allowed : 13.96 % Favored : 84.52 % 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: -0.57 (0.27), residues: 1004 helix: 0.81 (0.23), residues: 568 sheet: -3.32 (1.03), residues: 20 loop : -1.95 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 36 TYR 0.015 0.001 TYR B 343 PHE 0.010 0.001 PHE A 368 TRP 0.006 0.001 TRP A 335 HIS 0.001 0.000 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 7608) covalent geometry : angle 0.51082 / 0.26 (10342) SS BOND : bond 0.00212 / 0.12 ( 6) SS BOND : angle 0.65559 / 0.38 ( 12) hydrogen bonds : bond 0.02899 / 1.87 ( 294) hydrogen bonds : angle 3.83663 / 2.59 ( 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 118 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.193 Fit side-chains REVERT: A 102 ILE cc_start: 0.9034 (tt) cc_final: 0.8805 (tt) REVERT: A 213 ASN cc_start: 0.8014 (m-40) cc_final: 0.7337 (p0) REVERT: B 102 ILE cc_start: 0.9034 (tt) cc_final: 0.8789 (tt) REVERT: B 212 MET cc_start: 0.7774 (pmm) cc_final: 0.7185 (mtt) REVERT: B 213 ASN cc_start: 0.8177 (m-40) cc_final: 0.7415 (p0) REVERT: B 479 SER cc_start: 0.9446 (t) cc_final: 0.9104 (p) REVERT: B 482 ASN cc_start: 0.8591 (m-40) cc_final: 0.8254 (m110) outliers start: 12 outliers final: 12 residues processed: 113 average time/residue: 0.0433 time to fit residues: 7.6291 Evaluate side-chains 112 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 ILE 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: 4.9990 chunk 35 optimal weight: 0.0170 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.0470 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116064 restraints weight = 9746.870| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.31 r_work: 0.3164 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3826 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= 0.082 Angle : 0.497 6.882 10354 Z= 0.257 Chirality : 0.039 0.139 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.196 15.664 1062 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.27 % Allowed : 14.21 % Favored : 84.52 % 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: -0.36 (0.28), residues: 1004 helix: 1.02 (0.23), residues: 568 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 36 TYR 0.015 0.001 TYR B 343 PHE 0.010 0.001 PHE B 368 TRP 0.006 0.001 TRP A 335 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.08 ( 7608) covalent geometry : angle 0.49687 / 0.26 (10342) SS BOND : bond 0.00199 / 0.11 ( 6) SS BOND : angle 0.61937 / 0.36 ( 12) hydrogen bonds : bond 0.02654 / 1.71 ( 294) hydrogen bonds : angle 3.74870 / 2.54 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1421.19 seconds wall clock time: 25 minutes 1.44 seconds (1501.44 seconds total)