Starting phenix.real_space_refine on Mon Apr 28 11:37:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j16_61069/04_2025/9j16_61069.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j16_61069/04_2025/9j16_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_61069/04_2025/9j16_61069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j16_61069/04_2025/9j16_61069.map" model { file = "/net/cci-nas-00/data/ceres_data/9j16_61069/04_2025/9j16_61069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j16_61069/04_2025/9j16_61069.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.050 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7458 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3718 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 487} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B Time building chain proxies: 6.50, per 1000 atoms: 0.87 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: 1.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 59.9% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 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: 1.91 Time building geometry restraints manager: 2.03 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.910 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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= 0.311 Angle : 0.965 8.377 10354 Z= 0.528 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 : 1.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.55 (0.15), residues: 1004 helix: -4.72 (0.07), residues: 558 sheet: None (None), residues: 0 loop : -3.72 (0.22), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 253 HIS 0.003 0.001 HIS B 315 PHE 0.022 0.002 PHE A 207 TYR 0.018 0.002 TYR B 146 ARG 0.005 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.35878 ( 294) hydrogen bonds : angle 11.18073 ( 846) SS BOND : bond 0.00648 ( 6) SS BOND : angle 1.53442 ( 12) covalent geometry : bond 0.00680 ( 7608) covalent geometry : angle 0.96456 (10342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.857 Fit side-chains REVERT: A 15 LYS cc_start: 0.8137 (mptt) cc_final: 0.7824 (mtpt) REVERT: A 26 PHE cc_start: 0.7466 (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: 0.9104 (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: 0.1951 time to fit residues: 53.0902 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 : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 147 ASN A 160 HIS A 482 ASN B 95 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121506 restraints weight = 9898.637| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.28 r_work: 0.3177 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7614 Z= 0.110 Angle : 0.583 6.373 10354 Z= 0.309 Chirality : 0.041 0.177 1250 Planarity : 0.005 0.032 1272 Dihedral : 5.426 19.404 1062 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.03 % Allowed : 9.14 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.20), residues: 1004 helix: -3.04 (0.15), residues: 572 sheet: None (None), residues: 0 loop : -3.25 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 253 HIS 0.003 0.001 HIS B 17 PHE 0.013 0.001 PHE B 132 TYR 0.015 0.001 TYR B 419 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 294) hydrogen bonds : angle 4.97723 ( 846) SS BOND : bond 0.00340 ( 6) SS BOND : angle 0.80732 ( 12) covalent geometry : bond 0.00244 ( 7608) covalent geometry : angle 0.58285 (10342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.738 Fit side-chains REVERT: A 15 LYS cc_start: 0.8224 (mptt) cc_final: 0.7875 (ttpt) REVERT: A 102 ILE cc_start: 0.8973 (tt) cc_final: 0.8708 (tt) REVERT: A 213 ASN cc_start: 0.8045 (m-40) cc_final: 0.7421 (p0) REVERT: A 247 MET cc_start: 0.9206 (mmm) cc_final: 0.8950 (tpp) REVERT: A 274 MET cc_start: 0.9009 (mtp) cc_final: 0.8764 (mtm) REVERT: A 314 PHE cc_start: 0.8607 (t80) cc_final: 0.8387 (t80) REVERT: A 479 SER cc_start: 0.9315 (t) cc_final: 0.8894 (p) REVERT: B 102 ILE cc_start: 0.8929 (tt) cc_final: 0.8653 (tt) REVERT: B 212 MET cc_start: 0.7691 (pmm) cc_final: 0.7142 (mtt) REVERT: B 213 ASN cc_start: 0.8098 (m-40) cc_final: 0.7472 (p0) REVERT: B 479 SER cc_start: 0.9353 (t) cc_final: 0.8883 (p) REVERT: B 482 ASN cc_start: 0.8619 (m-40) cc_final: 0.8338 (m110) outliers start: 16 outliers final: 10 residues processed: 142 average time/residue: 0.1577 time to fit residues: 31.8719 Evaluate side-chains 107 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 353 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN B 147 ASN B 432 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115739 restraints weight = 9954.105| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.27 r_work: 0.3054 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7614 Z= 0.150 Angle : 0.581 5.387 10354 Z= 0.309 Chirality : 0.042 0.163 1250 Planarity : 0.004 0.032 1272 Dihedral : 5.131 18.676 1062 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.92 % Allowed : 10.91 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.23), residues: 1004 helix: -1.90 (0.19), residues: 582 sheet: None (None), residues: 0 loop : -3.03 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.002 0.001 HIS A 17 PHE 0.014 0.002 PHE A 368 TYR 0.012 0.001 TYR B 343 ARG 0.003 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 294) hydrogen bonds : angle 4.41648 ( 846) SS BOND : bond 0.00360 ( 6) SS BOND : angle 0.88082 ( 12) covalent geometry : bond 0.00364 ( 7608) covalent geometry : angle 0.58063 (10342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.808 Fit side-chains REVERT: A 15 LYS cc_start: 0.8029 (mptt) cc_final: 0.7654 (ttpt) REVERT: A 102 ILE cc_start: 0.9013 (tt) cc_final: 0.8706 (tt) REVERT: A 163 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8361 (mmm) REVERT: A 213 ASN cc_start: 0.8083 (m-40) cc_final: 0.7333 (p0) REVERT: A 479 SER cc_start: 0.9389 (t) cc_final: 0.9165 (p) REVERT: B 102 ILE cc_start: 0.9006 (tt) cc_final: 0.8692 (tt) REVERT: B 163 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8333 (mmm) REVERT: B 213 ASN cc_start: 0.8125 (m-40) cc_final: 0.7423 (p0) REVERT: B 324 ILE cc_start: 0.8451 (mm) cc_final: 0.8205 (mt) REVERT: B 479 SER cc_start: 0.9489 (t) cc_final: 0.9026 (p) REVERT: B 482 ASN cc_start: 0.8771 (m-40) cc_final: 0.8401 (m110) outliers start: 23 outliers final: 12 residues processed: 119 average time/residue: 0.1332 time to fit residues: 24.1713 Evaluate side-chains 112 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3715 r_free = 0.3715 target = 0.149563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118505 restraints weight = 9975.778| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.30 r_work: 0.3089 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3314 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= 0.107 Angle : 0.522 5.271 10354 Z= 0.277 Chirality : 0.040 0.150 1250 Planarity : 0.003 0.031 1272 Dihedral : 4.740 17.216 1062 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.28 % Allowed : 11.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.24), residues: 1004 helix: -1.14 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -2.81 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 335 HIS 0.001 0.001 HIS A 17 PHE 0.012 0.001 PHE A 132 TYR 0.012 0.001 TYR B 343 ARG 0.002 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 294) hydrogen bonds : angle 4.07148 ( 846) SS BOND : bond 0.00258 ( 6) SS BOND : angle 0.70896 ( 12) covalent geometry : bond 0.00251 ( 7608) covalent geometry : angle 0.52146 (10342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.740 Fit side-chains REVERT: A 15 LYS cc_start: 0.7996 (mptt) cc_final: 0.7710 (ttpt) REVERT: A 102 ILE cc_start: 0.9002 (tt) cc_final: 0.8704 (tt) REVERT: A 213 ASN cc_start: 0.8065 (m-40) cc_final: 0.7338 (p0) REVERT: A 274 MET cc_start: 0.9045 (mtp) cc_final: 0.8834 (mtm) REVERT: B 102 ILE cc_start: 0.9000 (tt) cc_final: 0.8681 (tt) REVERT: B 163 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8390 (mmp) REVERT: B 213 ASN cc_start: 0.8225 (m-40) cc_final: 0.7463 (p0) REVERT: B 274 MET cc_start: 0.9069 (mtp) cc_final: 0.8851 (mtm) REVERT: B 324 ILE cc_start: 0.8353 (mm) cc_final: 0.8069 (mt) REVERT: B 479 SER cc_start: 0.9438 (t) cc_final: 0.9022 (p) REVERT: B 482 ASN cc_start: 0.8677 (m-40) cc_final: 0.8345 (m110) outliers start: 18 outliers final: 13 residues processed: 120 average time/residue: 0.1328 time to fit residues: 24.0155 Evaluate side-chains 116 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 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 163 MET Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.0670 chunk 51 optimal weight: 7.9990 chunk 80 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 315 HIS B 211 GLN B 315 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116476 restraints weight = 9847.748| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.32 r_work: 0.3171 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3706 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= 0.077 Angle : 0.479 5.557 10354 Z= 0.253 Chirality : 0.039 0.140 1250 Planarity : 0.003 0.032 1272 Dihedral : 4.331 15.588 1062 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.16 % Allowed : 12.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.26), residues: 1004 helix: -0.40 (0.22), residues: 570 sheet: None (None), residues: 0 loop : -2.41 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS A 17 PHE 0.009 0.001 PHE A 368 TYR 0.011 0.001 TYR B 343 ARG 0.003 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.02489 ( 294) hydrogen bonds : angle 3.84354 ( 846) SS BOND : bond 0.00179 ( 6) SS BOND : angle 0.53058 ( 12) covalent geometry : bond 0.00162 ( 7608) covalent geometry : angle 0.47865 (10342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.794 Fit side-chains REVERT: A 15 LYS cc_start: 0.7898 (mptt) cc_final: 0.7656 (ttpt) REVERT: A 102 ILE cc_start: 0.9020 (tt) cc_final: 0.8725 (tt) REVERT: A 163 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8360 (mmp) REVERT: A 212 MET cc_start: 0.7772 (pmm) cc_final: 0.7274 (mtt) REVERT: A 213 ASN cc_start: 0.7987 (m-40) cc_final: 0.7312 (p0) REVERT: A 274 MET cc_start: 0.8997 (mtp) cc_final: 0.8783 (mtm) REVERT: B 102 ILE cc_start: 0.9043 (tt) cc_final: 0.8738 (tt) REVERT: B 213 ASN cc_start: 0.7976 (m-40) cc_final: 0.7229 (p0) REVERT: B 424 MET cc_start: 0.8656 (ptp) cc_final: 0.8447 (ttp) REVERT: B 479 SER cc_start: 0.9448 (t) cc_final: 0.9091 (p) REVERT: B 482 ASN cc_start: 0.8546 (m-40) cc_final: 0.8256 (m110) outliers start: 17 outliers final: 13 residues processed: 138 average time/residue: 0.1566 time to fit residues: 31.3371 Evaluate side-chains 123 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 390 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 0.0270 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113490 restraints weight = 9934.642| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.34 r_work: 0.3127 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7614 Z= 0.101 Angle : 0.498 6.360 10354 Z= 0.263 Chirality : 0.041 0.141 1250 Planarity : 0.003 0.032 1272 Dihedral : 4.325 17.066 1062 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.16 % Allowed : 13.71 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.26), residues: 1004 helix: -0.04 (0.22), residues: 570 sheet: -3.35 (1.03), residues: 20 loop : -2.11 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 253 HIS 0.001 0.000 HIS A 17 PHE 0.012 0.001 PHE B 132 TYR 0.015 0.001 TYR A 343 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 294) hydrogen bonds : angle 3.80899 ( 846) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.60364 ( 12) covalent geometry : bond 0.00240 ( 7608) covalent geometry : angle 0.49772 (10342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.913 Fit side-chains REVERT: A 15 LYS cc_start: 0.7893 (mptt) cc_final: 0.7668 (ttpt) REVERT: A 102 ILE cc_start: 0.9063 (tt) cc_final: 0.8826 (tt) REVERT: A 163 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8361 (mmp) REVERT: A 212 MET cc_start: 0.7779 (pmm) cc_final: 0.7264 (mtt) REVERT: A 213 ASN cc_start: 0.8046 (m-40) cc_final: 0.7345 (p0) REVERT: B 102 ILE cc_start: 0.9060 (tt) cc_final: 0.8821 (tt) REVERT: B 213 ASN cc_start: 0.8034 (m-40) cc_final: 0.7264 (p0) REVERT: B 424 MET cc_start: 0.8677 (ptp) cc_final: 0.8413 (ttp) REVERT: B 479 SER cc_start: 0.9486 (t) cc_final: 0.9131 (p) REVERT: B 482 ASN cc_start: 0.8590 (m-40) cc_final: 0.8254 (m110) outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.1445 time to fit residues: 25.7409 Evaluate side-chains 120 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 390 VAL 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 171 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 8 optimal weight: 0.0170 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114662 restraints weight = 9914.144| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.34 r_work: 0.3143 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3911 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 : 0.486 6.736 10354 Z= 0.256 Chirality : 0.040 0.142 1250 Planarity : 0.003 0.033 1272 Dihedral : 4.229 16.072 1062 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.54 % Allowed : 13.32 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.27), residues: 1004 helix: 0.31 (0.23), residues: 570 sheet: -3.33 (1.03), residues: 20 loop : -1.91 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 335 HIS 0.001 0.000 HIS A 17 PHE 0.010 0.001 PHE B 132 TYR 0.013 0.001 TYR B 343 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.02788 ( 294) hydrogen bonds : angle 3.70151 ( 846) SS BOND : bond 0.00218 ( 6) SS BOND : angle 0.54530 ( 12) covalent geometry : bond 0.00207 ( 7608) covalent geometry : angle 0.48589 (10342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.826 Fit side-chains REVERT: A 15 LYS cc_start: 0.7811 (mptt) cc_final: 0.7591 (tttt) REVERT: A 102 ILE cc_start: 0.9040 (tt) cc_final: 0.8813 (tt) REVERT: A 124 MET cc_start: 0.8694 (tpp) cc_final: 0.8457 (tpp) REVERT: A 163 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8304 (mmp) REVERT: A 212 MET cc_start: 0.7776 (pmm) cc_final: 0.7220 (mtt) REVERT: A 213 ASN cc_start: 0.7995 (m-40) cc_final: 0.7302 (p0) REVERT: B 102 ILE cc_start: 0.9063 (tt) cc_final: 0.8828 (tt) REVERT: B 213 ASN cc_start: 0.8035 (m-40) cc_final: 0.7266 (p0) REVERT: B 356 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7363 (mpp) REVERT: B 479 SER cc_start: 0.9482 (t) cc_final: 0.9214 (p) REVERT: B 482 ASN cc_start: 0.8497 (m-40) cc_final: 0.8184 (m110) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.1467 time to fit residues: 26.2574 Evaluate side-chains 123 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 390 VAL 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 229 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 0.0060 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 71 optimal weight: 0.0050 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.149020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117108 restraints weight = 10058.060| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.36 r_work: 0.3174 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4135 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= 0.078 Angle : 0.466 6.334 10354 Z= 0.245 Chirality : 0.040 0.136 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.039 15.159 1062 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.41 % Allowed : 13.83 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.27), residues: 1004 helix: 0.64 (0.23), residues: 570 sheet: None (None), residues: 0 loop : -1.96 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 335 HIS 0.001 0.000 HIS A 297 PHE 0.008 0.001 PHE B 132 TYR 0.010 0.001 TYR A 343 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.02488 ( 294) hydrogen bonds : angle 3.56095 ( 846) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.47147 ( 12) covalent geometry : bond 0.00172 ( 7608) covalent geometry : angle 0.46552 (10342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.729 Fit side-chains REVERT: A 15 LYS cc_start: 0.7726 (mptt) cc_final: 0.7521 (ttpt) REVERT: A 102 ILE cc_start: 0.9056 (tt) cc_final: 0.8834 (tt) REVERT: A 124 MET cc_start: 0.8583 (tpp) cc_final: 0.8383 (tpp) REVERT: A 163 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8281 (mmp) REVERT: A 213 ASN cc_start: 0.7956 (m-40) cc_final: 0.7179 (p0) REVERT: B 102 ILE cc_start: 0.9051 (tt) cc_final: 0.8754 (tt) REVERT: B 124 MET cc_start: 0.8674 (tpp) cc_final: 0.8407 (tpp) REVERT: B 163 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8296 (mmp) REVERT: B 213 ASN cc_start: 0.7997 (m-40) cc_final: 0.7240 (p0) REVERT: B 479 SER cc_start: 0.9446 (t) cc_final: 0.9206 (p) REVERT: B 482 ASN cc_start: 0.8403 (m-40) cc_final: 0.8128 (m110) outliers start: 19 outliers final: 11 residues processed: 127 average time/residue: 0.1452 time to fit residues: 26.9299 Evaluate side-chains 117 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 390 VAL 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 163 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110867 restraints weight = 9989.727| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.34 r_work: 0.3092 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7614 Z= 0.143 Angle : 0.549 6.566 10354 Z= 0.286 Chirality : 0.043 0.149 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.336 17.552 1062 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.66 % Allowed : 14.47 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.27), residues: 1004 helix: 0.58 (0.22), residues: 576 sheet: -3.29 (1.08), residues: 20 loop : -1.93 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 335 HIS 0.002 0.001 HIS A 297 PHE 0.015 0.001 PHE B 132 TYR 0.008 0.001 TYR A 343 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 294) hydrogen bonds : angle 3.78001 ( 846) SS BOND : bond 0.00282 ( 6) SS BOND : angle 0.66690 ( 12) covalent geometry : bond 0.00351 ( 7608) covalent geometry : angle 0.54898 (10342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.813 Fit side-chains REVERT: A 15 LYS cc_start: 0.7754 (mptt) cc_final: 0.7548 (ttpt) REVERT: A 102 ILE cc_start: 0.9092 (tt) cc_final: 0.8856 (tt) REVERT: A 163 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8319 (mmp) REVERT: A 213 ASN cc_start: 0.8075 (m-40) cc_final: 0.7309 (p0) REVERT: B 102 ILE cc_start: 0.9080 (tt) cc_final: 0.8844 (tt) REVERT: B 213 ASN cc_start: 0.8120 (m-40) cc_final: 0.7401 (p0) REVERT: B 356 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7376 (mpp) REVERT: B 479 SER cc_start: 0.9488 (t) cc_final: 0.9214 (p) REVERT: B 482 ASN cc_start: 0.8580 (m-40) cc_final: 0.8218 (m110) outliers start: 21 outliers final: 17 residues processed: 127 average time/residue: 0.1451 time to fit residues: 27.1252 Evaluate side-chains 132 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 341 LEU 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 208 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5816 > 50: distance: 122 - 123: 7.545 distance: 123 - 124: 5.935 distance: 123 - 126: 7.832 distance: 124 - 125: 4.897 distance: 124 - 130: 6.974 distance: 126 - 127: 7.156 distance: 128 - 129: 8.848 distance: 130 - 131: 3.869 distance: 130 - 136: 7.297 distance: 131 - 132: 7.919 distance: 131 - 134: 7.918 distance: 132 - 133: 7.885 distance: 132 - 137: 6.454 distance: 134 - 135: 11.444 distance: 135 - 136: 7.353 distance: 137 - 138: 8.880 distance: 138 - 139: 8.388 distance: 138 - 141: 19.605 distance: 139 - 140: 11.538 distance: 139 - 145: 9.098 distance: 141 - 142: 20.106 distance: 142 - 143: 12.748 distance: 142 - 144: 15.216 distance: 145 - 146: 10.511 distance: 146 - 147: 11.216 distance: 146 - 149: 8.308 distance: 147 - 148: 20.874 distance: 147 - 152: 32.600 distance: 149 - 150: 7.260 distance: 149 - 151: 10.793 distance: 152 - 153: 6.280 distance: 153 - 154: 6.480 distance: 153 - 156: 10.396 distance: 154 - 155: 9.442 distance: 156 - 157: 11.431 distance: 157 - 159: 5.319 distance: 158 - 160: 7.150 distance: 159 - 161: 6.801 distance: 160 - 162: 4.120 distance: 162 - 163: 6.194 distance: 164 - 165: 4.304 distance: 165 - 166: 5.995 distance: 165 - 168: 4.784 distance: 166 - 167: 14.642 distance: 166 - 170: 8.182 distance: 168 - 169: 6.777 distance: 170 - 171: 8.191 distance: 171 - 172: 6.625 distance: 171 - 174: 5.328 distance: 172 - 173: 4.165 distance: 172 - 178: 5.221 distance: 173 - 195: 15.164 distance: 174 - 175: 13.071 distance: 174 - 176: 14.832 distance: 175 - 177: 10.675 distance: 178 - 179: 9.996 distance: 179 - 180: 8.113 distance: 179 - 182: 16.249 distance: 180 - 181: 8.180 distance: 180 - 183: 9.753 distance: 181 - 203: 21.641 distance: 183 - 184: 5.475 distance: 184 - 185: 3.174 distance: 184 - 187: 6.614 distance: 185 - 186: 4.858 distance: 185 - 191: 5.098 distance: 187 - 188: 9.039 distance: 188 - 189: 3.774 distance: 188 - 190: 32.278 distance: 191 - 192: 9.466 distance: 192 - 193: 4.310 distance: 193 - 194: 6.980 distance: 194 - 215: 11.773