Starting phenix.real_space_refine on Wed Sep 17 09:03:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j16_61069/09_2025/9j16_61069.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j16_61069/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j16_61069/09_2025/9j16_61069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j16_61069/09_2025/9j16_61069.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j16_61069/09_2025/9j16_61069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j16_61069/09_2025/9j16_61069.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.050 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-2.0-5805/lib/python3.9/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: 2.28, per 1000 atoms: 0.31 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: 0.52 Conformation dependent library (CDL) restraints added in 351.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 59.9% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 24 removed outlier: 4.150A pdb=" N MET A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 15 " --> pdb=" O TRP A 11 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 3.995A 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: 0.95 Time building geometry restraints manager: 0.70 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: 0.01 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: 0.850 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.070 Find NCS groups from input model: 0.050 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- 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 : 1.33 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 aren 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 covalent geometry : bond 0.00680 ( 7608) covalent geometry : angle 0.96456 (10342) SS BOND : bond 0.00648 ( 6) SS BOND : angle 1.53442 ( 12) hydrogen bonds : bond 0.35878 ( 294) hydrogen bonds : angle 11.18073 ( 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 : 0.258 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: 0.0827 time to fit residues: 22.5776 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 : 0.209 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 147 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.151624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121263 restraints weight = 10046.691| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.30 r_work: 0.3123 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7614 Z= 0.117 Angle : 0.585 6.624 10354 Z= 0.310 Chirality : 0.041 0.181 1250 Planarity : 0.005 0.032 1272 Dihedral : 5.433 19.350 1062 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.03 % Allowed : 9.26 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.79 (0.20), residues: 1004 helix: -3.05 (0.15), residues: 572 sheet: None (None), residues: 0 loop : -3.26 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.016 0.002 TYR B 419 PHE 0.013 0.001 PHE B 132 TRP 0.008 0.001 TRP B 253 HIS 0.003 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7608) covalent geometry : angle 0.58489 (10342) SS BOND : bond 0.00328 ( 6) SS BOND : angle 0.78784 ( 12) hydrogen bonds : bond 0.04288 ( 294) hydrogen bonds : angle 4.96504 ( 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 148 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.262 Fit side-chains REVERT: A 15 LYS cc_start: 0.8205 (mptt) cc_final: 0.7860 (ttpt) REVERT: A 102 ILE cc_start: 0.8964 (tt) cc_final: 0.8703 (tt) REVERT: A 213 ASN cc_start: 0.8036 (m-40) cc_final: 0.7394 (p0) REVERT: A 247 MET cc_start: 0.9190 (mmm) cc_final: 0.8938 (tpp) REVERT: A 274 MET cc_start: 0.9017 (mtp) cc_final: 0.8764 (mtm) REVERT: A 314 PHE cc_start: 0.8622 (t80) cc_final: 0.8399 (t80) REVERT: A 479 SER cc_start: 0.9322 (t) cc_final: 0.8988 (p) REVERT: B 102 ILE cc_start: 0.8920 (tt) cc_final: 0.8647 (tt) REVERT: B 212 MET cc_start: 0.7700 (pmm) cc_final: 0.7132 (mtt) REVERT: B 213 ASN cc_start: 0.8090 (m-40) cc_final: 0.7455 (p0) REVERT: B 479 SER cc_start: 0.9362 (t) cc_final: 0.8881 (p) REVERT: B 482 ASN cc_start: 0.8633 (m-40) cc_final: 0.8340 (m110) outliers start: 16 outliers final: 9 residues processed: 142 average time/residue: 0.0654 time to fit residues: 13.4276 Evaluate side-chains 106 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 A 482 ASN B 147 ASN B 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117534 restraints weight = 9839.413| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.27 r_work: 0.3078 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7614 Z= 0.125 Angle : 0.555 5.300 10354 Z= 0.296 Chirality : 0.041 0.158 1250 Planarity : 0.004 0.030 1272 Dihedral : 4.998 18.131 1062 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.54 % Allowed : 11.55 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.23), residues: 1004 helix: -1.83 (0.19), residues: 580 sheet: None (None), residues: 0 loop : -3.01 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 187 TYR 0.013 0.001 TYR B 343 PHE 0.013 0.001 PHE A 368 TRP 0.008 0.001 TRP B 253 HIS 0.002 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7608) covalent geometry : angle 0.55470 (10342) SS BOND : bond 0.00311 ( 6) SS BOND : angle 0.80798 ( 12) hydrogen bonds : bond 0.03950 ( 294) hydrogen bonds : angle 4.32540 ( 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 125 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.423 Fit side-chains REVERT: A 15 LYS cc_start: 0.8021 (mptt) cc_final: 0.7646 (ttpt) REVERT: A 102 ILE cc_start: 0.8996 (tt) cc_final: 0.8703 (tt) REVERT: A 163 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8438 (mmp) REVERT: A 213 ASN cc_start: 0.8077 (m-40) cc_final: 0.7339 (p0) REVERT: A 479 SER cc_start: 0.9391 (t) cc_final: 0.9115 (p) REVERT: B 102 ILE cc_start: 0.8999 (tt) cc_final: 0.8708 (tt) REVERT: B 163 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8451 (mmp) REVERT: B 213 ASN cc_start: 0.8204 (m-40) cc_final: 0.7481 (p0) REVERT: B 324 ILE cc_start: 0.8334 (mm) cc_final: 0.8078 (mt) REVERT: B 479 SER cc_start: 0.9451 (t) cc_final: 0.8992 (p) REVERT: B 482 ASN cc_start: 0.8678 (m-40) cc_final: 0.8338 (m110) outliers start: 20 outliers final: 12 residues processed: 117 average time/residue: 0.0525 time to fit residues: 9.6864 Evaluate side-chains 115 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL 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 311 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 78 optimal weight: 2.9990 chunk 1 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.0040 chunk 11 optimal weight: 4.9990 overall best weight: 1.1214 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.147071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115937 restraints weight = 10084.443| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.30 r_work: 0.3147 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7614 Z= 0.139 Angle : 0.550 5.353 10354 Z= 0.292 Chirality : 0.042 0.154 1250 Planarity : 0.004 0.031 1272 Dihedral : 4.870 18.368 1062 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.17 % Allowed : 11.04 % 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 aren not related in a simple way. whole: -2.78 (0.24), residues: 1004 helix: -1.17 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -2.79 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.011 0.001 TYR B 343 PHE 0.014 0.001 PHE B 368 TRP 0.008 0.001 TRP B 335 HIS 0.002 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7608) covalent geometry : angle 0.54988 (10342) SS BOND : bond 0.00313 ( 6) SS BOND : angle 0.78427 ( 12) hydrogen bonds : bond 0.03788 ( 294) hydrogen bonds : angle 4.18785 ( 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 134 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.266 Fit side-chains REVERT: A 15 LYS cc_start: 0.8054 (mptt) cc_final: 0.7754 (ttpt) REVERT: A 102 ILE cc_start: 0.9046 (tt) cc_final: 0.8806 (tt) REVERT: A 163 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8459 (mmp) REVERT: A 213 ASN cc_start: 0.8105 (m-40) cc_final: 0.7375 (p0) REVERT: B 102 ILE cc_start: 0.9044 (tt) cc_final: 0.8781 (tt) REVERT: B 163 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8451 (mmp) REVERT: B 213 ASN cc_start: 0.8258 (m-40) cc_final: 0.7526 (p0) REVERT: B 324 ILE cc_start: 0.8431 (mm) cc_final: 0.8144 (mt) REVERT: B 479 SER cc_start: 0.9467 (t) cc_final: 0.9038 (p) REVERT: B 482 ASN cc_start: 0.8731 (m-40) cc_final: 0.8391 (m110) outliers start: 25 outliers final: 15 residues processed: 123 average time/residue: 0.0553 time to fit residues: 10.2641 Evaluate side-chains 114 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 22 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 163 MET 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 352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.141313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109388 restraints weight = 9937.476| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.40 r_work: 0.3064 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3545 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= 0.093 Angle : 0.503 5.463 10354 Z= 0.266 Chirality : 0.040 0.148 1250 Planarity : 0.003 0.033 1272 Dihedral : 4.532 16.715 1062 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.41 % Allowed : 12.69 % 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 aren not related in a simple way. whole: -2.01 (0.26), residues: 1004 helix: -0.54 (0.22), residues: 570 sheet: None (None), residues: 0 loop : -2.42 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.018 0.001 TYR A 343 PHE 0.010 0.001 PHE A 132 TRP 0.007 0.001 TRP B 335 HIS 0.001 0.000 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7608) covalent geometry : angle 0.50260 (10342) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.61868 ( 12) hydrogen bonds : bond 0.02957 ( 294) hydrogen bonds : angle 3.95670 ( 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 135 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.251 Fit side-chains REVERT: A 15 LYS cc_start: 0.7939 (mptt) cc_final: 0.7676 (ttpt) REVERT: A 102 ILE cc_start: 0.9033 (tt) cc_final: 0.8809 (tt) REVERT: A 213 ASN cc_start: 0.8028 (m-40) cc_final: 0.7263 (p0) REVERT: B 102 ILE cc_start: 0.9021 (tt) cc_final: 0.8770 (tt) REVERT: B 213 ASN cc_start: 0.8202 (m-40) cc_final: 0.7311 (p0) REVERT: B 324 ILE cc_start: 0.8360 (mm) cc_final: 0.8079 (mt) REVERT: B 479 SER cc_start: 0.9495 (t) cc_final: 0.9111 (p) REVERT: B 482 ASN cc_start: 0.8618 (m-40) cc_final: 0.8312 (m110) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 0.0546 time to fit residues: 10.4329 Evaluate side-chains 119 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 284 ILE 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 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104022 restraints weight = 10077.673| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.38 r_work: 0.2976 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7614 Z= 0.177 Angle : 0.575 5.653 10354 Z= 0.302 Chirality : 0.043 0.156 1250 Planarity : 0.003 0.033 1272 Dihedral : 4.794 19.149 1062 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.81 % Allowed : 12.69 % Favored : 83.50 % 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 aren not related in a simple way. whole: -1.91 (0.26), residues: 1004 helix: -0.45 (0.22), residues: 580 sheet: -3.40 (1.03), residues: 20 loop : -2.32 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.013 0.001 TYR A 343 PHE 0.016 0.002 PHE B 132 TRP 0.009 0.001 TRP B 335 HIS 0.002 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 7608) covalent geometry : angle 0.57423 (10342) SS BOND : bond 0.00359 ( 6) SS BOND : angle 0.80705 ( 12) hydrogen bonds : bond 0.04148 ( 294) hydrogen bonds : angle 4.14041 ( 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 138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.275 Fit side-chains REVERT: A 15 LYS cc_start: 0.7890 (mptt) cc_final: 0.7682 (tttt) REVERT: A 102 ILE cc_start: 0.9082 (tt) cc_final: 0.8858 (tt) REVERT: A 163 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8394 (mmp) REVERT: A 176 VAL cc_start: 0.8389 (p) cc_final: 0.8146 (p) REVERT: A 213 ASN cc_start: 0.8211 (m-40) cc_final: 0.7385 (p0) REVERT: A 324 ILE cc_start: 0.8613 (mm) cc_final: 0.8354 (mt) REVERT: B 102 ILE cc_start: 0.9106 (tt) cc_final: 0.8875 (tt) REVERT: B 163 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8414 (mmp) REVERT: B 176 VAL cc_start: 0.8475 (p) cc_final: 0.8257 (p) REVERT: B 212 MET cc_start: 0.7803 (pmm) cc_final: 0.7126 (mtt) REVERT: B 213 ASN cc_start: 0.8254 (m-40) cc_final: 0.7515 (p0) REVERT: B 324 ILE cc_start: 0.8623 (mm) cc_final: 0.8398 (mt) REVERT: B 356 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7594 (mpp) REVERT: B 479 SER cc_start: 0.9543 (t) cc_final: 0.9126 (p) REVERT: B 482 ASN cc_start: 0.8790 (m-40) cc_final: 0.8387 (m110) outliers start: 30 outliers final: 20 residues processed: 128 average time/residue: 0.0631 time to fit residues: 12.0152 Evaluate side-chains 131 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 341 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 163 MET 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 317 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.0070 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 315 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113279 restraints weight = 9985.882| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.34 r_work: 0.3129 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3851 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= 0.089 Angle : 0.496 5.940 10354 Z= 0.263 Chirality : 0.041 0.144 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.409 16.697 1062 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.65 % Allowed : 14.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.27), residues: 1004 helix: 0.07 (0.22), residues: 570 sheet: None (None), residues: 0 loop : -2.16 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.015 0.001 TYR B 343 PHE 0.010 0.001 PHE A 132 TRP 0.007 0.001 TRP A 335 HIS 0.001 0.000 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 7608) covalent geometry : angle 0.49566 (10342) SS BOND : bond 0.00215 ( 6) SS BOND : angle 0.60358 ( 12) hydrogen bonds : bond 0.02788 ( 294) hydrogen bonds : angle 3.82421 ( 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 133 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.268 Fit side-chains REVERT: A 15 LYS cc_start: 0.7816 (mptt) cc_final: 0.7566 (ttpt) REVERT: A 102 ILE cc_start: 0.9052 (tt) cc_final: 0.8828 (tt) REVERT: A 213 ASN cc_start: 0.8169 (m-40) cc_final: 0.7325 (p0) REVERT: B 102 ILE cc_start: 0.9060 (tt) cc_final: 0.8833 (tt) REVERT: B 213 ASN cc_start: 0.8058 (m-40) cc_final: 0.7322 (p0) REVERT: B 424 MET cc_start: 0.8650 (ptp) cc_final: 0.8429 (ttp) REVERT: B 463 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8418 (mm-30) REVERT: B 479 SER cc_start: 0.9493 (t) cc_final: 0.9207 (p) REVERT: B 482 ASN cc_start: 0.8661 (m-40) cc_final: 0.8307 (m110) outliers start: 13 outliers final: 12 residues processed: 129 average time/residue: 0.0689 time to fit residues: 12.8816 Evaluate side-chains 126 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 284 ILE 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 349 THR Chi-restraints excluded: chain B residue 463 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.142491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110559 restraints weight = 10014.351| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.34 r_work: 0.3091 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7614 Z= 0.124 Angle : 0.526 6.350 10354 Z= 0.277 Chirality : 0.042 0.148 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.434 17.756 1062 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.30 % Allowed : 13.45 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.27), residues: 1004 helix: 0.21 (0.22), residues: 574 sheet: -3.48 (1.01), residues: 20 loop : -1.96 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.013 0.001 TYR B 343 PHE 0.013 0.001 PHE B 132 TRP 0.008 0.001 TRP B 335 HIS 0.002 0.000 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7608) covalent geometry : angle 0.52604 (10342) SS BOND : bond 0.00278 ( 6) SS BOND : angle 0.65570 ( 12) hydrogen bonds : bond 0.03430 ( 294) hydrogen bonds : angle 3.87328 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.227 Fit side-chains REVERT: A 15 LYS cc_start: 0.7787 (mptt) cc_final: 0.7573 (ttpt) REVERT: A 102 ILE cc_start: 0.9065 (tt) cc_final: 0.8835 (tt) REVERT: A 213 ASN cc_start: 0.8200 (m-40) cc_final: 0.7400 (p0) REVERT: A 243 LEU cc_start: 0.6777 (mt) cc_final: 0.6562 (mt) REVERT: B 102 ILE cc_start: 0.9082 (tt) cc_final: 0.8849 (tt) REVERT: B 163 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8440 (mmp) REVERT: B 213 ASN cc_start: 0.8160 (m-40) cc_final: 0.7325 (p0) REVERT: B 356 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7498 (mpp) REVERT: B 479 SER cc_start: 0.9495 (t) cc_final: 0.9218 (p) REVERT: B 482 ASN cc_start: 0.8734 (m-40) cc_final: 0.8362 (m110) outliers start: 26 outliers final: 19 residues processed: 128 average time/residue: 0.0585 time to fit residues: 11.1665 Evaluate side-chains 132 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 132 PHE 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 A residue 479 SER 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 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 341 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.144256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112302 restraints weight = 9889.904| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.33 r_work: 0.3114 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3986 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= 0.103 Angle : 0.514 6.553 10354 Z= 0.269 Chirality : 0.041 0.146 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.344 16.348 1062 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.92 % Allowed : 13.83 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.27), residues: 1004 helix: 0.47 (0.23), residues: 572 sheet: None (None), residues: 0 loop : -2.07 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.013 0.001 TYR B 343 PHE 0.011 0.001 PHE B 132 TRP 0.007 0.001 TRP B 335 HIS 0.001 0.000 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7608) covalent geometry : angle 0.51421 (10342) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.62431 ( 12) hydrogen bonds : bond 0.03103 ( 294) hydrogen bonds : angle 3.82409 ( 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 137 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.266 Fit side-chains REVERT: A 102 ILE cc_start: 0.9045 (tt) cc_final: 0.8815 (tt) REVERT: A 124 MET cc_start: 0.8781 (tpp) cc_final: 0.8510 (tpp) REVERT: A 213 ASN cc_start: 0.8087 (m-40) cc_final: 0.7339 (p0) REVERT: B 102 ILE cc_start: 0.9066 (tt) cc_final: 0.8834 (tt) REVERT: B 163 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8486 (mmp) REVERT: B 213 ASN cc_start: 0.8070 (m-40) cc_final: 0.7344 (p0) REVERT: B 356 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7433 (mpp) REVERT: B 479 SER cc_start: 0.9496 (t) cc_final: 0.9225 (p) REVERT: B 482 ASN cc_start: 0.8650 (m-40) cc_final: 0.8274 (m110) outliers start: 23 outliers final: 20 residues processed: 125 average time/residue: 0.0734 time to fit residues: 13.0816 Evaluate side-chains 132 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 64 ILE 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 171 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 349 THR 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 ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 22 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.146269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114071 restraints weight = 9917.430| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.35 r_work: 0.3137 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7614 Z= 0.092 Angle : 0.509 7.244 10354 Z= 0.265 Chirality : 0.040 0.147 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.235 15.663 1062 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.41 % Allowed : 14.59 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.27), residues: 1004 helix: 0.74 (0.23), residues: 572 sheet: None (None), residues: 0 loop : -2.02 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 182 TYR 0.013 0.001 TYR B 343 PHE 0.010 0.001 PHE B 132 TRP 0.007 0.001 TRP B 335 HIS 0.001 0.000 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 7608) covalent geometry : angle 0.50890 (10342) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.69840 ( 12) hydrogen bonds : bond 0.02892 ( 294) hydrogen bonds : angle 3.75068 ( 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 139 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.237 Fit side-chains REVERT: A 24 LYS cc_start: 0.8438 (mmmt) cc_final: 0.7834 (mmmt) REVERT: A 102 ILE cc_start: 0.9054 (tt) cc_final: 0.8818 (tt) REVERT: A 124 MET cc_start: 0.8790 (tpp) cc_final: 0.8554 (tpp) REVERT: A 213 ASN cc_start: 0.8037 (m-40) cc_final: 0.7277 (p0) REVERT: B 102 ILE cc_start: 0.9047 (tt) cc_final: 0.8822 (tt) REVERT: B 124 MET cc_start: 0.8783 (tpp) cc_final: 0.8527 (tpp) REVERT: B 163 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8417 (mmp) REVERT: B 213 ASN cc_start: 0.8050 (m-40) cc_final: 0.7264 (p0) REVERT: B 356 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7348 (mpp) REVERT: B 479 SER cc_start: 0.9480 (t) cc_final: 0.9222 (p) REVERT: B 482 ASN cc_start: 0.8530 (m-40) cc_final: 0.8195 (m110) outliers start: 19 outliers final: 15 residues processed: 128 average time/residue: 0.0680 time to fit residues: 12.6799 Evaluate side-chains 127 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 39 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 171 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112184 restraints weight = 9823.254| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.33 r_work: 0.3110 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7614 Z= 0.114 Angle : 0.529 6.794 10354 Z= 0.273 Chirality : 0.041 0.149 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.317 16.736 1062 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.92 % Allowed : 14.59 % Favored : 82.49 % 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 aren not related in a simple way. whole: -0.46 (0.27), residues: 1004 helix: 0.85 (0.23), residues: 572 sheet: -3.63 (1.01), residues: 20 loop : -1.81 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.009 0.001 TYR A 343 PHE 0.012 0.001 PHE A 132 TRP 0.007 0.001 TRP A 335 HIS 0.001 0.000 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7608) covalent geometry : angle 0.52844 (10342) SS BOND : bond 0.00276 ( 6) SS BOND : angle 0.72044 ( 12) hydrogen bonds : bond 0.03327 ( 294) hydrogen bonds : angle 3.84648 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.77 seconds wall clock time: 29 minutes 41.15 seconds (1781.15 seconds total)