Starting phenix.real_space_refine on Wed Sep 17 09:04:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j15_61068/09_2025/9j15_61068.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j15_61068/09_2025/9j15_61068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j15_61068/09_2025/9j15_61068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j15_61068/09_2025/9j15_61068.map" model { file = "/net/cci-nas-00/data/ceres_data/9j15_61068/09_2025/9j15_61068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j15_61068/09_2025/9j15_61068.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 4836 2.51 5 N 1202 2.21 5 O 1364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-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: 2.77, per 1000 atoms: 0.37 Number of scatterers: 7458 At special positions: 0 Unit cell: (111.1, 95.7, 88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1364 8.00 N 1202 7.00 C 4836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 101 " distance=2.04 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 101 " distance=2.04 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 242 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 340.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 24 removed outlier: 4.150A pdb=" N MET A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 15 " --> pdb=" O TRP A 11 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.727A pdb=" N PHE A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 53 removed outlier: 3.650A pdb=" N THR A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.330A pdb=" N CYS A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 106 through 129 removed outlier: 4.215A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.662A pdb=" N ILE A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 175 removed outlier: 3.522A pdb=" N ALA A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.910A pdb=" N ARG A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 209 removed outlier: 4.176A pdb=" N ALA A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 3.746A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.563A pdb=" N ILE A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 4.070A pdb=" N SER A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.656A pdb=" N TRP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.706A pdb=" N ILE A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 removed outlier: 4.491A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.531A pdb=" N GLY A 402 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 422 removed outlier: 3.519A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.636A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.661A pdb=" N ILE A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 477 removed outlier: 3.684A pdb=" N ALA A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix Processing helix chain 'A' and resid 480 through 494 removed outlier: 3.961A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 507 Processing helix chain 'B' and resid 6 through 24 removed outlier: 4.150A pdb=" N MET B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 15 " --> pdb=" O TRP B 11 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 removed outlier: 3.727A pdb=" N PHE B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.650A pdb=" N THR B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.329A pdb=" N CYS B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 91' Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 106 through 129 removed outlier: 4.215A pdb=" N VAL B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.661A pdb=" N ILE B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.522A pdb=" N ALA B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 167 " --> pdb=" O MET B 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.909A pdb=" N ARG B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 removed outlier: 4.176A pdb=" N ALA B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 removed outlier: 3.745A pdb=" N ALA B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.563A pdb=" N ILE B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 4.070A pdb=" N SER B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 352 removed outlier: 4.656A pdb=" N TRP B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.705A pdb=" N ILE B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 387 removed outlier: 4.490A pdb=" N SER B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 387 " --> pdb=" O VAL B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.531A pdb=" N GLY B 402 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 422 removed outlier: 3.520A pdb=" N ILE B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 438 through 451 removed outlier: 3.635A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.662A pdb=" N ILE B 456 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 477 removed outlier: 3.684A pdb=" N ALA B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) Proline residue: B 475 - end of helix Processing helix chain 'B' and resid 480 through 494 removed outlier: 3.962A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 507 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 136 removed outlier: 4.070A pdb=" N ALA A 135 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 removed outlier: 7.307A pdb=" N GLU A 234 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 136 removed outlier: 4.071A pdb=" N ALA B 135 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 235 removed outlier: 7.308A pdb=" N GLU B 234 " --> pdb=" O LEU B 243 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1296 1.33 - 1.45: 2008 1.45 - 1.58: 4210 1.58 - 1.70: 0 1.70 - 1.83: 94 Bond restraints: 7608 Sorted by residual: bond pdb=" CA VAL A 397 " pdb=" CB VAL A 397 " ideal model delta sigma weight residual 1.540 1.503 0.037 1.15e-02 7.56e+03 1.06e+01 bond pdb=" CA VAL B 397 " pdb=" CB VAL B 397 " ideal model delta sigma weight residual 1.540 1.504 0.036 1.15e-02 7.56e+03 9.94e+00 bond pdb=" C PHE A 396 " pdb=" O PHE A 396 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.23e-02 6.61e+03 7.61e+00 bond pdb=" C PHE B 396 " pdb=" O PHE B 396 " ideal model delta sigma weight residual 1.234 1.201 0.034 1.23e-02 6.61e+03 7.52e+00 bond pdb=" N PHE B 396 " pdb=" CA PHE B 396 " ideal model delta sigma weight residual 1.455 1.422 0.033 1.30e-02 5.92e+03 6.38e+00 ... (remaining 7603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 9648 1.68 - 3.36: 551 3.36 - 5.04: 85 5.04 - 6.71: 42 6.71 - 8.39: 16 Bond angle restraints: 10342 Sorted by residual: angle pdb=" N VAL A 227 " pdb=" CA VAL A 227 " pdb=" CB VAL A 227 " ideal model delta sigma weight residual 111.19 118.82 -7.63 1.35e+00 5.49e-01 3.19e+01 angle pdb=" N VAL B 227 " pdb=" CA VAL B 227 " pdb=" CB VAL B 227 " ideal model delta sigma weight residual 111.19 118.78 -7.59 1.35e+00 5.49e-01 3.16e+01 angle pdb=" N PHE A 396 " pdb=" CA PHE A 396 " pdb=" CB PHE A 396 " ideal model delta sigma weight residual 110.06 102.22 7.84 1.51e+00 4.39e-01 2.69e+01 angle pdb=" N PHE B 396 " pdb=" CA PHE B 396 " pdb=" CB PHE B 396 " ideal model delta sigma weight residual 110.06 102.32 7.74 1.51e+00 4.39e-01 2.63e+01 angle pdb=" N PHE B 396 " pdb=" CA PHE B 396 " pdb=" C PHE B 396 " ideal model delta sigma weight residual 110.20 118.06 -7.86 1.58e+00 4.01e-01 2.47e+01 ... (remaining 10337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.49: 3804 9.49 - 18.98: 452 18.98 - 28.47: 126 28.47 - 37.96: 36 37.96 - 47.45: 8 Dihedral angle restraints: 4426 sinusoidal: 1588 harmonic: 2838 Sorted by residual: dihedral pdb=" CA ARG A 36 " pdb=" C ARG A 36 " pdb=" N LYS A 37 " pdb=" CA LYS A 37 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ARG B 36 " pdb=" C ARG B 36 " pdb=" N LYS B 37 " pdb=" CA LYS B 37 " ideal model delta harmonic sigma weight residual 180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA PHE B 362 " pdb=" C PHE B 362 " pdb=" N VAL B 363 " pdb=" CA VAL B 363 " ideal model delta harmonic sigma weight residual 180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 4423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1142 0.091 - 0.182: 96 0.182 - 0.272: 10 0.272 - 0.363: 0 0.363 - 0.454: 2 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CB ILE A 57 " pdb=" CA ILE A 57 " pdb=" CG1 ILE A 57 " pdb=" CG2 ILE A 57 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CB ILE B 57 " pdb=" CA ILE B 57 " pdb=" CG1 ILE B 57 " pdb=" CG2 ILE B 57 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CA ASN B 432 " pdb=" N ASN B 432 " pdb=" C ASN B 432 " pdb=" CB ASN B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1247 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 430 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C VAL B 430 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL B 430 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 431 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 430 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C VAL A 430 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL A 430 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 431 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 135 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO A 136 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.027 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2548 2.85 - 3.37: 6790 3.37 - 3.88: 11256 3.88 - 4.39: 13228 4.39 - 4.90: 23079 Nonbonded interactions: 56901 Sorted by model distance: nonbonded pdb=" OG1 THR B 192 " pdb=" OE1 GLU B 463 " model vdw 2.342 3.040 nonbonded pdb=" OG1 THR A 192 " pdb=" OE1 GLU A 463 " model vdw 2.343 3.040 nonbonded pdb=" OE1 GLU B 43 " pdb=" OG1 THR B 412 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLU A 43 " pdb=" OG1 THR A 412 " model vdw 2.371 3.040 nonbonded pdb=" OG SER A 73 " pdb=" OD1 ASN A 75 " model vdw 2.435 3.040 ... (remaining 56896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 7614 Z= 0.312 Angle : 0.965 8.393 10354 Z= 0.529 Chirality : 0.059 0.454 1250 Planarity : 0.006 0.049 1272 Dihedral : 9.605 47.445 2608 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they 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 A 36 TYR 0.018 0.002 TYR A 146 PHE 0.022 0.002 PHE A 207 TRP 0.012 0.002 TRP A 253 HIS 0.003 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00681 ( 7608) covalent geometry : angle 0.96440 (10342) SS BOND : bond 0.00652 ( 6) SS BOND : angle 1.53956 ( 12) hydrogen bonds : bond 0.35879 ( 294) hydrogen bonds : angle 11.18167 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7896 (mtm180) REVERT: A 108 ASP cc_start: 0.8623 (m-30) cc_final: 0.8307 (m-30) REVERT: A 187 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7550 (mtm180) REVERT: A 228 THR cc_start: 0.8693 (t) cc_final: 0.8338 (m) REVERT: A 353 LEU cc_start: 0.8542 (tp) cc_final: 0.8319 (tp) REVERT: A 354 TYR cc_start: 0.8125 (t80) cc_final: 0.7705 (t80) REVERT: A 378 ASP cc_start: 0.8031 (t0) cc_final: 0.7711 (t0) REVERT: A 404 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8119 (mtpp) REVERT: A 482 ASN cc_start: 0.8347 (m-40) cc_final: 0.7997 (m110) REVERT: A 496 MET cc_start: 0.6570 (ttp) cc_final: 0.6188 (ttm) REVERT: B 104 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7814 (mtm-85) REVERT: B 108 ASP cc_start: 0.8689 (m-30) cc_final: 0.8299 (m-30) REVERT: B 187 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7660 (mtm180) REVERT: B 228 THR cc_start: 0.8707 (t) cc_final: 0.8322 (m) REVERT: B 353 LEU cc_start: 0.8532 (tp) cc_final: 0.8307 (tp) REVERT: B 354 TYR cc_start: 0.8085 (t80) cc_final: 0.7632 (t80) REVERT: B 378 ASP cc_start: 0.8078 (t0) cc_final: 0.7740 (t0) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1058 time to fit residues: 31.6186 Evaluate side-chains 138 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 147 ASN A 160 HIS A 315 HIS B 95 ASN B 147 ASN B 160 HIS B 432 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.146256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.116405 restraints weight = 9192.732| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.87 r_work: 0.2992 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7614 Z= 0.125 Angle : 0.593 5.334 10354 Z= 0.315 Chirality : 0.041 0.135 1250 Planarity : 0.005 0.032 1272 Dihedral : 5.536 19.276 1062 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.05 % Allowed : 11.17 % 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: -4.64 (0.20), residues: 1004 helix: -2.95 (0.16), residues: 554 sheet: None (None), residues: 0 loop : -3.17 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.017 0.002 TYR B 419 PHE 0.016 0.001 PHE B 280 TRP 0.008 0.001 TRP B 253 HIS 0.002 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7608) covalent geometry : angle 0.59246 (10342) SS BOND : bond 0.00347 ( 6) SS BOND : angle 0.78615 ( 12) hydrogen bonds : bond 0.04667 ( 294) hydrogen bonds : angle 5.07523 ( 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 161 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8869 (m-30) cc_final: 0.8609 (m-30) REVERT: A 132 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8051 (p90) REVERT: A 187 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7735 (mtm180) REVERT: A 228 THR cc_start: 0.8790 (t) cc_final: 0.8458 (m) REVERT: A 378 ASP cc_start: 0.7892 (t0) cc_final: 0.7527 (t0) REVERT: A 404 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8399 (mtpp) REVERT: A 482 ASN cc_start: 0.8724 (m-40) cc_final: 0.8274 (m110) REVERT: A 496 MET cc_start: 0.6831 (ttp) cc_final: 0.6327 (ttm) REVERT: B 108 ASP cc_start: 0.8909 (m-30) cc_final: 0.8609 (m-30) REVERT: B 132 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8039 (p90) REVERT: B 187 ARG cc_start: 0.8126 (mtm110) cc_final: 0.7753 (mtm180) REVERT: B 228 THR cc_start: 0.8846 (t) cc_final: 0.8514 (m) REVERT: B 311 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8586 (mt) REVERT: B 378 ASP cc_start: 0.7896 (t0) cc_final: 0.7521 (t0) REVERT: B 482 ASN cc_start: 0.8780 (m-40) cc_final: 0.8333 (m110) outliers start: 24 outliers final: 8 residues processed: 152 average time/residue: 0.0737 time to fit residues: 15.9382 Evaluate side-chains 145 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.0060 chunk 24 optimal weight: 0.0370 chunk 73 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 432 ASN B 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.136936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106529 restraints weight = 9128.967| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.85 r_work: 0.2989 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7614 Z= 0.089 Angle : 0.513 5.142 10354 Z= 0.273 Chirality : 0.040 0.154 1250 Planarity : 0.004 0.030 1272 Dihedral : 4.884 16.825 1062 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.17 % Allowed : 12.69 % 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 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: -3.36 (0.23), residues: 1004 helix: -1.72 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -2.89 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.014 0.001 TYR B 343 PHE 0.013 0.001 PHE B 280 TRP 0.008 0.001 TRP B 11 HIS 0.001 0.000 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 7608) covalent geometry : angle 0.51238 (10342) SS BOND : bond 0.00240 ( 6) SS BOND : angle 0.67527 ( 12) hydrogen bonds : bond 0.03255 ( 294) hydrogen bonds : angle 4.30240 ( 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 167 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8895 (m-30) cc_final: 0.8626 (m-30) REVERT: A 122 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8629 (mp) REVERT: A 163 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7656 (mmm) REVERT: A 187 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7607 (mtm180) REVERT: A 378 ASP cc_start: 0.7935 (t0) cc_final: 0.7618 (t0) REVERT: A 482 ASN cc_start: 0.8701 (m-40) cc_final: 0.8314 (m110) REVERT: A 496 MET cc_start: 0.6724 (ttp) cc_final: 0.6184 (ttm) REVERT: B 108 ASP cc_start: 0.8919 (m-30) cc_final: 0.8610 (m-30) REVERT: B 122 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8697 (mp) REVERT: B 187 ARG cc_start: 0.8083 (mtm110) cc_final: 0.7688 (mtm180) REVERT: B 228 THR cc_start: 0.8709 (t) cc_final: 0.8444 (m) REVERT: B 313 ASP cc_start: 0.8755 (t0) cc_final: 0.8551 (t0) REVERT: B 378 ASP cc_start: 0.7877 (t0) cc_final: 0.7551 (t0) REVERT: B 482 ASN cc_start: 0.8717 (m-40) cc_final: 0.8322 (m110) outliers start: 25 outliers final: 6 residues processed: 158 average time/residue: 0.0869 time to fit residues: 18.6272 Evaluate side-chains 133 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 147 ASN A 211 GLN B 147 ASN B 211 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.131621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.100404 restraints weight = 9465.335| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.87 r_work: 0.2912 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7614 Z= 0.186 Angle : 0.602 6.758 10354 Z= 0.313 Chirality : 0.044 0.168 1250 Planarity : 0.004 0.034 1272 Dihedral : 5.094 19.944 1062 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.92 % Allowed : 14.47 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.68 (0.25), residues: 1004 helix: -1.10 (0.21), residues: 568 sheet: -3.06 (1.13), residues: 20 loop : -2.63 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 36 TYR 0.008 0.002 TYR B 419 PHE 0.015 0.002 PHE A 368 TRP 0.008 0.001 TRP B 335 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 7608) covalent geometry : angle 0.60149 (10342) SS BOND : bond 0.00397 ( 6) SS BOND : angle 0.89155 ( 12) hydrogen bonds : bond 0.04606 ( 294) hydrogen bonds : angle 4.42872 ( 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 155 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9121 (tt) cc_final: 0.8864 (tt) REVERT: A 108 ASP cc_start: 0.8893 (m-30) cc_final: 0.8611 (m-30) REVERT: A 187 ARG cc_start: 0.8141 (mtm110) cc_final: 0.7700 (mtm180) REVERT: A 378 ASP cc_start: 0.7901 (t0) cc_final: 0.7483 (t0) REVERT: A 496 MET cc_start: 0.6725 (ttp) cc_final: 0.6237 (ttm) REVERT: B 15 LYS cc_start: 0.7173 (mtmt) cc_final: 0.6714 (mtmm) REVERT: B 102 ILE cc_start: 0.9120 (tt) cc_final: 0.8861 (tt) REVERT: B 108 ASP cc_start: 0.8922 (m-30) cc_final: 0.8609 (m-30) REVERT: B 187 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7737 (mtm180) REVERT: B 228 THR cc_start: 0.8896 (t) cc_final: 0.8632 (m) REVERT: B 313 ASP cc_start: 0.8695 (t0) cc_final: 0.8491 (t0) REVERT: B 332 SER cc_start: 0.8851 (m) cc_final: 0.8650 (t) REVERT: B 378 ASP cc_start: 0.7944 (t0) cc_final: 0.7545 (t0) outliers start: 23 outliers final: 11 residues processed: 147 average time/residue: 0.0898 time to fit residues: 17.8411 Evaluate side-chains 137 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 496 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 64 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.134787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103599 restraints weight = 9245.639| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.85 r_work: 0.2940 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7614 Z= 0.097 Angle : 0.540 8.989 10354 Z= 0.276 Chirality : 0.040 0.150 1250 Planarity : 0.003 0.034 1272 Dihedral : 4.667 17.204 1062 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.90 % Allowed : 14.85 % 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: -2.02 (0.26), residues: 1004 helix: -0.49 (0.22), residues: 574 sheet: -3.13 (1.07), residues: 20 loop : -2.46 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 36 TYR 0.012 0.001 TYR A 343 PHE 0.011 0.001 PHE B 132 TRP 0.007 0.001 TRP B 335 HIS 0.001 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 7608) covalent geometry : angle 0.53963 (10342) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.93844 ( 12) hydrogen bonds : bond 0.03026 ( 294) hydrogen bonds : angle 3.93570 ( 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 164 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9035 (tt) cc_final: 0.8799 (tt) REVERT: A 108 ASP cc_start: 0.8854 (m-30) cc_final: 0.8574 (m-30) REVERT: A 122 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8722 (mp) REVERT: A 187 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7614 (mtm180) REVERT: A 378 ASP cc_start: 0.7677 (t0) cc_final: 0.7354 (t0) REVERT: A 496 MET cc_start: 0.6688 (ttp) cc_final: 0.6151 (ttm) REVERT: B 15 LYS cc_start: 0.6960 (mtmt) cc_final: 0.6662 (mtmm) REVERT: B 102 ILE cc_start: 0.9052 (tt) cc_final: 0.8811 (tt) REVERT: B 108 ASP cc_start: 0.8894 (m-30) cc_final: 0.8568 (m-30) REVERT: B 122 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8736 (mp) REVERT: B 187 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7638 (mtm180) REVERT: B 228 THR cc_start: 0.8691 (t) cc_final: 0.8476 (m) REVERT: B 313 ASP cc_start: 0.8633 (t0) cc_final: 0.8427 (t0) REVERT: B 332 SER cc_start: 0.8770 (m) cc_final: 0.8522 (t) REVERT: B 378 ASP cc_start: 0.7735 (t0) cc_final: 0.7383 (t0) outliers start: 15 outliers final: 5 residues processed: 158 average time/residue: 0.1022 time to fit residues: 21.1601 Evaluate side-chains 147 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 327 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.102078 restraints weight = 9333.194| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.83 r_work: 0.2910 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7614 Z= 0.105 Angle : 0.531 7.938 10354 Z= 0.271 Chirality : 0.040 0.146 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.535 17.035 1062 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.27 % Allowed : 16.88 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.27), residues: 1004 helix: -0.03 (0.23), residues: 572 sheet: -3.29 (1.04), residues: 20 loop : -2.30 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.009 0.001 TYR B 343 PHE 0.012 0.001 PHE B 132 TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7608) covalent geometry : angle 0.52960 (10342) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.24508 ( 12) hydrogen bonds : bond 0.03212 ( 294) hydrogen bonds : angle 3.82854 ( 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 151 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7156 (mmt) cc_final: 0.6335 (mtm) REVERT: A 102 ILE cc_start: 0.8998 (tt) cc_final: 0.8758 (tt) REVERT: A 108 ASP cc_start: 0.8868 (m-30) cc_final: 0.8606 (m-30) REVERT: A 122 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 187 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7522 (mtm180) REVERT: A 378 ASP cc_start: 0.7676 (t0) cc_final: 0.7329 (t0) REVERT: A 496 MET cc_start: 0.6640 (ttp) cc_final: 0.6087 (ttm) REVERT: B 102 ILE cc_start: 0.9029 (tt) cc_final: 0.8796 (tt) REVERT: B 108 ASP cc_start: 0.8846 (m-30) cc_final: 0.8534 (m-30) REVERT: B 122 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 187 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7566 (mtm180) REVERT: B 228 THR cc_start: 0.8702 (t) cc_final: 0.8428 (m) REVERT: B 313 ASP cc_start: 0.8639 (t0) cc_final: 0.8416 (t0) REVERT: B 332 SER cc_start: 0.8778 (m) cc_final: 0.8470 (t) REVERT: B 378 ASP cc_start: 0.7677 (t0) cc_final: 0.7339 (t0) outliers start: 10 outliers final: 5 residues processed: 146 average time/residue: 0.0967 time to fit residues: 18.9284 Evaluate side-chains 139 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.134708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103602 restraints weight = 9314.790| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.88 r_work: 0.2914 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4090 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= 0.110 Angle : 0.537 8.082 10354 Z= 0.272 Chirality : 0.041 0.149 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.503 16.781 1062 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.78 % Allowed : 16.12 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.27), residues: 1004 helix: 0.17 (0.23), residues: 574 sheet: -3.45 (0.98), residues: 20 loop : -2.25 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 36 TYR 0.008 0.001 TYR A 343 PHE 0.011 0.001 PHE B 132 TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7608) covalent geometry : angle 0.53547 (10342) SS BOND : bond 0.00250 ( 6) SS BOND : angle 1.26369 ( 12) hydrogen bonds : bond 0.03228 ( 294) hydrogen bonds : angle 3.78728 ( 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 150 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7110 (mmt) cc_final: 0.6302 (mtm) REVERT: A 102 ILE cc_start: 0.9105 (tt) cc_final: 0.8859 (tt) REVERT: A 108 ASP cc_start: 0.8945 (m-30) cc_final: 0.8673 (m-30) REVERT: A 122 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 187 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7865 (mtm180) REVERT: A 378 ASP cc_start: 0.7764 (t0) cc_final: 0.7336 (t0) REVERT: A 496 MET cc_start: 0.6677 (ttp) cc_final: 0.6164 (ttm) REVERT: B 102 ILE cc_start: 0.9086 (tt) cc_final: 0.8838 (tt) REVERT: B 108 ASP cc_start: 0.8929 (m-30) cc_final: 0.8635 (m-30) REVERT: B 122 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8812 (mp) REVERT: B 187 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7837 (mtm180) REVERT: B 228 THR cc_start: 0.8860 (t) cc_final: 0.8578 (m) REVERT: B 332 SER cc_start: 0.8851 (m) cc_final: 0.8539 (t) REVERT: B 378 ASP cc_start: 0.7738 (t0) cc_final: 0.7329 (t0) outliers start: 14 outliers final: 8 residues processed: 140 average time/residue: 0.0922 time to fit residues: 17.3006 Evaluate side-chains 146 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 496 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 39 optimal weight: 0.2980 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 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 = 0.3449 r_free = 0.3449 target = 0.134179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.102479 restraints weight = 9353.407| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.96 r_work: 0.2913 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7614 Z= 0.102 Angle : 0.528 8.641 10354 Z= 0.269 Chirality : 0.040 0.145 1250 Planarity : 0.003 0.035 1272 Dihedral : 4.388 16.387 1062 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.90 % Allowed : 16.37 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.27), residues: 1004 helix: 0.43 (0.23), residues: 572 sheet: -3.10 (1.10), residues: 20 loop : -2.07 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 36 TYR 0.009 0.001 TYR A 343 PHE 0.009 0.001 PHE B 368 TRP 0.006 0.001 TRP B 335 HIS 0.002 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7608) covalent geometry : angle 0.52727 (10342) SS BOND : bond 0.00194 ( 6) SS BOND : angle 1.11354 ( 12) hydrogen bonds : bond 0.03022 ( 294) hydrogen bonds : angle 3.70648 ( 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 155 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7080 (mmt) cc_final: 0.6256 (mtm) REVERT: A 102 ILE cc_start: 0.9092 (tt) cc_final: 0.8849 (tt) REVERT: A 108 ASP cc_start: 0.8985 (m-30) cc_final: 0.8724 (m-30) REVERT: A 122 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8818 (mp) REVERT: A 187 ARG cc_start: 0.8125 (mtm110) cc_final: 0.7839 (mtm180) REVERT: A 378 ASP cc_start: 0.7758 (t0) cc_final: 0.7323 (t0) REVERT: A 496 MET cc_start: 0.6630 (ttp) cc_final: 0.6118 (ttm) REVERT: B 102 ILE cc_start: 0.9068 (tt) cc_final: 0.8824 (tt) REVERT: B 108 ASP cc_start: 0.9012 (m-30) cc_final: 0.8731 (m-30) REVERT: B 122 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8821 (mp) REVERT: B 187 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7884 (mtm180) REVERT: B 228 THR cc_start: 0.8770 (t) cc_final: 0.8483 (m) REVERT: B 332 SER cc_start: 0.8840 (m) cc_final: 0.8517 (t) REVERT: B 378 ASP cc_start: 0.7714 (t0) cc_final: 0.7312 (t0) outliers start: 15 outliers final: 7 residues processed: 146 average time/residue: 0.0951 time to fit residues: 18.5403 Evaluate side-chains 143 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 327 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.133543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.101640 restraints weight = 9272.920| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.96 r_work: 0.2904 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7614 Z= 0.116 Angle : 0.539 8.319 10354 Z= 0.275 Chirality : 0.041 0.148 1250 Planarity : 0.004 0.044 1272 Dihedral : 4.412 17.149 1062 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.40 % Allowed : 17.01 % Favored : 81.60 % 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: -0.96 (0.27), residues: 1004 helix: 0.38 (0.23), residues: 586 sheet: None (None), residues: 0 loop : -2.16 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 182 TYR 0.034 0.001 TYR A 375 PHE 0.010 0.001 PHE A 368 TRP 0.006 0.001 TRP A 335 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7608) covalent geometry : angle 0.53728 (10342) SS BOND : bond 0.00248 ( 6) SS BOND : angle 1.19482 ( 12) hydrogen bonds : bond 0.03270 ( 294) hydrogen bonds : angle 3.74257 ( 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 143 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9100 (tt) cc_final: 0.8855 (tt) REVERT: A 108 ASP cc_start: 0.9007 (m-30) cc_final: 0.8734 (m-30) REVERT: A 122 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8811 (mp) REVERT: A 378 ASP cc_start: 0.7833 (t0) cc_final: 0.7348 (t0) REVERT: A 496 MET cc_start: 0.6632 (ttp) cc_final: 0.6115 (ttm) REVERT: B 102 ILE cc_start: 0.9078 (tt) cc_final: 0.8834 (tt) REVERT: B 108 ASP cc_start: 0.9027 (m-30) cc_final: 0.8742 (m-30) REVERT: B 122 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8811 (mp) REVERT: B 187 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7883 (mtm180) REVERT: B 228 THR cc_start: 0.8974 (t) cc_final: 0.8736 (m) REVERT: B 332 SER cc_start: 0.8871 (m) cc_final: 0.8579 (t) REVERT: B 378 ASP cc_start: 0.7752 (t0) cc_final: 0.7314 (t0) outliers start: 11 outliers final: 5 residues processed: 139 average time/residue: 0.0984 time to fit residues: 18.1501 Evaluate side-chains 135 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.134147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.102453 restraints weight = 9248.656| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.94 r_work: 0.2907 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4359 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= 0.106 Angle : 0.527 8.717 10354 Z= 0.269 Chirality : 0.041 0.147 1250 Planarity : 0.003 0.036 1272 Dihedral : 4.328 16.719 1062 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.14 % Allowed : 17.39 % Favored : 81.47 % 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: -0.80 (0.27), residues: 1004 helix: 0.52 (0.23), residues: 586 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.017 0.001 TYR A 375 PHE 0.009 0.001 PHE A 368 TRP 0.006 0.001 TRP A 335 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7608) covalent geometry : angle 0.52621 (10342) SS BOND : bond 0.00211 ( 6) SS BOND : angle 1.11174 ( 12) hydrogen bonds : bond 0.03052 ( 294) hydrogen bonds : angle 3.69456 ( 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 141 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9097 (tt) cc_final: 0.8855 (tt) REVERT: A 108 ASP cc_start: 0.8987 (m-30) cc_final: 0.8725 (m-30) REVERT: A 122 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8844 (mp) REVERT: A 378 ASP cc_start: 0.7817 (t0) cc_final: 0.7331 (t0) REVERT: A 496 MET cc_start: 0.6674 (ttp) cc_final: 0.6122 (ttm) REVERT: B 102 ILE cc_start: 0.9077 (tt) cc_final: 0.8837 (tt) REVERT: B 108 ASP cc_start: 0.9004 (m-30) cc_final: 0.8734 (m-30) REVERT: B 122 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8832 (mp) REVERT: B 228 THR cc_start: 0.8966 (t) cc_final: 0.8707 (m) REVERT: B 332 SER cc_start: 0.8856 (m) cc_final: 0.8563 (t) REVERT: B 378 ASP cc_start: 0.7706 (t0) cc_final: 0.7276 (t0) outliers start: 9 outliers final: 5 residues processed: 138 average time/residue: 0.0814 time to fit residues: 15.7664 Evaluate side-chains 134 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 THR 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: 3.9990 chunk 42 optimal weight: 0.1980 chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.133981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.102360 restraints weight = 9118.541| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.93 r_work: 0.2905 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4380 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= 0.107 Angle : 0.525 8.747 10354 Z= 0.268 Chirality : 0.041 0.148 1250 Planarity : 0.003 0.036 1272 Dihedral : 4.322 16.547 1062 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.40 % Allowed : 17.51 % Favored : 81.09 % 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: -0.68 (0.27), residues: 1004 helix: 0.65 (0.23), residues: 586 sheet: None (None), residues: 0 loop : -2.10 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.013 0.001 TYR A 375 PHE 0.009 0.001 PHE A 368 TRP 0.006 0.001 TRP A 335 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7608) covalent geometry : angle 0.52331 (10342) SS BOND : bond 0.00269 ( 6) SS BOND : angle 1.37292 ( 12) hydrogen bonds : bond 0.03137 ( 294) hydrogen bonds : angle 3.70226 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.22 seconds wall clock time: 32 minutes 44.19 seconds (1964.19 seconds total)