Starting phenix.real_space_refine on Wed Feb 4 11:47:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mky_48342/02_2026/9mky_48342.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mky_48342/02_2026/9mky_48342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mky_48342/02_2026/9mky_48342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mky_48342/02_2026/9mky_48342.map" model { file = "/net/cci-nas-00/data/ceres_data/9mky_48342/02_2026/9mky_48342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mky_48342/02_2026/9mky_48342.cif" } resolution = 3.0 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= 0.000 sd= 0.013 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 27 5.16 5 C 6537 2.51 5 N 1680 2.21 5 O 1899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10143 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3311 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3311 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3311 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.46, per 1000 atoms: 0.24 Number of scatterers: 10143 At special positions: 0 Unit cell: (104.656, 103.812, 130.82, 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 27 16.00 O 1899 8.00 N 1680 7.00 C 6537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 207 " distance=2.03 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: 0.85 Conformation dependent library (CDL) restraints added in 480.9 milliseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 15 sheets defined 46.0% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.507A pdb=" N VAL C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 88 removed outlier: 4.178A pdb=" N LEU C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 127 through 136 Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 148 through 161 removed outlier: 3.526A pdb=" N SER C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.651A pdb=" N LEU C 246 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 311 through 328 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.800A pdb=" N TYR C 338 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY C 339 " --> pdb=" O PRO C 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 335 through 339' Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.625A pdb=" N TYR C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 362 removed outlier: 3.512A pdb=" N VAL C 354 " --> pdb=" O CYS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 removed outlier: 3.917A pdb=" N LYS C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 402 " --> pdb=" O LYS C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 437 through 454 removed outlier: 3.517A pdb=" N ALA C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 471 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.542A pdb=" N VAL A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 88 removed outlier: 4.205A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 311 through 328 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.860A pdb=" N TYR A 338 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 339' Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.627A pdb=" N TYR A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 393 through 405 removed outlier: 3.777A pdb=" N LYS A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 437 through 454 removed outlier: 3.515A pdb=" N ASP A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 471 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 49 through 56 removed outlier: 3.531A pdb=" N VAL B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 88 removed outlier: 4.146A pdb=" N LEU B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 148 through 161 removed outlier: 3.509A pdb=" N SER B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 311 through 328 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.800A pdb=" N TYR B 338 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 335 through 339' Processing helix chain 'B' and resid 343 through 350 removed outlier: 3.623A pdb=" N TYR B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.515A pdb=" N VAL B 354 " --> pdb=" O CYS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 removed outlier: 3.849A pdb=" N LYS B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 437 through 454 removed outlier: 3.532A pdb=" N ALA B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 471 Processing sheet with id=AA1, first strand: chain 'C' and resid 92 through 99 removed outlier: 3.597A pdb=" N GLN C 99 " --> pdb=" O TYR C 427 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N MET C 277 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 417 " --> pdb=" O MET C 277 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN C 285 " --> pdb=" O SER C 423 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N LEU C 425 " --> pdb=" O GLN C 285 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N LYS C 287 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N TYR C 427 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 12.987A pdb=" N VAL C 289 " --> pdb=" O TYR C 427 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N ILE C 429 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 190 through 191 removed outlier: 5.907A pdb=" N LEU C 182 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN C 234 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N MET C 277 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 417 " --> pdb=" O MET C 277 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN C 285 " --> pdb=" O SER C 423 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N LEU C 425 " --> pdb=" O GLN C 285 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N LYS C 287 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N TYR C 427 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 12.987A pdb=" N VAL C 289 " --> pdb=" O TYR C 427 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N ILE C 429 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 197 through 202 removed outlier: 7.387A pdb=" N ASN C 206 " --> pdb=" O ASN C 113 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASN C 113 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'C' and resid 366 through 367 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 99 removed outlier: 3.614A pdb=" N GLN A 99 " --> pdb=" O TYR A 427 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N MET A 277 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 417 " --> pdb=" O MET A 277 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLN A 285 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU A 425 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N LYS A 287 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N TYR A 427 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 12.961A pdb=" N VAL A 289 " --> pdb=" O TYR A 427 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N ILE A 429 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 190 through 191 removed outlier: 5.939A pdb=" N LEU A 182 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN A 234 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 184 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N MET A 277 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 417 " --> pdb=" O MET A 277 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLN A 285 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU A 425 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N LYS A 287 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N TYR A 427 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 12.961A pdb=" N VAL A 289 " --> pdb=" O TYR A 427 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N ILE A 429 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 197 through 202 removed outlier: 7.314A pdb=" N ASN A 206 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASN A 113 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AB2, first strand: chain 'B' and resid 92 through 99 removed outlier: 3.606A pdb=" N GLN B 99 " --> pdb=" O TYR B 427 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET B 277 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 417 " --> pdb=" O MET B 277 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLN B 285 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LEU B 425 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N LYS B 287 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N TYR B 427 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 12.982A pdb=" N VAL B 289 " --> pdb=" O TYR B 427 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N ILE B 429 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 191 removed outlier: 5.975A pdb=" N LEU B 182 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN B 234 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET B 277 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 417 " --> pdb=" O MET B 277 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLN B 285 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LEU B 425 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N LYS B 287 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N TYR B 427 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 12.982A pdb=" N VAL B 289 " --> pdb=" O TYR B 427 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N ILE B 429 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 197 through 202 removed outlier: 7.462A pdb=" N ASN B 206 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN B 113 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB6, first strand: chain 'B' and resid 366 through 367 529 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3204 1.34 - 1.46: 2316 1.46 - 1.57: 4833 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 10386 Sorted by residual: bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C1 NAG C 603 " pdb=" O5 NAG C 603 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C1 NAG B 604 " pdb=" O5 NAG B 604 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.34e+00 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 13250 0.87 - 1.74: 695 1.74 - 2.61: 88 2.61 - 3.48: 47 3.48 - 4.35: 23 Bond angle restraints: 14103 Sorted by residual: angle pdb=" N VAL B 69 " pdb=" CA VAL B 69 " pdb=" C VAL B 69 " ideal model delta sigma weight residual 110.42 108.50 1.92 9.60e-01 1.09e+00 4.02e+00 angle pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 110.42 108.51 1.91 9.60e-01 1.09e+00 3.97e+00 angle pdb=" N VAL C 69 " pdb=" CA VAL C 69 " pdb=" C VAL C 69 " ideal model delta sigma weight residual 110.42 108.58 1.84 9.60e-01 1.09e+00 3.66e+00 angle pdb=" N VAL A 54 " pdb=" CA VAL A 54 " pdb=" C VAL A 54 " ideal model delta sigma weight residual 111.45 109.71 1.74 9.30e-01 1.16e+00 3.48e+00 angle pdb=" N VAL B 54 " pdb=" CA VAL B 54 " pdb=" C VAL B 54 " ideal model delta sigma weight residual 111.45 109.73 1.72 9.30e-01 1.16e+00 3.42e+00 ... (remaining 14098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 5525 13.80 - 27.60: 546 27.60 - 41.41: 156 41.41 - 55.21: 55 55.21 - 69.01: 21 Dihedral angle restraints: 6303 sinusoidal: 2613 harmonic: 3690 Sorted by residual: dihedral pdb=" CA LEU B 335 " pdb=" C LEU B 335 " pdb=" N PRO B 336 " pdb=" CA PRO B 336 " ideal model delta harmonic sigma weight residual -180.00 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU C 335 " pdb=" C LEU C 335 " pdb=" N PRO C 336 " pdb=" CA PRO C 336 " ideal model delta harmonic sigma weight residual 180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU A 335 " pdb=" C LEU A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta harmonic sigma weight residual -180.00 -157.13 -22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 6300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 986 0.027 - 0.054: 396 0.054 - 0.081: 94 0.081 - 0.107: 88 0.107 - 0.134: 53 Chirality restraints: 1617 Sorted by residual: chirality pdb=" CA VAL A 263 " pdb=" N VAL A 263 " pdb=" C VAL A 263 " pdb=" CB VAL A 263 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA VAL B 263 " pdb=" N VAL B 263 " pdb=" C VAL B 263 " pdb=" CB VAL B 263 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL C 263 " pdb=" N VAL C 263 " pdb=" C VAL C 263 " pdb=" CB VAL C 263 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1614 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 193 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO B 194 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 193 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO C 194 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 193 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 194 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 194 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 194 " 0.015 5.00e-02 4.00e+02 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 142 2.68 - 3.24: 10052 3.24 - 3.79: 14805 3.79 - 4.35: 20682 4.35 - 4.90: 35383 Nonbonded interactions: 81064 Sorted by model distance: nonbonded pdb=" O GLY B 337 " pdb=" O3 NAG B 603 " model vdw 2.125 3.040 nonbonded pdb=" O GLY C 337 " pdb=" O3 NAG C 603 " model vdw 2.146 3.040 nonbonded pdb=" O GLY A 337 " pdb=" O3 NAG A 603 " model vdw 2.148 3.040 nonbonded pdb=" O VAL A 249 " pdb=" OG SER B 393 " model vdw 2.197 3.040 nonbonded pdb=" OG SER C 393 " pdb=" O VAL B 249 " model vdw 2.202 3.040 ... (remaining 81059 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = 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: 2.580 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.003 0.024 10389 Z= 0.151 Angle : 0.474 4.349 14109 Z= 0.252 Chirality : 0.041 0.134 1617 Planarity : 0.002 0.029 1779 Dihedral : 13.334 69.009 3912 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.19 % Allowed : 7.26 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.24), residues: 1254 helix: 1.15 (0.24), residues: 468 sheet: 1.02 (0.30), residues: 276 loop : -0.55 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 62 TYR 0.007 0.001 TYR B 422 PHE 0.008 0.001 PHE B 175 TRP 0.004 0.001 TRP C 90 HIS 0.002 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00318 (10386) covalent geometry : angle 0.47364 (14103) SS BOND : bond 0.00278 ( 3) SS BOND : angle 0.30953 ( 6) hydrogen bonds : bond 0.22642 ( 511) hydrogen bonds : angle 8.24025 ( 1521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.398 Fit side-chains REVERT: C 86 ASN cc_start: 0.9020 (t0) cc_final: 0.8585 (t0) REVERT: C 330 CYS cc_start: 0.8314 (m) cc_final: 0.7978 (p) REVERT: A 65 TRP cc_start: 0.8090 (m100) cc_final: 0.7293 (m100) REVERT: A 330 CYS cc_start: 0.8298 (m) cc_final: 0.7989 (p) REVERT: B 65 TRP cc_start: 0.8137 (m100) cc_final: 0.7581 (m100) REVERT: B 86 ASN cc_start: 0.9005 (t0) cc_final: 0.8576 (t0) REVERT: B 330 CYS cc_start: 0.8300 (m) cc_final: 0.7960 (p) outliers start: 2 outliers final: 2 residues processed: 91 average time/residue: 0.4493 time to fit residues: 44.9304 Evaluate side-chains 48 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 424 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN A 48 HIS A 133 HIS B 48 HIS B 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.098571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.071016 restraints weight = 23762.494| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.75 r_work: 0.3002 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10389 Z= 0.131 Angle : 0.547 5.341 14109 Z= 0.297 Chirality : 0.044 0.177 1617 Planarity : 0.003 0.035 1779 Dihedral : 4.911 30.225 1662 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.68 % Allowed : 10.89 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1254 helix: 1.51 (0.24), residues: 489 sheet: 1.17 (0.30), residues: 270 loop : -0.19 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 284 TYR 0.015 0.001 TYR A 100 PHE 0.010 0.001 PHE B 233 TRP 0.010 0.001 TRP A 65 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00294 (10386) covalent geometry : angle 0.54701 (14103) SS BOND : bond 0.00525 ( 3) SS BOND : angle 0.36272 ( 6) hydrogen bonds : bond 0.04164 ( 511) hydrogen bonds : angle 5.49636 ( 1521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.397 Fit side-chains REVERT: C 51 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6941 (p90) REVERT: C 86 ASN cc_start: 0.9079 (t0) cc_final: 0.8701 (t0) REVERT: A 84 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 86 ASN cc_start: 0.9030 (t0) cc_final: 0.8665 (t0) REVERT: B 86 ASN cc_start: 0.9095 (t0) cc_final: 0.8680 (t0) outliers start: 18 outliers final: 10 residues processed: 66 average time/residue: 0.2279 time to fit residues: 18.1580 Evaluate side-chains 44 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 145 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN A 133 HIS B 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.095472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067660 restraints weight = 24020.310| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.75 r_work: 0.2927 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10389 Z= 0.191 Angle : 0.548 7.172 14109 Z= 0.297 Chirality : 0.044 0.169 1617 Planarity : 0.003 0.035 1779 Dihedral : 5.011 42.163 1661 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.58 % Allowed : 12.76 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1254 helix: 1.48 (0.24), residues: 489 sheet: 1.06 (0.29), residues: 270 loop : -0.30 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 57 TYR 0.013 0.001 TYR B 100 PHE 0.011 0.001 PHE A 266 TRP 0.006 0.001 TRP B 65 HIS 0.007 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00453 (10386) covalent geometry : angle 0.54753 (14103) SS BOND : bond 0.00593 ( 3) SS BOND : angle 0.52065 ( 6) hydrogen bonds : bond 0.04106 ( 511) hydrogen bonds : angle 5.26231 ( 1521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.471 Fit side-chains REVERT: C 86 ASN cc_start: 0.9118 (t0) cc_final: 0.8651 (t0) REVERT: A 84 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8329 (mm) REVERT: A 86 ASN cc_start: 0.9079 (t0) cc_final: 0.8658 (t0) REVERT: B 86 ASN cc_start: 0.9079 (t0) cc_final: 0.8673 (t0) outliers start: 17 outliers final: 9 residues processed: 53 average time/residue: 0.2810 time to fit residues: 17.7153 Evaluate side-chains 39 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 438 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 90 optimal weight: 0.0040 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.099052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.069694 restraints weight = 24471.416| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.91 r_work: 0.2965 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10389 Z= 0.105 Angle : 0.493 5.767 14109 Z= 0.270 Chirality : 0.042 0.166 1617 Planarity : 0.003 0.035 1779 Dihedral : 4.440 27.385 1659 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.14 % Allowed : 12.20 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.24), residues: 1254 helix: 1.54 (0.24), residues: 489 sheet: 1.06 (0.29), residues: 270 loop : -0.12 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 284 TYR 0.013 0.001 TYR C 100 PHE 0.011 0.001 PHE B 233 TRP 0.024 0.001 TRP C 65 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00231 (10386) covalent geometry : angle 0.49320 (14103) SS BOND : bond 0.00346 ( 3) SS BOND : angle 0.42999 ( 6) hydrogen bonds : bond 0.03335 ( 511) hydrogen bonds : angle 4.88971 ( 1521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.400 Fit side-chains REVERT: C 65 TRP cc_start: 0.7383 (t-100) cc_final: 0.6641 (t60) REVERT: C 86 ASN cc_start: 0.9092 (t0) cc_final: 0.8627 (t0) REVERT: A 84 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 86 ASN cc_start: 0.9058 (t0) cc_final: 0.8596 (t0) REVERT: B 65 TRP cc_start: 0.7623 (t-100) cc_final: 0.7388 (t-100) REVERT: B 86 ASN cc_start: 0.9057 (t0) cc_final: 0.8646 (t0) outliers start: 23 outliers final: 9 residues processed: 54 average time/residue: 0.2755 time to fit residues: 17.6205 Evaluate side-chains 34 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 438 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 HIS A 133 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067487 restraints weight = 24491.111| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.90 r_work: 0.2927 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10389 Z= 0.184 Angle : 0.533 5.836 14109 Z= 0.290 Chirality : 0.044 0.165 1617 Planarity : 0.003 0.036 1779 Dihedral : 4.811 32.591 1659 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.61 % Allowed : 12.76 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.24), residues: 1254 helix: 1.47 (0.24), residues: 495 sheet: 0.99 (0.29), residues: 270 loop : -0.24 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.010 0.001 TYR B 100 PHE 0.010 0.001 PHE A 266 TRP 0.012 0.001 TRP A 65 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00439 (10386) covalent geometry : angle 0.53296 (14103) SS BOND : bond 0.00586 ( 3) SS BOND : angle 0.48977 ( 6) hydrogen bonds : bond 0.03723 ( 511) hydrogen bonds : angle 5.05588 ( 1521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 27 time to evaluate : 0.441 Fit side-chains REVERT: C 86 ASN cc_start: 0.9115 (t0) cc_final: 0.8665 (t0) REVERT: A 84 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8382 (mm) REVERT: A 86 ASN cc_start: 0.9064 (t0) cc_final: 0.8635 (t0) REVERT: B 86 ASN cc_start: 0.9075 (t0) cc_final: 0.8669 (t0) outliers start: 28 outliers final: 12 residues processed: 54 average time/residue: 0.4278 time to fit residues: 25.9427 Evaluate side-chains 37 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 438 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 61 optimal weight: 0.0770 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.097840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068686 restraints weight = 24186.651| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.96 r_work: 0.2952 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10389 Z= 0.103 Angle : 0.489 4.887 14109 Z= 0.269 Chirality : 0.042 0.135 1617 Planarity : 0.003 0.038 1779 Dihedral : 4.487 30.881 1659 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.77 % Allowed : 13.41 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.24), residues: 1254 helix: 1.59 (0.24), residues: 495 sheet: 0.98 (0.29), residues: 270 loop : -0.19 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.008 0.001 TYR C 100 PHE 0.011 0.001 PHE B 233 TRP 0.023 0.001 TRP C 65 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00226 (10386) covalent geometry : angle 0.48868 (14103) SS BOND : bond 0.00367 ( 3) SS BOND : angle 0.31744 ( 6) hydrogen bonds : bond 0.03178 ( 511) hydrogen bonds : angle 4.79975 ( 1521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 26 time to evaluate : 0.493 Fit side-chains REVERT: C 86 ASN cc_start: 0.9081 (t0) cc_final: 0.8655 (t0) REVERT: A 84 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (mm) REVERT: A 86 ASN cc_start: 0.9045 (t0) cc_final: 0.8624 (t0) REVERT: B 86 ASN cc_start: 0.9056 (t0) cc_final: 0.8676 (t0) outliers start: 19 outliers final: 11 residues processed: 45 average time/residue: 0.2901 time to fit residues: 15.5890 Evaluate side-chains 38 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 438 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.097131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067945 restraints weight = 23865.013| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.96 r_work: 0.2940 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10389 Z= 0.125 Angle : 0.492 5.168 14109 Z= 0.270 Chirality : 0.042 0.136 1617 Planarity : 0.003 0.037 1779 Dihedral : 4.493 31.107 1659 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.58 % Allowed : 13.78 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1254 helix: 1.63 (0.24), residues: 495 sheet: 0.93 (0.29), residues: 270 loop : -0.17 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.010 0.001 TYR B 100 PHE 0.009 0.001 PHE C 233 TRP 0.044 0.002 TRP B 65 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00289 (10386) covalent geometry : angle 0.49212 (14103) SS BOND : bond 0.00456 ( 3) SS BOND : angle 0.36575 ( 6) hydrogen bonds : bond 0.03233 ( 511) hydrogen bonds : angle 4.81855 ( 1521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.276 Fit side-chains REVERT: C 86 ASN cc_start: 0.9085 (t0) cc_final: 0.8662 (t0) REVERT: C 428 LYS cc_start: 0.9083 (tttt) cc_final: 0.8777 (tttm) REVERT: A 84 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8274 (mm) REVERT: A 86 ASN cc_start: 0.9044 (t0) cc_final: 0.8628 (t0) REVERT: A 428 LYS cc_start: 0.9069 (tttt) cc_final: 0.8802 (tttm) REVERT: B 86 ASN cc_start: 0.9047 (t0) cc_final: 0.8682 (t0) outliers start: 17 outliers final: 15 residues processed: 49 average time/residue: 0.3440 time to fit residues: 19.4318 Evaluate side-chains 44 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 438 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068726 restraints weight = 24021.135| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.97 r_work: 0.2954 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10389 Z= 0.108 Angle : 0.496 9.033 14109 Z= 0.267 Chirality : 0.041 0.135 1617 Planarity : 0.003 0.037 1779 Dihedral : 4.407 30.805 1659 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.86 % Allowed : 13.87 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1254 helix: 1.68 (0.24), residues: 495 sheet: 0.91 (0.29), residues: 270 loop : -0.08 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.008 0.001 TYR C 100 PHE 0.011 0.001 PHE B 233 TRP 0.026 0.001 TRP C 65 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00247 (10386) covalent geometry : angle 0.49655 (14103) SS BOND : bond 0.00375 ( 3) SS BOND : angle 0.28421 ( 6) hydrogen bonds : bond 0.03080 ( 511) hydrogen bonds : angle 4.71990 ( 1521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 0.407 Fit side-chains REVERT: C 86 ASN cc_start: 0.9072 (t0) cc_final: 0.8655 (t0) REVERT: C 428 LYS cc_start: 0.9093 (tttt) cc_final: 0.8794 (tttm) REVERT: A 86 ASN cc_start: 0.9051 (t0) cc_final: 0.8634 (t0) REVERT: A 428 LYS cc_start: 0.9031 (tttt) cc_final: 0.8763 (tttp) REVERT: B 86 ASN cc_start: 0.9057 (t0) cc_final: 0.8681 (t0) outliers start: 20 outliers final: 13 residues processed: 52 average time/residue: 0.4025 time to fit residues: 23.6567 Evaluate side-chains 42 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 438 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 92 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 77 optimal weight: 0.0270 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- 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 = 0.097352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068175 restraints weight = 23828.522| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.94 r_work: 0.2908 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10389 Z= 0.135 Angle : 0.508 8.712 14109 Z= 0.274 Chirality : 0.042 0.137 1617 Planarity : 0.003 0.036 1779 Dihedral : 4.526 32.115 1659 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.49 % Allowed : 14.43 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1254 helix: 1.64 (0.24), residues: 495 sheet: 0.93 (0.29), residues: 267 loop : -0.11 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.011 0.001 TYR B 100 PHE 0.009 0.001 PHE B 233 TRP 0.030 0.001 TRP C 65 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00318 (10386) covalent geometry : angle 0.50791 (14103) SS BOND : bond 0.00491 ( 3) SS BOND : angle 0.37450 ( 6) hydrogen bonds : bond 0.03236 ( 511) hydrogen bonds : angle 4.81099 ( 1521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.407 Fit side-chains REVERT: C 86 ASN cc_start: 0.9088 (t0) cc_final: 0.8678 (t0) REVERT: C 428 LYS cc_start: 0.9099 (tttt) cc_final: 0.8797 (tttm) REVERT: A 86 ASN cc_start: 0.9067 (t0) cc_final: 0.8671 (t0) REVERT: A 428 LYS cc_start: 0.9069 (tttt) cc_final: 0.8807 (tttm) REVERT: B 86 ASN cc_start: 0.9057 (t0) cc_final: 0.8671 (t0) outliers start: 16 outliers final: 15 residues processed: 44 average time/residue: 0.3896 time to fit residues: 19.3898 Evaluate side-chains 43 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 438 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 63 optimal weight: 0.0010 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.098338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.069307 restraints weight = 23502.335| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.91 r_work: 0.2934 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10389 Z= 0.108 Angle : 0.490 8.672 14109 Z= 0.264 Chirality : 0.042 0.136 1617 Planarity : 0.003 0.037 1779 Dihedral : 4.395 31.353 1659 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.30 % Allowed : 14.90 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1254 helix: 1.66 (0.24), residues: 495 sheet: 0.91 (0.29), residues: 267 loop : -0.05 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 62 TYR 0.008 0.001 TYR C 100 PHE 0.010 0.001 PHE B 233 TRP 0.030 0.001 TRP C 65 HIS 0.003 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00245 (10386) covalent geometry : angle 0.49027 (14103) SS BOND : bond 0.00394 ( 3) SS BOND : angle 0.29565 ( 6) hydrogen bonds : bond 0.03053 ( 511) hydrogen bonds : angle 4.72219 ( 1521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.279 Fit side-chains REVERT: C 86 ASN cc_start: 0.9071 (t0) cc_final: 0.8664 (t0) REVERT: C 419 GLU cc_start: 0.8781 (tt0) cc_final: 0.8544 (tt0) REVERT: C 428 LYS cc_start: 0.9079 (tttt) cc_final: 0.8779 (tttm) REVERT: A 86 ASN cc_start: 0.9065 (t0) cc_final: 0.8683 (t0) REVERT: A 428 LYS cc_start: 0.9028 (tttt) cc_final: 0.8754 (tttp) REVERT: B 86 ASN cc_start: 0.9078 (t0) cc_final: 0.8692 (t0) REVERT: B 330 CYS cc_start: 0.8449 (p) cc_final: 0.8129 (p) outliers start: 14 outliers final: 13 residues processed: 46 average time/residue: 0.3331 time to fit residues: 17.4992 Evaluate side-chains 47 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 438 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 0.0670 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 405 ASN B 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.097310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068231 restraints weight = 23874.904| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.93 r_work: 0.2910 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10389 Z= 0.134 Angle : 0.503 8.510 14109 Z= 0.272 Chirality : 0.042 0.139 1617 Planarity : 0.003 0.037 1779 Dihedral : 4.513 32.351 1659 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.40 % Allowed : 14.99 % Favored : 83.61 % 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 are not related in a simple way. whole: 1.20 (0.24), residues: 1254 helix: 1.67 (0.24), residues: 495 sheet: 0.89 (0.29), residues: 267 loop : -0.08 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.011 0.001 TYR B 100 PHE 0.009 0.001 PHE B 233 TRP 0.030 0.001 TRP C 65 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00315 (10386) covalent geometry : angle 0.50297 (14103) SS BOND : bond 0.00483 ( 3) SS BOND : angle 0.36589 ( 6) hydrogen bonds : bond 0.03197 ( 511) hydrogen bonds : angle 4.77587 ( 1521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.49 seconds wall clock time: 44 minutes 18.25 seconds (2658.25 seconds total)