Starting phenix.real_space_refine on Sat Jul 4 15:21:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x1y_32952/07_2026/7x1y_32952.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1y_32952/07_2026/7x1y_32952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x1y_32952/07_2026/7x1y_32952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1y_32952/07_2026/7x1y_32952.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x1y_32952/07_2026/7x1y_32952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1y_32952/07_2026/7x1y_32952.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7x1y_32952/07_2026/7x1y_32952.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x1y_32952/07_2026/7x1y_32952.cif" } resolution = 3.3 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= 0.003 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 84 5.16 5 C 13806 2.51 5 N 3852 2.21 5 O 4242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22032 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "B" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "C" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "D" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "E" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.45, per 1000 atoms: 0.20 Number of scatterers: 22032 At special positions: 0 Unit cell: (121.245, 119.875, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 36 15.00 Mg 12 11.99 O 4242 8.00 N 3852 7.00 C 13806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 690.9 milliseconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 20 sheets defined 36.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 52 through 66 removed outlier: 4.055A pdb=" N SER A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.569A pdb=" N ILE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.744A pdb=" N GLU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 267 through 273 removed outlier: 3.687A pdb=" N MET A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.731A pdb=" N LEU A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 321 through 332 Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.740A pdb=" N MET A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 4.107A pdb=" N ALA A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.741A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'B' and resid 52 through 66 removed outlier: 4.059A pdb=" N SER B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.564A pdb=" N ILE B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.750A pdb=" N GLU B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 267 through 273 removed outlier: 3.552A pdb=" N MET B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 removed outlier: 3.724A pdb=" N LEU B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 321 through 332 Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.703A pdb=" N MET B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 4.082A pdb=" N ALA B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.737A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'C' and resid 52 through 66 removed outlier: 4.074A pdb=" N SER C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 63 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.536A pdb=" N ILE C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 removed outlier: 3.809A pdb=" N PHE C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.743A pdb=" N GLU C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 267 through 273 removed outlier: 3.550A pdb=" N MET C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.868A pdb=" N LEU C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 321 through 332 Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.732A pdb=" N MET C 338 " --> pdb=" O ASP C 334 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.121A pdb=" N ALA C 354 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 371 Processing helix chain 'C' and resid 379 through 384 removed outlier: 3.713A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'D' and resid 52 through 66 removed outlier: 4.055A pdb=" N SER D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 88 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.576A pdb=" N ILE D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.738A pdb=" N GLU D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 268 through 273 removed outlier: 3.769A pdb=" N MET D 273 " --> pdb=" O ARG D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 removed outlier: 3.734A pdb=" N LEU D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 321 through 332 Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.742A pdb=" N MET D 338 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.081A pdb=" N ALA D 354 " --> pdb=" O PRO D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 371 Processing helix chain 'D' and resid 379 through 384 removed outlier: 3.745A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'E' and resid 52 through 66 removed outlier: 4.061A pdb=" N SER E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY E 63 " --> pdb=" O PHE E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 88 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 94 through 100 Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.564A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 159 through 175 removed outlier: 3.749A pdb=" N GLU E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 200 Processing helix chain 'E' and resid 267 through 273 removed outlier: 3.552A pdb=" N MET E 273 " --> pdb=" O ARG E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 removed outlier: 3.771A pdb=" N LEU E 297 " --> pdb=" O GLY E 293 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA E 305 " --> pdb=" O PHE E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 321 through 332 Processing helix chain 'E' and resid 334 through 341 removed outlier: 3.705A pdb=" N MET E 338 " --> pdb=" O ASP E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 4.084A pdb=" N ALA E 354 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 371 Processing helix chain 'E' and resid 379 through 384 removed outlier: 3.761A pdb=" N LEU E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'F' and resid 52 through 66 removed outlier: 4.080A pdb=" N SER F 56 " --> pdb=" O LYS F 52 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 63 " --> pdb=" O PHE F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 88 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 94 through 100 Processing helix chain 'F' and resid 125 through 138 removed outlier: 3.533A pdb=" N ILE F 130 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 159 through 175 removed outlier: 3.749A pdb=" N GLU F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 200 Processing helix chain 'F' and resid 267 through 273 removed outlier: 3.551A pdb=" N MET F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 removed outlier: 3.731A pdb=" N LEU F 297 " --> pdb=" O GLY F 293 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA F 305 " --> pdb=" O PHE F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'F' and resid 334 through 341 removed outlier: 3.744A pdb=" N MET F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 4.118A pdb=" N ALA F 354 " --> pdb=" O PRO F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 371 Processing helix chain 'F' and resid 379 through 384 removed outlier: 3.701A pdb=" N LEU F 383 " --> pdb=" O SER F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 406 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 7.109A pdb=" N GLY A 71 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU A 106 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE A 73 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU A 43 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 207 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 45 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ASN A 209 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 12.999A pdb=" N ARG A 216 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N ILE A 239 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG A 218 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 346 removed outlier: 6.397A pdb=" N ILE A 284 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN A 414 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA A 286 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 283 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 438 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 285 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU A 440 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A 287 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR A 442 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 441 " --> pdb=" O ALA A 452 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 107 removed outlier: 7.124A pdb=" N GLY B 71 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU B 106 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE B 73 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU B 43 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 207 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER B 45 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ASN B 209 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 13.056A pdb=" N ARG B 216 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ILE B 239 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG B 218 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.404A pdb=" N ILE B 284 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN B 414 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA B 286 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 283 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE B 438 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 285 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU B 440 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 287 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR B 442 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 4.329A pdb=" N GLU B 469 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 471 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AA9, first strand: chain 'C' and resid 103 through 107 removed outlier: 7.103A pdb=" N GLY C 71 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU C 106 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE C 73 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU C 43 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU C 207 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER C 45 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN C 209 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 13.013A pdb=" N ARG C 216 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N ILE C 239 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG C 218 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 344 through 346 removed outlier: 6.394A pdb=" N ILE C 284 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASN C 414 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA C 286 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 283 " --> pdb=" O THR C 436 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ILE C 438 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU C 285 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU C 440 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR C 287 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N TYR C 442 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 441 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB3, first strand: chain 'D' and resid 103 through 107 removed outlier: 7.101A pdb=" N GLY D 71 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU D 106 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE D 73 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU D 43 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU D 207 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER D 45 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASN D 209 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 12.999A pdb=" N ARG D 216 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N ILE D 239 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG D 218 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 344 through 346 removed outlier: 6.404A pdb=" N ILE D 284 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN D 414 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA D 286 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 283 " --> pdb=" O THR D 436 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE D 438 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 285 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU D 440 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR D 287 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR D 442 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 441 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AB6, first strand: chain 'E' and resid 103 through 107 removed outlier: 7.125A pdb=" N GLY E 71 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU E 106 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE E 73 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU E 43 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU E 207 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER E 45 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ASN E 209 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 13.052A pdb=" N ARG E 216 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N ILE E 239 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG E 218 " --> pdb=" O PHE E 237 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 344 through 346 removed outlier: 6.401A pdb=" N ILE E 284 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN E 414 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA E 286 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 283 " --> pdb=" O THR E 436 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE E 438 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU E 285 " --> pdb=" O ILE E 438 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU E 440 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR E 287 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR E 442 " --> pdb=" O THR E 287 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN E 441 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 468 through 472 removed outlier: 4.310A pdb=" N GLU E 469 " --> pdb=" O LYS E 480 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 471 " --> pdb=" O ASP E 478 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AC1, first strand: chain 'F' and resid 103 through 107 removed outlier: 7.104A pdb=" N GLY F 71 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU F 106 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE F 73 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU F 43 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU F 207 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER F 45 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN F 209 " --> pdb=" O SER F 45 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 13.011A pdb=" N ARG F 216 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N ILE F 239 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG F 218 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 344 through 346 removed outlier: 6.402A pdb=" N ILE F 284 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN F 414 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA F 286 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE F 283 " --> pdb=" O THR F 436 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE F 438 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU F 285 " --> pdb=" O ILE F 438 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU F 440 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR F 287 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N TYR F 442 " --> pdb=" O THR F 287 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN F 441 " --> pdb=" O ALA F 452 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2295 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: 3.69 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6820 1.34 - 1.45: 3350 1.45 - 1.57: 12016 1.57 - 1.69: 62 1.69 - 1.81: 150 Bond restraints: 22398 Sorted by residual: bond pdb=" CB PRO C 110 " pdb=" CG PRO C 110 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.77e+00 bond pdb=" CB PRO F 110 " pdb=" CG PRO F 110 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.73e+00 bond pdb=" CB PRO D 110 " pdb=" CG PRO D 110 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.86e+00 bond pdb=" CB PRO A 110 " pdb=" CG PRO A 110 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.58e+00 bond pdb=" CB PRO D 248 " pdb=" CG PRO D 248 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.55e+00 ... (remaining 22393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 29625 2.38 - 4.76: 482 4.76 - 7.14: 129 7.14 - 9.52: 17 9.52 - 11.89: 11 Bond angle restraints: 30264 Sorted by residual: angle pdb=" CA PRO C 110 " pdb=" N PRO C 110 " pdb=" CD PRO C 110 " ideal model delta sigma weight residual 112.00 100.11 11.89 1.40e+00 5.10e-01 7.22e+01 angle pdb=" CA PRO F 110 " pdb=" N PRO F 110 " pdb=" CD PRO F 110 " ideal model delta sigma weight residual 112.00 100.14 11.86 1.40e+00 5.10e-01 7.18e+01 angle pdb=" CA PRO B 110 " pdb=" N PRO B 110 " pdb=" CD PRO B 110 " ideal model delta sigma weight residual 112.00 100.48 11.52 1.40e+00 5.10e-01 6.78e+01 angle pdb=" CA PRO E 110 " pdb=" N PRO E 110 " pdb=" CD PRO E 110 " ideal model delta sigma weight residual 112.00 100.56 11.44 1.40e+00 5.10e-01 6.68e+01 angle pdb=" CA PRO A 248 " pdb=" N PRO A 248 " pdb=" CD PRO A 248 " ideal model delta sigma weight residual 112.00 101.20 10.80 1.40e+00 5.10e-01 5.96e+01 ... (remaining 30259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 11995 18.02 - 36.04: 1031 36.04 - 54.06: 198 54.06 - 72.08: 52 72.08 - 90.10: 20 Dihedral angle restraints: 13296 sinusoidal: 5448 harmonic: 7848 Sorted by residual: dihedral pdb=" CA GLU E 319 " pdb=" C GLU E 319 " pdb=" N SER E 320 " pdb=" CA SER E 320 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU F 319 " pdb=" C GLU F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" C ASP B 478 " pdb=" N ASP B 478 " pdb=" CA ASP B 478 " pdb=" CB ASP B 478 " ideal model delta harmonic sigma weight residual -122.60 -132.46 9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 13293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2424 0.047 - 0.093: 680 0.093 - 0.140: 235 0.140 - 0.186: 33 0.186 - 0.233: 6 Chirality restraints: 3378 Sorted by residual: chirality pdb=" CA PRO B 110 " pdb=" N PRO B 110 " pdb=" C PRO B 110 " pdb=" CB PRO B 110 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PRO E 110 " pdb=" N PRO E 110 " pdb=" C PRO E 110 " pdb=" CB PRO E 110 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP E 478 " pdb=" N ASP E 478 " pdb=" C ASP E 478 " pdb=" CB ASP E 478 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3375 not shown) Planarity restraints: 3858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 478 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" CG ASP E 478 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASP E 478 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP E 478 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 478 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" CG ASP B 478 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASP B 478 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP B 478 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 247 " 0.061 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO D 248 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 248 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 248 " 0.047 5.00e-02 4.00e+02 ... (remaining 3855 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 4 2.01 - 2.74: 1675 2.74 - 3.46: 29160 3.46 - 4.18: 48850 4.18 - 4.90: 91873 Nonbonded interactions: 171562 Sorted by model distance: nonbonded pdb=" OE2 GLU D 318 " pdb=" OG SER D 379 " model vdw 1.293 3.040 nonbonded pdb=" OE2 GLU B 318 " pdb=" OG SER B 379 " model vdw 1.608 3.040 nonbonded pdb=" OE2 GLU C 318 " pdb=" OG SER C 379 " model vdw 1.671 3.040 nonbonded pdb=" OE2 GLU A 318 " pdb=" OG SER A 379 " model vdw 1.675 3.040 nonbonded pdb=" OG1 THR B 53 " pdb="MG MG B 904 " model vdw 2.037 2.170 ... (remaining 171557 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.610 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.410 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.006 0.156 22404 Z= 0.245 Angle : 0.854 11.894 30264 Z= 0.492 Chirality : 0.050 0.233 3378 Planarity : 0.006 0.086 3858 Dihedral : 14.651 90.104 8256 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.48 % Favored : 91.30 % Rotamer: Outliers : 0.52 % Allowed : 0.82 % Favored : 98.66 % Cbeta Deviations : 0.08 % 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: -1.68 (0.15), residues: 2724 helix: -0.39 (0.17), residues: 876 sheet: -0.68 (0.20), residues: 672 loop : -1.88 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 140 TYR 0.019 0.002 TYR C 442 PHE 0.019 0.002 PHE C 237 TRP 0.018 0.003 TRP E 92 HIS 0.006 0.002 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.24 (22398) covalent geometry : angle 0.85353 / 0.49 (30264) hydrogen bonds : bond 0.20257 / 13.52 ( 824) hydrogen bonds : angle 7.30016 / 5.16 ( 2295) Misc. bond : bond 0.00295 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 247 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: C 321 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8002 (ttt-90) REVERT: D 321 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8277 (tpt-90) REVERT: E 321 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7871 (tpt-90) REVERT: F 321 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7820 (tpt-90) outliers start: 12 outliers final: 7 residues processed: 259 average time/residue: 0.1978 time to fit residues: 74.3737 Evaluate side-chains 200 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 321 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 463 HIS C 463 HIS E 463 HIS F 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.083411 restraints weight = 36107.616| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.67 r_work: 0.2822 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22404 Z= 0.169 Angle : 0.545 8.029 30264 Z= 0.292 Chirality : 0.042 0.145 3378 Planarity : 0.004 0.036 3858 Dihedral : 7.489 83.087 3097 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 1.16 % Allowed : 7.19 % Favored : 91.65 % 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: -0.94 (0.16), residues: 2724 helix: 0.43 (0.18), residues: 912 sheet: -0.35 (0.21), residues: 666 loop : -1.62 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 170 TYR 0.017 0.001 TYR C 442 PHE 0.015 0.001 PHE F 237 TRP 0.014 0.002 TRP B 92 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (22398) covalent geometry : angle 0.54515 / 0.29 (30264) hydrogen bonds : bond 0.03830 / 2.60 ( 824) hydrogen bonds : angle 4.81205 / 3.43 ( 2295) Misc. bond : bond 0.00194 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 152 GLN cc_start: 0.8122 (tp40) cc_final: 0.7809 (pp30) REVERT: B 152 GLN cc_start: 0.8074 (tp40) cc_final: 0.7782 (pp30) REVERT: C 152 GLN cc_start: 0.8170 (tp40) cc_final: 0.7667 (pp30) REVERT: C 458 MET cc_start: 0.8453 (ttt) cc_final: 0.8179 (ttt) REVERT: D 152 GLN cc_start: 0.8119 (tp40) cc_final: 0.7801 (pp30) REVERT: D 458 MET cc_start: 0.8365 (mmm) cc_final: 0.8103 (mtp) REVERT: E 152 GLN cc_start: 0.8064 (tp40) cc_final: 0.7780 (pp30) REVERT: F 152 GLN cc_start: 0.8135 (tp40) cc_final: 0.7780 (pp30) REVERT: F 458 MET cc_start: 0.8498 (ttt) cc_final: 0.8248 (ttt) outliers start: 27 outliers final: 25 residues processed: 234 average time/residue: 0.1608 time to fit residues: 57.3870 Evaluate side-chains 224 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 215 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.082356 restraints weight = 36067.895| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.70 r_work: 0.2795 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22404 Z= 0.186 Angle : 0.541 7.260 30264 Z= 0.286 Chirality : 0.042 0.146 3378 Planarity : 0.003 0.036 3858 Dihedral : 7.238 82.729 3078 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.86 % Favored : 91.92 % Rotamer: Outliers : 1.29 % Allowed : 10.64 % Favored : 88.07 % 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 (0.17), residues: 2724 helix: 0.86 (0.18), residues: 912 sheet: -0.32 (0.21), residues: 666 loop : -1.52 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 340 TYR 0.015 0.001 TYR C 442 PHE 0.015 0.002 PHE E 237 TRP 0.015 0.002 TRP D 92 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (22398) covalent geometry : angle 0.54088 / 0.29 (30264) hydrogen bonds : bond 0.03719 / 2.53 ( 824) hydrogen bonds : angle 4.50062 / 3.20 ( 2295) Misc. bond : bond 0.00200 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.949 Fit side-chains REVERT: A 152 GLN cc_start: 0.8077 (tp40) cc_final: 0.7802 (pp30) REVERT: B 152 GLN cc_start: 0.8107 (tp40) cc_final: 0.7845 (pp30) REVERT: C 152 GLN cc_start: 0.8166 (tp40) cc_final: 0.7694 (pp30) REVERT: C 170 ARG cc_start: 0.8204 (tpt-90) cc_final: 0.7993 (tpt-90) REVERT: D 152 GLN cc_start: 0.8075 (tp40) cc_final: 0.7799 (pp30) REVERT: E 152 GLN cc_start: 0.8101 (tp40) cc_final: 0.7841 (pp30) REVERT: F 152 GLN cc_start: 0.8160 (tp40) cc_final: 0.7846 (pp30) outliers start: 30 outliers final: 26 residues processed: 214 average time/residue: 0.1692 time to fit residues: 55.4553 Evaluate side-chains 218 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.084446 restraints weight = 35771.379| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.72 r_work: 0.2830 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22404 Z= 0.111 Angle : 0.468 5.837 30264 Z= 0.248 Chirality : 0.041 0.145 3378 Planarity : 0.003 0.034 3858 Dihedral : 6.802 78.135 3078 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.32 % Rotamer: Outliers : 1.08 % Allowed : 11.58 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2724 helix: 1.20 (0.18), residues: 906 sheet: -0.23 (0.21), residues: 672 loop : -1.41 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 340 TYR 0.011 0.001 TYR C 442 PHE 0.012 0.001 PHE C 151 TRP 0.011 0.002 TRP D 92 HIS 0.002 0.000 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (22398) covalent geometry : angle 0.46767 / 0.25 (30264) hydrogen bonds : bond 0.02876 / 1.95 ( 824) hydrogen bonds : angle 4.20361 / 2.98 ( 2295) Misc. bond : bond 0.00132 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.766 Fit side-chains REVERT: A 152 GLN cc_start: 0.8025 (tp40) cc_final: 0.7752 (pp30) REVERT: B 152 GLN cc_start: 0.8069 (tp40) cc_final: 0.7789 (pp30) REVERT: B 272 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8034 (mm-30) REVERT: C 152 GLN cc_start: 0.8095 (tp40) cc_final: 0.7676 (pp30) REVERT: D 152 GLN cc_start: 0.8020 (tp40) cc_final: 0.7752 (pp30) REVERT: D 458 MET cc_start: 0.8361 (mmm) cc_final: 0.8065 (mtp) REVERT: E 152 GLN cc_start: 0.8053 (tp40) cc_final: 0.7787 (pp30) REVERT: E 272 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8041 (mm-30) REVERT: F 152 GLN cc_start: 0.8109 (tp40) cc_final: 0.7788 (pp30) outliers start: 25 outliers final: 23 residues processed: 229 average time/residue: 0.1563 time to fit residues: 54.9520 Evaluate side-chains 227 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 220 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 250 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.083187 restraints weight = 35701.295| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.70 r_work: 0.2808 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22404 Z= 0.149 Angle : 0.492 5.915 30264 Z= 0.261 Chirality : 0.041 0.143 3378 Planarity : 0.003 0.033 3858 Dihedral : 6.671 79.635 3075 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.97 % Favored : 91.92 % Rotamer: Outliers : 1.38 % Allowed : 12.10 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2724 helix: 1.35 (0.19), residues: 906 sheet: -0.16 (0.21), residues: 666 loop : -1.35 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 170 TYR 0.011 0.001 TYR C 442 PHE 0.013 0.001 PHE B 237 TRP 0.013 0.002 TRP A 92 HIS 0.003 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (22398) covalent geometry : angle 0.49217 / 0.26 (30264) hydrogen bonds : bond 0.03201 / 2.18 ( 824) hydrogen bonds : angle 4.18712 / 2.97 ( 2295) Misc. bond : bond 0.00169 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.729 Fit side-chains REVERT: A 152 GLN cc_start: 0.8060 (tp40) cc_final: 0.7758 (pp30) REVERT: A 458 MET cc_start: 0.8443 (mmm) cc_final: 0.8162 (mtp) REVERT: B 152 GLN cc_start: 0.8065 (tp40) cc_final: 0.7790 (pp30) REVERT: B 272 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8061 (mm-30) REVERT: C 152 GLN cc_start: 0.8132 (tp40) cc_final: 0.7696 (pp30) REVERT: C 272 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7974 (mm-30) REVERT: D 152 GLN cc_start: 0.8055 (tp40) cc_final: 0.7756 (pp30) REVERT: D 272 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: D 319 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: D 458 MET cc_start: 0.8394 (mmm) cc_final: 0.8135 (mtp) REVERT: E 152 GLN cc_start: 0.8073 (tp40) cc_final: 0.7790 (pp30) REVERT: E 272 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8061 (mm-30) REVERT: F 152 GLN cc_start: 0.8133 (tp40) cc_final: 0.7790 (pp30) REVERT: F 272 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7973 (mm-30) outliers start: 32 outliers final: 24 residues processed: 225 average time/residue: 0.1582 time to fit residues: 54.1310 Evaluate side-chains 226 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 155 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 117 optimal weight: 0.5980 chunk 203 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 overall best weight: 2.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 ASN E 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.083269 restraints weight = 35964.565| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.72 r_work: 0.2809 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22404 Z= 0.140 Angle : 0.483 5.553 30264 Z= 0.256 Chirality : 0.041 0.143 3378 Planarity : 0.003 0.033 3858 Dihedral : 6.625 79.423 3075 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 1.64 % Allowed : 12.83 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.15 (0.17), residues: 2724 helix: 1.42 (0.18), residues: 906 sheet: -0.21 (0.20), residues: 672 loop : -1.26 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 170 TYR 0.010 0.001 TYR C 442 PHE 0.014 0.001 PHE C 151 TRP 0.013 0.002 TRP D 92 HIS 0.002 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (22398) covalent geometry : angle 0.48261 / 0.26 (30264) hydrogen bonds : bond 0.03059 / 2.08 ( 824) hydrogen bonds : angle 4.13515 / 2.93 ( 2295) Misc. bond : bond 0.00155 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.886 Fit side-chains REVERT: A 152 GLN cc_start: 0.8085 (tp40) cc_final: 0.7730 (pp30) REVERT: B 152 GLN cc_start: 0.8067 (tp40) cc_final: 0.7781 (pp30) REVERT: B 272 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8052 (mm-30) REVERT: B 321 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7942 (tpt-90) REVERT: B 458 MET cc_start: 0.8102 (mtp) cc_final: 0.7831 (ttt) REVERT: C 152 GLN cc_start: 0.8142 (tp40) cc_final: 0.7658 (pp30) REVERT: C 272 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7965 (mm-30) REVERT: D 152 GLN cc_start: 0.8043 (tp40) cc_final: 0.7743 (pp30) REVERT: D 272 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: E 152 GLN cc_start: 0.8074 (tp40) cc_final: 0.7778 (pp30) REVERT: E 272 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8074 (mm-30) REVERT: E 458 MET cc_start: 0.8110 (mtp) cc_final: 0.7875 (ttt) REVERT: F 152 GLN cc_start: 0.8139 (tp40) cc_final: 0.7765 (pp30) REVERT: F 272 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7975 (mm-30) outliers start: 38 outliers final: 27 residues processed: 228 average time/residue: 0.1788 time to fit residues: 62.2514 Evaluate side-chains 230 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 65 optimal weight: 0.3980 chunk 183 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.081629 restraints weight = 36130.116| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.70 r_work: 0.2785 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22404 Z= 0.202 Angle : 0.539 7.886 30264 Z= 0.284 Chirality : 0.043 0.142 3378 Planarity : 0.004 0.036 3858 Dihedral : 6.942 86.495 3075 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.19 % Favored : 91.74 % Rotamer: Outliers : 1.94 % Allowed : 13.01 % Favored : 85.06 % 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: -0.19 (0.17), residues: 2724 helix: 1.36 (0.18), residues: 912 sheet: -0.21 (0.20), residues: 666 loop : -1.28 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 170 TYR 0.011 0.001 TYR C 442 PHE 0.015 0.001 PHE E 237 TRP 0.016 0.002 TRP A 92 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (22398) covalent geometry : angle 0.53915 / 0.28 (30264) hydrogen bonds : bond 0.03594 / 2.45 ( 824) hydrogen bonds : angle 4.27928 / 3.04 ( 2295) Misc. bond : bond 0.00196 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.789 Fit side-chains REVERT: A 152 GLN cc_start: 0.8086 (tp40) cc_final: 0.7776 (pp30) REVERT: A 350 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 474 ASP cc_start: 0.8455 (t0) cc_final: 0.8025 (t0) REVERT: B 152 GLN cc_start: 0.8111 (tp40) cc_final: 0.7785 (pp30) REVERT: B 272 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8138 (mm-30) REVERT: B 321 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7976 (ttt-90) REVERT: B 350 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8016 (t80) REVERT: B 458 MET cc_start: 0.8152 (mtp) cc_final: 0.7901 (ttt) REVERT: B 474 ASP cc_start: 0.8510 (t0) cc_final: 0.8026 (t0) REVERT: C 152 GLN cc_start: 0.8193 (tp40) cc_final: 0.7695 (pp30) REVERT: C 170 ARG cc_start: 0.8208 (tpt-90) cc_final: 0.7990 (tpt-90) REVERT: C 272 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8130 (mm-30) REVERT: C 336 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8795 (mm-30) REVERT: C 344 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9454 (tp) REVERT: C 350 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.8141 (t80) REVERT: D 152 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7758 (pp30) REVERT: D 272 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: D 319 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: D 350 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8127 (t80) REVERT: E 152 GLN cc_start: 0.8132 (tp40) cc_final: 0.7784 (pp30) REVERT: E 272 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8120 (mm-30) REVERT: E 350 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.8027 (t80) REVERT: E 458 MET cc_start: 0.8157 (mtp) cc_final: 0.7948 (ttt) REVERT: E 483 PHE cc_start: 0.8440 (m-10) cc_final: 0.8189 (m-10) REVERT: F 152 GLN cc_start: 0.8172 (tp40) cc_final: 0.7777 (pp30) REVERT: F 272 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8145 (mm-30) REVERT: F 344 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9455 (tp) REVERT: F 350 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8057 (t80) outliers start: 45 outliers final: 28 residues processed: 232 average time/residue: 0.1610 time to fit residues: 57.2919 Evaluate side-chains 245 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 50 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.082553 restraints weight = 35708.731| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.71 r_work: 0.2797 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22404 Z= 0.161 Angle : 0.516 9.035 30264 Z= 0.269 Chirality : 0.042 0.144 3378 Planarity : 0.003 0.033 3858 Dihedral : 6.716 84.312 3072 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 2.07 % Allowed : 12.96 % Favored : 84.97 % 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: -0.15 (0.17), residues: 2724 helix: 1.41 (0.18), residues: 912 sheet: -0.25 (0.20), residues: 672 loop : -1.23 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 170 TYR 0.011 0.001 TYR F 442 PHE 0.019 0.001 PHE F 151 TRP 0.015 0.002 TRP A 92 HIS 0.003 0.001 HIS D 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (22398) covalent geometry : angle 0.51554 / 0.27 (30264) hydrogen bonds : bond 0.03236 / 2.20 ( 824) hydrogen bonds : angle 4.18717 / 2.98 ( 2295) Misc. bond : bond 0.00168 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.662 Fit side-chains REVERT: A 152 GLN cc_start: 0.8074 (tp40) cc_final: 0.7764 (pp30) REVERT: A 350 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8146 (t80) REVERT: A 474 ASP cc_start: 0.8465 (t0) cc_final: 0.8028 (t0) REVERT: B 15 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7432 (m170) REVERT: B 152 GLN cc_start: 0.8087 (tp40) cc_final: 0.7786 (pp30) REVERT: B 272 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 321 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7946 (ttt-90) REVERT: B 350 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8020 (t80) REVERT: B 458 MET cc_start: 0.8125 (mtp) cc_final: 0.7852 (ttt) REVERT: B 474 ASP cc_start: 0.8482 (t0) cc_final: 0.8006 (t0) REVERT: C 152 GLN cc_start: 0.8177 (tp40) cc_final: 0.7700 (pp30) REVERT: C 170 ARG cc_start: 0.8232 (tpt-90) cc_final: 0.7957 (tpt-90) REVERT: C 272 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8141 (mm-30) REVERT: C 344 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9439 (tp) REVERT: C 350 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8144 (t80) REVERT: D 152 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7744 (pp30) REVERT: D 272 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: D 319 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: D 350 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8241 (t80) REVERT: E 15 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7428 (m170) REVERT: E 152 GLN cc_start: 0.8095 (tp40) cc_final: 0.7783 (pp30) REVERT: E 272 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8124 (mm-30) REVERT: E 350 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8034 (t80) REVERT: E 458 MET cc_start: 0.8145 (mtp) cc_final: 0.7906 (ttt) REVERT: E 483 PHE cc_start: 0.8413 (m-10) cc_final: 0.8201 (m-10) REVERT: F 152 GLN cc_start: 0.8152 (tp40) cc_final: 0.7795 (pp30) REVERT: F 272 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8116 (mm-30) REVERT: F 344 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9444 (tp) REVERT: F 350 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.8222 (t80) outliers start: 48 outliers final: 30 residues processed: 242 average time/residue: 0.1647 time to fit residues: 59.8050 Evaluate side-chains 250 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 15 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 95 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.081061 restraints weight = 36195.780| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.70 r_work: 0.2774 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 22404 Z= 0.231 Angle : 0.575 9.054 30264 Z= 0.299 Chirality : 0.043 0.142 3378 Planarity : 0.004 0.039 3858 Dihedral : 6.996 89.796 3072 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.26 % Favored : 91.67 % Rotamer: Outliers : 2.20 % Allowed : 12.96 % Favored : 84.84 % 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: -0.23 (0.17), residues: 2724 helix: 1.34 (0.18), residues: 912 sheet: -0.41 (0.20), residues: 678 loop : -1.19 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 170 TYR 0.016 0.001 TYR D 154 PHE 0.016 0.002 PHE F 151 TRP 0.017 0.002 TRP A 92 HIS 0.004 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (22398) covalent geometry : angle 0.57463 / 0.30 (30264) hydrogen bonds : bond 0.03728 / 2.54 ( 824) hydrogen bonds : angle 4.33935 / 3.10 ( 2295) Misc. bond : bond 0.00204 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.805 Fit side-chains REVERT: A 15 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7187 (m170) REVERT: A 152 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7759 (pp30) REVERT: A 350 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 474 ASP cc_start: 0.8516 (t0) cc_final: 0.8066 (t0) REVERT: B 15 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7451 (m170) REVERT: B 152 GLN cc_start: 0.8120 (tp40) cc_final: 0.7795 (pp30) REVERT: B 272 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8200 (mm-30) REVERT: B 321 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8005 (ttt-90) REVERT: B 350 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8027 (t80) REVERT: B 458 MET cc_start: 0.8157 (mtp) cc_final: 0.7906 (ttt) REVERT: C 15 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7388 (m170) REVERT: C 152 GLN cc_start: 0.8223 (tp40) cc_final: 0.7741 (pp30) REVERT: C 272 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8166 (mm-30) REVERT: C 344 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9456 (tp) REVERT: C 350 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8119 (t80) REVERT: D 15 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7161 (m170) REVERT: D 272 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: D 319 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: D 350 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8092 (t80) REVERT: E 15 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.7446 (m170) REVERT: E 152 GLN cc_start: 0.8149 (tp40) cc_final: 0.7798 (pp30) REVERT: E 272 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8191 (mm-30) REVERT: E 350 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8034 (t80) REVERT: E 458 MET cc_start: 0.8173 (mtp) cc_final: 0.7951 (ttt) REVERT: F 15 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7376 (m170) REVERT: F 152 GLN cc_start: 0.8202 (tp40) cc_final: 0.7819 (pp30) REVERT: F 272 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8181 (mm-30) REVERT: F 344 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9464 (tp) REVERT: F 350 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8138 (t80) outliers start: 51 outliers final: 31 residues processed: 238 average time/residue: 0.1555 time to fit residues: 56.5617 Evaluate side-chains 252 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 15 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 15 HIS Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 183 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 136 optimal weight: 0.2980 chunk 150 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.083806 restraints weight = 35953.006| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.69 r_work: 0.2825 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22404 Z= 0.113 Angle : 0.491 8.328 30264 Z= 0.256 Chirality : 0.041 0.145 3378 Planarity : 0.003 0.038 3858 Dihedral : 6.618 80.666 3072 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 1.68 % Allowed : 13.35 % Favored : 84.97 % 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: -0.09 (0.17), residues: 2724 helix: 1.44 (0.19), residues: 906 sheet: -0.20 (0.20), residues: 672 loop : -1.18 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 170 TYR 0.010 0.001 TYR F 442 PHE 0.015 0.001 PHE F 151 TRP 0.013 0.002 TRP A 462 HIS 0.001 0.000 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (22398) covalent geometry : angle 0.49125 / 0.26 (30264) hydrogen bonds : bond 0.02787 / 1.89 ( 824) hydrogen bonds : angle 4.13693 / 2.95 ( 2295) Misc. bond : bond 0.00125 / 0.08 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.894 Fit side-chains REVERT: A 15 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7144 (m170) REVERT: A 152 GLN cc_start: 0.8032 (tp40) cc_final: 0.7713 (pp30) REVERT: A 350 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.8260 (t80) REVERT: A 474 ASP cc_start: 0.8493 (t0) cc_final: 0.8048 (t0) REVERT: B 15 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7408 (m170) REVERT: B 152 GLN cc_start: 0.8091 (tp40) cc_final: 0.7764 (pp30) REVERT: B 272 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 350 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7995 (t80) REVERT: B 458 MET cc_start: 0.8051 (mtp) cc_final: 0.7725 (ttt) REVERT: B 474 ASP cc_start: 0.8446 (t0) cc_final: 0.7967 (t0) REVERT: C 15 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7355 (m170) REVERT: C 152 GLN cc_start: 0.8172 (tp40) cc_final: 0.7655 (pp30) REVERT: C 272 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7904 (mm-30) REVERT: C 344 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9424 (tp) REVERT: C 350 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8281 (t80) REVERT: D 15 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.7176 (m170) REVERT: D 272 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: D 350 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8275 (t80) REVERT: E 15 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7407 (m170) REVERT: E 152 GLN cc_start: 0.8110 (tp40) cc_final: 0.7741 (pp30) REVERT: E 272 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8060 (mm-30) REVERT: E 350 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7996 (t80) REVERT: E 458 MET cc_start: 0.8037 (mtp) cc_final: 0.7741 (ttt) REVERT: E 474 ASP cc_start: 0.8415 (t0) cc_final: 0.7919 (t0) REVERT: F 15 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7331 (m170) REVERT: F 152 GLN cc_start: 0.8160 (tp40) cc_final: 0.7767 (pp30) REVERT: F 272 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7974 (mm-30) REVERT: F 344 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9422 (tp) outliers start: 39 outliers final: 20 residues processed: 237 average time/residue: 0.1556 time to fit residues: 56.6168 Evaluate side-chains 231 residues out of total 2322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 15 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 15 HIS Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 230 optimal weight: 0.4980 chunk 34 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.081554 restraints weight = 36047.131| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.71 r_work: 0.2786 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22404 Z= 0.205 Angle : 0.565 8.823 30264 Z= 0.293 Chirality : 0.043 0.142 3378 Planarity : 0.004 0.037 3858 Dihedral : 6.860 89.284 3069 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.08 % Favored : 91.85 % Rotamer: Outliers : 1.89 % Allowed : 13.31 % Favored : 84.80 % 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: -0.16 (0.17), residues: 2724 helix: 1.40 (0.19), residues: 906 sheet: -0.26 (0.20), residues: 666 loop : -1.21 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 170 TYR 0.012 0.001 TYR B 442 PHE 0.020 0.002 PHE C 151 TRP 0.017 0.002 TRP A 92 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.20 (22398) covalent geometry : angle 0.56499 / 0.29 (30264) hydrogen bonds : bond 0.03556 / 2.41 ( 824) hydrogen bonds : angle 4.31455 / 3.09 ( 2295) Misc. bond : bond 0.00189 / 0.12 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3596.81 seconds wall clock time: 62 minutes 54.40 seconds (3774.40 seconds total)