Starting phenix.real_space_refine on Thu Sep 18 07:24:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxq_38758/09_2025/8xxq_38758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxq_38758/09_2025/8xxq_38758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxq_38758/09_2025/8xxq_38758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxq_38758/09_2025/8xxq_38758.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxq_38758/09_2025/8xxq_38758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxq_38758/09_2025/8xxq_38758.cif" } resolution = 2.75 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= 0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 9620 2.51 5 N 2608 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15172 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3793 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3793 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Chain: "C" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3793 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Chain: "D" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3793 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Time building chain proxies: 3.78, per 1000 atoms: 0.25 Number of scatterers: 15172 At special positions: 0 Unit cell: (108.712, 107, 101.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2840 8.00 N 2608 7.00 C 9620 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=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 527.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 46.0% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 43 through 64 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 157 through 170 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.514A pdb=" N THR A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.675A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.783A pdb=" N HIS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 296 through 299 Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 328 through 345 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'B' and resid 43 through 64 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 157 through 170 Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.465A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.740A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.772A pdb=" N HIS B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 328 through 345 Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 466 through 474 removed outlier: 3.583A pdb=" N TYR B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'C' and resid 43 through 64 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 65 through 83 Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 98 through 117 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 157 through 170 Proline residue: C 165 - end of helix removed outlier: 3.616A pdb=" N CYS C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.491A pdb=" N THR C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.679A pdb=" N HIS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 279 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 296 through 299 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 328 through 345 Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.547A pdb=" N TYR C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'D' and resid 43 through 64 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 65 through 83 Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 98 through 117 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 157 through 170 Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.477A pdb=" N THR D 186 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.819A pdb=" N HIS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 296 through 299 Processing helix chain 'D' and resid 300 through 310 Processing helix chain 'D' and resid 328 through 345 Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 398 through 409 Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 467 through 474 Processing helix chain 'D' and resid 485 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 132 removed outlier: 3.851A pdb=" N GLU A 126 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET A 135 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS B 257 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N PHE B 418 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 259 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY B 258 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 294 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 260 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA B 291 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR B 396 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 293 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 371 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.669A pdb=" N CYS A 147 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LYS A 177 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A 149 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 146 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 225 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 148 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE A 227 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 150 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS A 223 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N GLN A 249 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 225 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ASN A 251 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 227 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 351 removed outlier: 6.496A pdb=" N ILE A 371 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY A 258 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 294 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 260 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS A 257 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE A 418 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 259 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 437 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLN B 483 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 439 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 126 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'B' and resid 24 through 28 Processing sheet with id=AA8, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.313A pdb=" N PHE B 174 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 146 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 224 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS B 223 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLN B 249 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 225 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ASN B 251 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE B 227 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 28 Processing sheet with id=AB2, first strand: chain 'C' and resid 127 through 132 removed outlier: 6.577A pdb=" N MET C 135 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N HIS D 257 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N PHE D 418 " --> pdb=" O HIS D 257 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D 259 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY D 258 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL D 294 " --> pdb=" O GLY D 258 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL D 260 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA D 291 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR D 396 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU D 293 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE D 371 " --> pdb=" O LEU D 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 203 through 205 removed outlier: 6.312A pdb=" N PHE C 174 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS C 147 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LYS C 177 " --> pdb=" O CYS C 147 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY C 149 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL C 146 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE C 225 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 148 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE C 227 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE C 150 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 348 through 351 removed outlier: 6.502A pdb=" N ILE C 371 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA C 291 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 396 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C 293 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLY C 258 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 294 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 260 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS C 257 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE C 418 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C 259 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 437 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLN D 483 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL C 439 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET D 135 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 137 " --> pdb=" O MET D 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'D' and resid 24 through 28 Processing sheet with id=AB7, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.381A pdb=" N PHE D 174 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS D 147 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LYS D 177 " --> pdb=" O CYS D 147 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY D 149 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL D 146 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA D 224 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS D 223 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLN D 249 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE D 225 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASN D 251 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE D 227 " --> pdb=" O ASN D 251 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 2124 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: 2.87 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5023 1.34 - 1.46: 3064 1.46 - 1.58: 7217 1.58 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 15480 Sorted by residual: bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N SER B 3 " pdb=" CA SER B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N SER D 3 " pdb=" CA SER D 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N SER C 3 " pdb=" CA SER C 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ARG D 456 " pdb=" CA ARG D 456 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.17e-02 7.31e+03 2.45e+00 ... (remaining 15475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 20435 1.16 - 2.32: 387 2.32 - 3.47: 107 3.47 - 4.63: 54 4.63 - 5.79: 5 Bond angle restraints: 20988 Sorted by residual: angle pdb=" C SER D 455 " pdb=" N ARG D 456 " pdb=" CA ARG D 456 " ideal model delta sigma weight residual 121.19 126.53 -5.34 1.59e+00 3.96e-01 1.13e+01 angle pdb=" C SER B 455 " pdb=" N ARG B 456 " pdb=" CA ARG B 456 " ideal model delta sigma weight residual 120.79 124.93 -4.14 1.39e+00 5.18e-01 8.87e+00 angle pdb=" C SER C 455 " pdb=" N ARG C 456 " pdb=" CA ARG C 456 " ideal model delta sigma weight residual 120.79 124.74 -3.95 1.39e+00 5.18e-01 8.07e+00 angle pdb=" CA GLN B 209 " pdb=" C GLN B 209 " pdb=" O GLN B 209 " ideal model delta sigma weight residual 121.50 118.02 3.48 1.25e+00 6.40e-01 7.74e+00 angle pdb=" C ARG C 456 " pdb=" CA ARG C 456 " pdb=" CB ARG C 456 " ideal model delta sigma weight residual 110.92 115.32 -4.40 1.59e+00 3.96e-01 7.65e+00 ... (remaining 20983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 9087 16.09 - 32.19: 221 32.19 - 48.28: 67 48.28 - 64.37: 2 64.37 - 80.46: 3 Dihedral angle restraints: 9380 sinusoidal: 3700 harmonic: 5680 Sorted by residual: dihedral pdb=" CA GLY D 454 " pdb=" C GLY D 454 " pdb=" N SER D 455 " pdb=" CA SER D 455 " ideal model delta harmonic sigma weight residual 180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA LEU D 161 " pdb=" C LEU D 161 " pdb=" N TRP D 162 " pdb=" CA TRP D 162 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 dihedral pdb=" N PHE D 465 " pdb=" CA PHE D 465 " pdb=" CB PHE D 465 " pdb=" CG PHE D 465 " ideal model delta sinusoidal sigma weight residual -60.00 -112.23 52.23 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1504 0.027 - 0.054: 528 0.054 - 0.081: 141 0.081 - 0.108: 130 0.108 - 0.135: 85 Chirality restraints: 2388 Sorted by residual: chirality pdb=" CA VAL C 5 " pdb=" N VAL C 5 " pdb=" C VAL C 5 " pdb=" CB VAL C 5 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL D 441 " pdb=" N VAL D 441 " pdb=" C VAL D 441 " pdb=" CB VAL D 441 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL C 441 " pdb=" N VAL C 441 " pdb=" C VAL C 441 " pdb=" CB VAL C 441 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 2385 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 159 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 160 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 159 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO C 160 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 159 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 160 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 160 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 160 " 0.016 5.00e-02 4.00e+02 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 286 2.69 - 3.25: 15580 3.25 - 3.80: 25034 3.80 - 4.35: 34175 4.35 - 4.90: 56264 Nonbonded interactions: 131339 Sorted by model distance: nonbonded pdb=" OD2 ASP A 462 " pdb=" OG1 THR B 463 " model vdw 2.142 3.040 nonbonded pdb=" OD1 ASN C 464 " pdb=" NE2 GLN C 469 " model vdw 2.153 3.120 nonbonded pdb=" ND2 ASN B 33 " pdb=" O ASN B 363 " model vdw 2.154 3.120 nonbonded pdb=" OD1 ASN B 464 " pdb=" NE2 GLN B 469 " model vdw 2.154 3.120 nonbonded pdb=" OD2 ASP C 462 " pdb=" OG1 THR D 463 " model vdw 2.161 3.040 ... (remaining 131334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.160 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.002 0.033 15480 Z= 0.111 Angle : 0.480 5.790 20988 Z= 0.273 Chirality : 0.041 0.135 2388 Planarity : 0.003 0.031 2732 Dihedral : 8.138 80.464 5732 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.04 % Rotamer: Outliers : 0.43 % Allowed : 1.58 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.19), residues: 1988 helix: 1.10 (0.18), residues: 812 sheet: -0.64 (0.25), residues: 396 loop : -1.07 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 75 TYR 0.006 0.001 TYR A 76 PHE 0.014 0.001 PHE D 164 TRP 0.002 0.000 TRP C 484 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00191 (15480) covalent geometry : angle 0.48011 (20988) hydrogen bonds : bond 0.15940 ( 741) hydrogen bonds : angle 6.61087 ( 2124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 254 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 501 MET cc_start: 0.0563 (mtm) cc_final: -0.0433 (mtp) outliers start: 7 outliers final: 1 residues processed: 261 average time/residue: 0.6071 time to fit residues: 175.2952 Evaluate side-chains 144 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 272 GLN B 41 GLN B 115 HIS B 172 ASN B 210 HIS B 272 GLN B 436 GLN B 440 ASN C 41 GLN C 115 HIS ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN C 272 GLN C 365 ASN C 413 ASN D 41 GLN D 115 HIS D 207 HIS D 272 GLN D 409 ASN D 440 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.079609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064843 restraints weight = 42408.480| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.19 r_work: 0.2866 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.066 15480 Z= 0.457 Angle : 0.776 7.242 20988 Z= 0.401 Chirality : 0.054 0.235 2388 Planarity : 0.005 0.046 2732 Dihedral : 4.938 27.983 2102 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.10 % Allowed : 9.18 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.19), residues: 1988 helix: 1.03 (0.18), residues: 864 sheet: -0.15 (0.27), residues: 368 loop : -0.29 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 75 TYR 0.031 0.003 TYR D 466 PHE 0.026 0.002 PHE A 465 TRP 0.010 0.002 TRP D 24 HIS 0.005 0.002 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.01045 (15480) covalent geometry : angle 0.77600 (20988) hydrogen bonds : bond 0.05116 ( 741) hydrogen bonds : angle 5.53995 ( 2124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8715 (p0) cc_final: 0.8495 (p0) REVERT: A 486 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7730 (tm-30) REVERT: A 498 MET cc_start: 0.1127 (ttt) cc_final: 0.0702 (ttt) REVERT: B 63 ASP cc_start: 0.8641 (p0) cc_final: 0.8385 (p0) REVERT: B 501 MET cc_start: -0.2044 (mtm) cc_final: -0.2664 (mtp) REVERT: C 63 ASP cc_start: 0.8642 (p0) cc_final: 0.8419 (p0) REVERT: C 379 MET cc_start: 0.8155 (mtt) cc_final: 0.7789 (mtt) REVERT: C 486 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7772 (tm-30) REVERT: C 488 ASP cc_start: 0.8429 (m-30) cc_final: 0.8196 (m-30) REVERT: C 498 MET cc_start: 0.1043 (ttt) cc_final: 0.0599 (ttt) REVERT: D 63 ASP cc_start: 0.8675 (p0) cc_final: 0.8435 (p0) REVERT: D 90 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8646 (tm) REVERT: D 486 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 51 outliers final: 20 residues processed: 159 average time/residue: 0.5406 time to fit residues: 96.5060 Evaluate side-chains 128 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 186 optimal weight: 7.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 231 ASN A 440 ASN A 483 GLN B 77 GLN B 231 ASN B 409 ASN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN D 483 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.086032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071851 restraints weight = 40255.534| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.14 r_work: 0.3010 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15480 Z= 0.112 Angle : 0.539 7.441 20988 Z= 0.273 Chirality : 0.044 0.175 2388 Planarity : 0.004 0.036 2732 Dihedral : 4.394 21.707 2100 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.19 % Allowed : 9.31 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 1988 helix: 1.71 (0.18), residues: 840 sheet: 0.01 (0.27), residues: 356 loop : -0.13 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.016 0.002 TYR C 466 PHE 0.018 0.001 PHE C 164 TRP 0.005 0.001 TRP D 162 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00247 (15480) covalent geometry : angle 0.53883 (20988) hydrogen bonds : bond 0.03335 ( 741) hydrogen bonds : angle 4.72083 ( 2124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8650 (p0) cc_final: 0.8386 (p0) REVERT: A 76 TYR cc_start: 0.9289 (t80) cc_final: 0.9022 (t80) REVERT: A 379 MET cc_start: 0.8111 (mtt) cc_final: 0.7772 (mtm) REVERT: A 486 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 63 ASP cc_start: 0.8585 (p0) cc_final: 0.8320 (p0) REVERT: B 463 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9126 (p) REVERT: B 486 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 501 MET cc_start: -0.1564 (mtm) cc_final: -0.2314 (mtp) REVERT: C 63 ASP cc_start: 0.8608 (p0) cc_final: 0.8358 (p0) REVERT: C 76 TYR cc_start: 0.9264 (t80) cc_final: 0.9003 (t80) REVERT: C 379 MET cc_start: 0.8142 (mtt) cc_final: 0.7804 (mtm) REVERT: C 486 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7802 (tm-30) REVERT: C 488 ASP cc_start: 0.8339 (m-30) cc_final: 0.8097 (m-30) REVERT: D 63 ASP cc_start: 0.8594 (p0) cc_final: 0.8366 (p0) REVERT: D 76 TYR cc_start: 0.9319 (t80) cc_final: 0.9090 (t80) REVERT: D 411 TYR cc_start: 0.8643 (m-80) cc_final: 0.8196 (m-80) REVERT: D 486 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7724 (tm-30) outliers start: 36 outliers final: 10 residues processed: 165 average time/residue: 0.5426 time to fit residues: 100.3925 Evaluate side-chains 136 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.081673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.066916 restraints weight = 41708.903| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 4.19 r_work: 0.2901 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 15480 Z= 0.292 Angle : 0.630 7.466 20988 Z= 0.318 Chirality : 0.047 0.204 2388 Planarity : 0.004 0.038 2732 Dihedral : 4.582 27.559 2100 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.10 % Allowed : 10.10 % Favored : 86.80 % 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 aren not related in a simple way. whole: 1.05 (0.20), residues: 1988 helix: 1.77 (0.18), residues: 840 sheet: -0.05 (0.27), residues: 368 loop : 0.01 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 75 TYR 0.021 0.002 TYR C 466 PHE 0.019 0.002 PHE B 164 TRP 0.005 0.001 TRP D 484 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00668 (15480) covalent geometry : angle 0.63038 (20988) hydrogen bonds : bond 0.04130 ( 741) hydrogen bonds : angle 4.89786 ( 2124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8668 (p0) cc_final: 0.8425 (p0) REVERT: A 379 MET cc_start: 0.8229 (mtt) cc_final: 0.7882 (mtm) REVERT: A 411 TYR cc_start: 0.8681 (m-80) cc_final: 0.8264 (m-80) REVERT: A 463 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9068 (p) REVERT: A 486 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 63 ASP cc_start: 0.8641 (p0) cc_final: 0.8381 (p0) REVERT: B 73 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8990 (tp) REVERT: B 77 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.9151 (pp30) REVERT: B 411 TYR cc_start: 0.8581 (m-80) cc_final: 0.8366 (m-80) REVERT: B 486 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 501 MET cc_start: -0.1914 (mtm) cc_final: -0.2621 (mtp) REVERT: C 63 ASP cc_start: 0.8649 (p0) cc_final: 0.8409 (p0) REVERT: C 81 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8663 (mttm) REVERT: C 379 MET cc_start: 0.8226 (mtt) cc_final: 0.7881 (mtm) REVERT: C 486 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7814 (tm-30) REVERT: C 488 ASP cc_start: 0.8468 (m-30) cc_final: 0.8196 (m-30) REVERT: D 63 ASP cc_start: 0.8607 (p0) cc_final: 0.8372 (p0) REVERT: D 81 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8610 (mttm) REVERT: D 251 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8160 (m110) REVERT: D 411 TYR cc_start: 0.8708 (m-80) cc_final: 0.8424 (m-80) REVERT: D 486 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7764 (tm-30) outliers start: 51 outliers final: 18 residues processed: 161 average time/residue: 0.5482 time to fit residues: 99.1306 Evaluate side-chains 134 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 118 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 77 GLN B 436 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 GLN C 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067817 restraints weight = 41897.634| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.04 r_work: 0.2949 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15480 Z= 0.139 Angle : 0.566 10.164 20988 Z= 0.278 Chirality : 0.044 0.184 2388 Planarity : 0.004 0.034 2732 Dihedral : 4.446 25.788 2100 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.19 % Allowed : 11.37 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.19), residues: 1988 helix: 1.90 (0.18), residues: 840 sheet: 0.07 (0.27), residues: 356 loop : -0.03 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 75 TYR 0.017 0.002 TYR C 466 PHE 0.019 0.001 PHE B 164 TRP 0.003 0.001 TRP D 484 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00315 (15480) covalent geometry : angle 0.56562 (20988) hydrogen bonds : bond 0.03510 ( 741) hydrogen bonds : angle 4.66185 ( 2124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8611 (p0) cc_final: 0.8353 (p0) REVERT: A 188 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8787 (mm) REVERT: A 379 MET cc_start: 0.8195 (mtt) cc_final: 0.7814 (mtm) REVERT: A 463 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9172 (p) REVERT: A 486 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 63 ASP cc_start: 0.8647 (p0) cc_final: 0.8389 (p0) REVERT: B 486 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 501 MET cc_start: -0.1213 (mtm) cc_final: -0.2087 (mtp) REVERT: C 63 ASP cc_start: 0.8631 (p0) cc_final: 0.8375 (p0) REVERT: C 76 TYR cc_start: 0.9297 (t80) cc_final: 0.8984 (t80) REVERT: C 81 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8684 (mttm) REVERT: C 379 MET cc_start: 0.8202 (mtt) cc_final: 0.7825 (mtm) REVERT: C 486 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7810 (tm-30) REVERT: C 488 ASP cc_start: 0.8423 (m-30) cc_final: 0.8158 (m-30) REVERT: D 63 ASP cc_start: 0.8626 (p0) cc_final: 0.8386 (p0) REVERT: D 81 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8586 (mttm) REVERT: D 251 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8152 (m110) REVERT: D 411 TYR cc_start: 0.8685 (m-80) cc_final: 0.8214 (m-80) REVERT: D 486 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7740 (tm-30) outliers start: 36 outliers final: 15 residues processed: 149 average time/residue: 0.5628 time to fit residues: 94.0534 Evaluate side-chains 136 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 163 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 191 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN C 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.084101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069740 restraints weight = 41396.834| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.01 r_work: 0.2991 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15480 Z= 0.105 Angle : 0.551 10.114 20988 Z= 0.267 Chirality : 0.044 0.170 2388 Planarity : 0.004 0.033 2732 Dihedral : 4.275 22.205 2100 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.13 % Allowed : 11.62 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.19), residues: 1988 helix: 2.06 (0.18), residues: 840 sheet: 0.08 (0.27), residues: 356 loop : 0.00 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.015 0.001 TYR C 466 PHE 0.018 0.001 PHE B 164 TRP 0.003 0.001 TRP B 24 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00235 (15480) covalent geometry : angle 0.55147 (20988) hydrogen bonds : bond 0.03112 ( 741) hydrogen bonds : angle 4.47702 ( 2124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8607 (p0) cc_final: 0.8336 (p0) REVERT: A 76 TYR cc_start: 0.9294 (t80) cc_final: 0.8993 (t80) REVERT: A 110 LEU cc_start: 0.9239 (tt) cc_final: 0.9035 (tm) REVERT: A 188 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8775 (mm) REVERT: A 379 MET cc_start: 0.8209 (mtt) cc_final: 0.7836 (mtm) REVERT: A 486 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7570 (tm-30) REVERT: B 63 ASP cc_start: 0.8615 (p0) cc_final: 0.8356 (p0) REVERT: B 486 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7662 (tm-30) REVERT: B 498 MET cc_start: 0.1275 (OUTLIER) cc_final: 0.0982 (mmm) REVERT: B 501 MET cc_start: -0.0783 (mtm) cc_final: -0.1808 (mtp) REVERT: C 63 ASP cc_start: 0.8607 (p0) cc_final: 0.8334 (p0) REVERT: C 76 TYR cc_start: 0.9284 (t80) cc_final: 0.8995 (t80) REVERT: C 379 MET cc_start: 0.8235 (mtt) cc_final: 0.7851 (mtm) REVERT: C 486 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7722 (tm-30) REVERT: C 488 ASP cc_start: 0.8375 (m-30) cc_final: 0.8100 (m-30) REVERT: C 498 MET cc_start: 0.2597 (mmm) cc_final: 0.2341 (tpp) REVERT: D 63 ASP cc_start: 0.8585 (p0) cc_final: 0.8349 (p0) REVERT: D 76 TYR cc_start: 0.9300 (t80) cc_final: 0.9031 (t80) REVERT: D 110 LEU cc_start: 0.9195 (tt) cc_final: 0.8947 (tm) REVERT: D 411 TYR cc_start: 0.8664 (m-80) cc_final: 0.8158 (m-80) REVERT: D 486 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7573 (tm-30) outliers start: 35 outliers final: 10 residues processed: 155 average time/residue: 0.5188 time to fit residues: 90.5989 Evaluate side-chains 134 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 1 optimal weight: 0.5980 chunk 184 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 overall best weight: 5.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN B 77 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065493 restraints weight = 42135.796| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.18 r_work: 0.2873 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 15480 Z= 0.321 Angle : 0.693 12.003 20988 Z= 0.342 Chirality : 0.049 0.221 2388 Planarity : 0.004 0.036 2732 Dihedral : 4.671 30.531 2100 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.13 % Allowed : 11.62 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.20), residues: 1988 helix: 1.88 (0.18), residues: 840 sheet: 0.04 (0.28), residues: 368 loop : -0.01 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 75 TYR 0.023 0.002 TYR C 466 PHE 0.022 0.002 PHE B 164 TRP 0.007 0.001 TRP D 24 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00735 (15480) covalent geometry : angle 0.69254 (20988) hydrogen bonds : bond 0.04233 ( 741) hydrogen bonds : angle 4.88959 ( 2124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.712 Fit side-chains REVERT: A 63 ASP cc_start: 0.8680 (p0) cc_final: 0.8440 (p0) REVERT: A 379 MET cc_start: 0.8230 (mtt) cc_final: 0.7915 (mtm) REVERT: A 411 TYR cc_start: 0.8697 (m-80) cc_final: 0.8440 (m-80) REVERT: A 486 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 498 MET cc_start: 0.3004 (mmm) cc_final: 0.2554 (mmm) REVERT: B 63 ASP cc_start: 0.8703 (p0) cc_final: 0.8450 (p0) REVERT: B 486 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 498 MET cc_start: 0.1329 (mmt) cc_final: 0.0996 (mmm) REVERT: B 501 MET cc_start: -0.1538 (mtm) cc_final: -0.2368 (mtp) REVERT: C 63 ASP cc_start: 0.8660 (p0) cc_final: 0.8414 (p0) REVERT: C 81 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8699 (mttm) REVERT: C 344 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8930 (mtpt) REVERT: C 379 MET cc_start: 0.8255 (mtt) cc_final: 0.7928 (mtm) REVERT: C 433 ASP cc_start: 0.8793 (t0) cc_final: 0.8136 (t70) REVERT: C 486 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7764 (tm-30) REVERT: C 488 ASP cc_start: 0.8575 (m-30) cc_final: 0.8353 (m-30) REVERT: D 63 ASP cc_start: 0.8683 (p0) cc_final: 0.8454 (p0) REVERT: D 486 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7770 (tm-30) REVERT: D 488 ASP cc_start: 0.8629 (m-30) cc_final: 0.8414 (m-30) outliers start: 35 outliers final: 15 residues processed: 145 average time/residue: 0.5672 time to fit residues: 92.0300 Evaluate side-chains 124 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 137 optimal weight: 0.4980 chunk 145 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN B 469 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.083941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069266 restraints weight = 41832.647| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.10 r_work: 0.2989 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15480 Z= 0.106 Angle : 0.597 14.779 20988 Z= 0.285 Chirality : 0.044 0.171 2388 Planarity : 0.003 0.032 2732 Dihedral : 4.363 22.608 2100 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.58 % Allowed : 12.29 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.19), residues: 1988 helix: 2.04 (0.18), residues: 840 sheet: 0.09 (0.27), residues: 356 loop : -0.01 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.014 0.001 TYR B 76 PHE 0.018 0.001 PHE B 164 TRP 0.006 0.001 TRP B 24 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00237 (15480) covalent geometry : angle 0.59692 (20988) hydrogen bonds : bond 0.03140 ( 741) hydrogen bonds : angle 4.53652 ( 2124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.624 Fit side-chains REVERT: A 63 ASP cc_start: 0.8612 (p0) cc_final: 0.8344 (p0) REVERT: A 76 TYR cc_start: 0.9288 (t80) cc_final: 0.9039 (t80) REVERT: A 110 LEU cc_start: 0.9261 (tt) cc_final: 0.9033 (tm) REVERT: A 188 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8792 (mm) REVERT: A 379 MET cc_start: 0.8193 (mtt) cc_final: 0.7836 (mtm) REVERT: A 486 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 498 MET cc_start: 0.2236 (mmm) cc_final: 0.1890 (mmm) REVERT: B 63 ASP cc_start: 0.8639 (p0) cc_final: 0.8363 (p0) REVERT: B 486 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 498 MET cc_start: 0.1135 (OUTLIER) cc_final: 0.0859 (mmt) REVERT: B 501 MET cc_start: -0.1226 (mtm) cc_final: -0.2168 (mtp) REVERT: C 63 ASP cc_start: 0.8609 (p0) cc_final: 0.8345 (p0) REVERT: C 76 TYR cc_start: 0.9291 (t80) cc_final: 0.9039 (t80) REVERT: C 81 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8655 (mttm) REVERT: C 252 MET cc_start: 0.8996 (mtp) cc_final: 0.8681 (mpp) REVERT: C 261 MET cc_start: 0.8856 (mmm) cc_final: 0.8640 (mmm) REVERT: C 379 MET cc_start: 0.8273 (mtt) cc_final: 0.7909 (mtm) REVERT: C 486 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7748 (tm-30) REVERT: C 488 ASP cc_start: 0.8449 (m-30) cc_final: 0.8202 (m-30) REVERT: D 63 ASP cc_start: 0.8616 (p0) cc_final: 0.8374 (p0) REVERT: D 76 TYR cc_start: 0.9305 (t80) cc_final: 0.9083 (t80) REVERT: D 110 LEU cc_start: 0.9230 (tt) cc_final: 0.9005 (tm) REVERT: D 486 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7598 (tm-30) outliers start: 26 outliers final: 11 residues processed: 137 average time/residue: 0.5921 time to fit residues: 90.1977 Evaluate side-chains 129 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 109 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 138 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.083024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068472 restraints weight = 41641.783| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.05 r_work: 0.2967 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15480 Z= 0.140 Angle : 0.609 14.557 20988 Z= 0.291 Chirality : 0.045 0.178 2388 Planarity : 0.003 0.032 2732 Dihedral : 4.329 23.513 2100 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.40 % Allowed : 12.77 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.19), residues: 1988 helix: 2.08 (0.18), residues: 840 sheet: 0.04 (0.27), residues: 368 loop : 0.11 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 75 TYR 0.016 0.001 TYR A 466 PHE 0.022 0.001 PHE A 155 TRP 0.004 0.001 TRP B 61 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00322 (15480) covalent geometry : angle 0.60854 (20988) hydrogen bonds : bond 0.03335 ( 741) hydrogen bonds : angle 4.56609 ( 2124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.657 Fit side-chains REVERT: A 63 ASP cc_start: 0.8612 (p0) cc_final: 0.8365 (p0) REVERT: A 76 TYR cc_start: 0.9298 (t80) cc_final: 0.9058 (t80) REVERT: A 110 LEU cc_start: 0.9260 (tt) cc_final: 0.9024 (tm) REVERT: A 188 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8801 (mm) REVERT: A 379 MET cc_start: 0.8216 (mtt) cc_final: 0.7871 (mtm) REVERT: A 486 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 488 ASP cc_start: 0.8541 (m-30) cc_final: 0.8333 (m-30) REVERT: A 498 MET cc_start: 0.2262 (mmm) cc_final: 0.2049 (mmm) REVERT: B 63 ASP cc_start: 0.8635 (p0) cc_final: 0.8364 (p0) REVERT: B 486 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 501 MET cc_start: -0.1204 (mtm) cc_final: -0.2131 (mtp) REVERT: C 63 ASP cc_start: 0.8614 (p0) cc_final: 0.8353 (p0) REVERT: C 76 TYR cc_start: 0.9323 (t80) cc_final: 0.9104 (t80) REVERT: C 81 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8699 (mttm) REVERT: C 252 MET cc_start: 0.9041 (mtp) cc_final: 0.8698 (mpp) REVERT: C 379 MET cc_start: 0.8238 (mtt) cc_final: 0.7892 (mtm) REVERT: C 486 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 488 ASP cc_start: 0.8457 (m-30) cc_final: 0.8204 (m-30) REVERT: D 63 ASP cc_start: 0.8602 (p0) cc_final: 0.8365 (p0) REVERT: D 76 TYR cc_start: 0.9346 (t80) cc_final: 0.9105 (t80) REVERT: D 110 LEU cc_start: 0.9214 (tt) cc_final: 0.8992 (tm) REVERT: D 128 MET cc_start: 0.8462 (tpp) cc_final: 0.8190 (ttm) REVERT: D 486 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7761 (tm-30) REVERT: D 488 ASP cc_start: 0.8524 (m-30) cc_final: 0.8312 (m-30) outliers start: 23 outliers final: 10 residues processed: 136 average time/residue: 0.5715 time to fit residues: 86.7170 Evaluate side-chains 127 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 107 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 159 optimal weight: 0.0570 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 31 optimal weight: 0.0870 chunk 35 optimal weight: 8.9990 chunk 85 optimal weight: 0.0870 overall best weight: 0.8456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069885 restraints weight = 41510.825| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.12 r_work: 0.3002 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15480 Z= 0.106 Angle : 0.601 13.373 20988 Z= 0.288 Chirality : 0.044 0.172 2388 Planarity : 0.003 0.032 2732 Dihedral : 4.287 21.378 2100 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.03 % Allowed : 13.02 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.19), residues: 1988 helix: 2.08 (0.18), residues: 840 sheet: 0.02 (0.27), residues: 368 loop : 0.13 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.016 0.001 TYR C 466 PHE 0.024 0.001 PHE D 164 TRP 0.006 0.001 TRP C 162 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00240 (15480) covalent geometry : angle 0.60103 (20988) hydrogen bonds : bond 0.03104 ( 741) hydrogen bonds : angle 4.51553 ( 2124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.521 Fit side-chains REVERT: A 63 ASP cc_start: 0.8595 (p0) cc_final: 0.8345 (p0) REVERT: A 76 TYR cc_start: 0.9281 (t80) cc_final: 0.9034 (t80) REVERT: A 110 LEU cc_start: 0.9247 (tt) cc_final: 0.9019 (tm) REVERT: A 379 MET cc_start: 0.8186 (mtt) cc_final: 0.7821 (mtm) REVERT: A 486 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 488 ASP cc_start: 0.8512 (m-30) cc_final: 0.8289 (m-30) REVERT: B 63 ASP cc_start: 0.8594 (p0) cc_final: 0.8340 (p0) REVERT: B 486 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 501 MET cc_start: -0.1170 (mtm) cc_final: -0.2104 (mtp) REVERT: C 63 ASP cc_start: 0.8575 (p0) cc_final: 0.8323 (p0) REVERT: C 76 TYR cc_start: 0.9291 (t80) cc_final: 0.9028 (t80) REVERT: C 128 MET cc_start: 0.8508 (tpt) cc_final: 0.8268 (tpp) REVERT: C 252 MET cc_start: 0.9028 (mtp) cc_final: 0.8707 (mpp) REVERT: C 379 MET cc_start: 0.8233 (mtt) cc_final: 0.7873 (mtm) REVERT: C 486 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 488 ASP cc_start: 0.8394 (m-30) cc_final: 0.8123 (m-30) REVERT: D 63 ASP cc_start: 0.8573 (p0) cc_final: 0.8331 (p0) REVERT: D 76 TYR cc_start: 0.9315 (t80) cc_final: 0.9073 (t80) REVERT: D 110 LEU cc_start: 0.9217 (tt) cc_final: 0.8991 (tm) REVERT: D 128 MET cc_start: 0.8416 (tpp) cc_final: 0.8100 (ttm) REVERT: D 486 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 488 ASP cc_start: 0.8496 (m-30) cc_final: 0.8265 (m-30) outliers start: 17 outliers final: 9 residues processed: 136 average time/residue: 0.5141 time to fit residues: 78.5007 Evaluate side-chains 130 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 113 optimal weight: 0.9990 chunk 85 optimal weight: 0.0010 chunk 184 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069174 restraints weight = 41774.318| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.14 r_work: 0.2987 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15480 Z= 0.131 Angle : 0.607 13.386 20988 Z= 0.293 Chirality : 0.045 0.178 2388 Planarity : 0.003 0.031 2732 Dihedral : 4.275 22.012 2100 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.16 % Allowed : 13.02 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.19), residues: 1988 helix: 2.05 (0.18), residues: 840 sheet: 0.04 (0.27), residues: 368 loop : 0.16 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 108 TYR 0.017 0.001 TYR A 466 PHE 0.021 0.001 PHE A 155 TRP 0.005 0.001 TRP C 162 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00302 (15480) covalent geometry : angle 0.60686 (20988) hydrogen bonds : bond 0.03268 ( 741) hydrogen bonds : angle 4.57133 ( 2124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3936.00 seconds wall clock time: 68 minutes 25.00 seconds (4105.00 seconds total)