Starting phenix.real_space_refine on Thu Mar 5 14:02:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x1z_32953/03_2026/7x1z_32953.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1z_32953/03_2026/7x1z_32953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x1z_32953/03_2026/7x1z_32953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1z_32953/03_2026/7x1z_32953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x1z_32953/03_2026/7x1z_32953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1z_32953/03_2026/7x1z_32953.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 90 5.16 5 C 14580 2.51 5 N 4080 2.21 5 O 4506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23304 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "B" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "C" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "D" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "E" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "F" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.59, per 1000 atoms: 0.24 Number of scatterers: 23304 At special positions: 0 Unit cell: (122.615, 119.875, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 36 15.00 Mg 12 11.99 O 4506 8.00 N 4080 7.00 C 14580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5328 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 18 sheets defined 32.0% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 51 through 68 removed outlier: 3.599A pdb=" N GLY A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.741A pdb=" N SER A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 122 through 138 removed outlier: 4.132A pdb=" N GLU A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.854A pdb=" N GLU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.741A pdb=" N VAL A 200 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 334 through 341 removed outlier: 4.056A pdb=" N MET A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 removed outlier: 3.516A pdb=" N HIS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.789A pdb=" N ILE B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 68 removed outlier: 3.588A pdb=" N GLY B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 89 removed outlier: 3.797A pdb=" N SER B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 122 through 138 removed outlier: 4.072A pdb=" N GLU B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.852A pdb=" N GLU B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.504A pdb=" N PHE B 199 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 200 " --> pdb=" O GLU B 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 196 through 200' Processing helix chain 'B' and resid 267 through 275 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 334 through 341 removed outlier: 4.069A pdb=" N MET B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 removed outlier: 4.008A pdb=" N LEU B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 405 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 51 through 68 removed outlier: 3.595A pdb=" N GLY C 63 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.825A pdb=" N SER C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 122 through 138 removed outlier: 4.221A pdb=" N GLU C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.775A pdb=" N GLU C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 275 Processing helix chain 'C' and resid 293 through 304 Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'C' and resid 334 through 341 removed outlier: 4.060A pdb=" N MET C 338 " --> pdb=" O ASP C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 371 removed outlier: 3.962A pdb=" N LEU C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 405 Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.599A pdb=" N GLY D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 89 removed outlier: 3.824A pdb=" N SER D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 122 through 138 removed outlier: 4.138A pdb=" N GLU D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.891A pdb=" N GLU D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 293 through 304 Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 334 through 341 removed outlier: 4.161A pdb=" N MET D 338 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 371 removed outlier: 3.848A pdb=" N LEU D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 405 Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.794A pdb=" N ILE E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 68 removed outlier: 3.589A pdb=" N GLY E 63 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 removed outlier: 3.722A pdb=" N SER E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 100 Processing helix chain 'E' and resid 122 through 138 removed outlier: 4.097A pdb=" N GLU E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 175 removed outlier: 3.811A pdb=" N GLU E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 275 Processing helix chain 'E' and resid 293 through 304 Processing helix chain 'E' and resid 305 through 307 No H-bonds generated for 'chain 'E' and resid 305 through 307' Processing helix chain 'E' and resid 320 through 330 removed outlier: 3.516A pdb=" N LEU E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 341 removed outlier: 4.070A pdb=" N MET E 338 " --> pdb=" O ASP E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 371 removed outlier: 4.005A pdb=" N LEU E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 405 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 51 through 68 removed outlier: 3.602A pdb=" N GLY F 63 " --> pdb=" O PHE F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 89 removed outlier: 3.865A pdb=" N SER F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 100 Processing helix chain 'F' and resid 122 through 138 removed outlier: 4.071A pdb=" N GLU F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 175 removed outlier: 3.869A pdb=" N GLU F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 275 Processing helix chain 'F' and resid 293 through 304 removed outlier: 3.506A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 321 through 330 Processing helix chain 'F' and resid 334 through 341 removed outlier: 4.050A pdb=" N MET F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 371 removed outlier: 3.822A pdb=" N LEU F 360 " --> pdb=" O LEU F 356 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 405 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.507A pdb=" N PHE A 104 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 181 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU A 43 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 207 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER A 45 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASN A 209 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 210 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 13.028A pdb=" N ARG A 216 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N ILE A 239 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG A 218 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.633A pdb=" N ALA A 376 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 375 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR A 413 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE A 377 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR A 415 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 288 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A 451 " --> pdb=" O PHE A 470 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 107 removed outlier: 7.118A pdb=" N GLY B 71 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 106 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE B 73 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 181 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU B 43 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 207 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER B 45 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ASN B 209 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 210 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 13.048A pdb=" N ARG B 216 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N ILE B 239 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG B 218 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 238 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.840A pdb=" N LYS B 345 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 376 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 375 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 413 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE B 377 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N THR B 415 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 288 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 283 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE B 438 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 285 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 440 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR B 287 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N TYR B 442 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG B 451 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 107 removed outlier: 7.062A pdb=" N GLY C 71 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 106 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE C 73 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 181 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU C 43 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU C 207 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER C 45 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASN C 209 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 210 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 13.043A pdb=" N ARG C 216 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N ILE C 239 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG C 218 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 238 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 312 through 315 removed outlier: 3.620A pdb=" N ALA C 376 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE C 375 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR C 413 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE C 377 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N THR C 415 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C 288 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE C 283 " --> pdb=" O THR C 436 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE C 438 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU C 285 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU C 440 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR C 287 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N TYR C 442 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB2, first strand: chain 'D' and resid 103 through 107 removed outlier: 7.079A pdb=" N GLY D 71 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU D 106 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE D 73 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 181 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU D 43 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU D 207 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER D 45 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASN D 209 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 210 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 13.017A pdb=" N ARG D 216 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N ILE D 239 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG D 218 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 344 through 346 removed outlier: 3.880A pdb=" N LYS D 345 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 376 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 375 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR D 413 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE D 377 " --> pdb=" O THR D 413 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N THR D 415 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY D 288 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG D 451 " --> pdb=" O PHE D 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain 'E' and resid 103 through 107 removed outlier: 7.150A pdb=" N GLY E 71 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU E 106 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE E 73 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 181 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU E 43 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU E 207 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER E 45 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASN E 209 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E 210 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 13.053A pdb=" N ARG E 216 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N ILE E 239 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG E 218 " --> pdb=" O PHE E 237 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 344 through 346 removed outlier: 3.826A pdb=" N LYS E 345 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 376 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 375 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR E 413 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE E 377 " --> pdb=" O THR E 413 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N THR E 415 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 288 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE E 283 " --> pdb=" O THR E 436 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE E 438 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU E 285 " --> pdb=" O ILE E 438 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 440 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR E 287 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N TYR E 442 " --> pdb=" O THR E 287 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG E 451 " --> pdb=" O PHE E 470 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'F' and resid 103 through 107 removed outlier: 7.096A pdb=" N GLY F 71 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU F 106 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE F 73 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR F 181 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU F 43 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU F 207 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER F 45 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ASN F 209 " --> pdb=" O SER F 45 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 210 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 13.036A pdb=" N ARG F 216 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ILE F 239 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG F 218 " --> pdb=" O PHE F 237 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 238 " --> pdb=" O ASN F 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 344 through 346 removed outlier: 3.854A pdb=" N LYS F 345 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA F 376 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE F 375 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR F 413 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE F 377 " --> pdb=" O THR F 413 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N THR F 415 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY F 288 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE F 283 " --> pdb=" O THR F 436 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE F 438 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F 285 " --> pdb=" O ILE F 438 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU F 440 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR F 287 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N TYR F 442 " --> pdb=" O THR F 287 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2406 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: 4.26 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7813 1.35 - 1.47: 5322 1.47 - 1.58: 10384 1.58 - 1.70: 25 1.70 - 1.82: 162 Bond restraints: 23706 Sorted by residual: bond pdb=" CA ASN B 245 " pdb=" CB ASN B 245 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.70e-02 3.46e+03 2.39e+00 bond pdb=" CB PRO B 248 " pdb=" CG PRO B 248 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.28e+00 bond pdb=" CB PRO E 248 " pdb=" CG PRO E 248 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.24e+00 bond pdb=" CG1 ILE A 490 " pdb=" CD1 ILE A 490 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 bond pdb=" CA SER D 320 " pdb=" C SER D 320 " ideal model delta sigma weight residual 1.533 1.521 0.013 9.60e-03 1.09e+04 1.71e+00 ... (remaining 23701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 31529 2.45 - 4.91: 435 4.91 - 7.36: 46 7.36 - 9.81: 15 9.81 - 12.27: 9 Bond angle restraints: 32034 Sorted by residual: angle pdb=" N ILE C 433 " pdb=" CA ILE C 433 " pdb=" C ILE C 433 " ideal model delta sigma weight residual 112.96 108.03 4.93 1.00e+00 1.00e+00 2.43e+01 angle pdb=" N ILE F 433 " pdb=" CA ILE F 433 " pdb=" C ILE F 433 " ideal model delta sigma weight residual 112.96 108.07 4.89 1.00e+00 1.00e+00 2.39e+01 angle pdb=" C PHE C 278 " pdb=" N PHE C 279 " pdb=" CA PHE C 279 " ideal model delta sigma weight residual 122.41 132.25 -9.84 2.09e+00 2.29e-01 2.22e+01 angle pdb=" C PHE F 278 " pdb=" N PHE F 279 " pdb=" CA PHE F 279 " ideal model delta sigma weight residual 122.41 132.20 -9.79 2.09e+00 2.29e-01 2.19e+01 angle pdb=" C PHE A 278 " pdb=" N PHE A 279 " pdb=" CA PHE A 279 " ideal model delta sigma weight residual 122.41 132.07 -9.66 2.09e+00 2.29e-01 2.14e+01 ... (remaining 32029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12616 17.99 - 35.97: 1357 35.97 - 53.95: 343 53.95 - 71.94: 78 71.94 - 89.92: 60 Dihedral angle restraints: 14454 sinusoidal: 6156 harmonic: 8298 Sorted by residual: dihedral pdb=" CA TRP C 462 " pdb=" C TRP C 462 " pdb=" N HIS C 463 " pdb=" CA HIS C 463 " ideal model delta harmonic sigma weight residual 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA TRP F 462 " pdb=" C TRP F 462 " pdb=" N HIS F 463 " pdb=" CA HIS F 463 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP E 462 " pdb=" C TRP E 462 " pdb=" N HIS E 463 " pdb=" CA HIS E 463 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 14451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2412 0.041 - 0.082: 798 0.082 - 0.123: 289 0.123 - 0.163: 43 0.163 - 0.204: 16 Chirality restraints: 3558 Sorted by residual: chirality pdb=" CB VAL A 196 " pdb=" CA VAL A 196 " pdb=" CG1 VAL A 196 " pdb=" CG2 VAL A 196 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL D 196 " pdb=" CA VAL D 196 " pdb=" CG1 VAL D 196 " pdb=" CG2 VAL D 196 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL C 196 " pdb=" CA VAL C 196 " pdb=" CG1 VAL C 196 " pdb=" CG2 VAL C 196 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3555 not shown) Planarity restraints: 4104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 279 " -0.010 2.00e-02 2.50e+03 1.66e-02 4.85e+00 pdb=" CG PHE F 279 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE F 279 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 279 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE F 279 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 279 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 279 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 279 " -0.010 2.00e-02 2.50e+03 1.65e-02 4.77e+00 pdb=" CG PHE C 279 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C 279 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE C 279 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE C 279 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 279 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 279 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 79 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO C 80 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.029 5.00e-02 4.00e+02 ... (remaining 4101 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 403 2.66 - 3.22: 20137 3.22 - 3.78: 34127 3.78 - 4.34: 47459 4.34 - 4.90: 79631 Nonbonded interactions: 181757 Sorted by model distance: nonbonded pdb=" OG1 THR B 295 " pdb="MG MG B 903 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR E 295 " pdb="MG MG E 903 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR D 53 " pdb="MG MG D 904 " model vdw 2.101 2.170 nonbonded pdb=" OG1 THR A 53 " pdb="MG MG A 904 " model vdw 2.102 2.170 nonbonded pdb=" OG1 THR E 53 " pdb="MG MG E 904 " model vdw 2.102 2.170 ... (remaining 181752 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' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.030 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23712 Z= 0.162 Angle : 0.756 12.268 32034 Z= 0.423 Chirality : 0.048 0.204 3558 Planarity : 0.005 0.069 4104 Dihedral : 17.098 89.925 9126 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 0.53 % Allowed : 0.44 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.14), residues: 2892 helix: -0.74 (0.15), residues: 912 sheet: -1.69 (0.20), residues: 708 loop : -2.49 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 88 TYR 0.014 0.001 TYR A 132 PHE 0.037 0.002 PHE F 279 TRP 0.031 0.003 TRP A 462 HIS 0.009 0.001 HIS F 463 Details of bonding type rmsd covalent geometry : bond 0.00337 (23706) covalent geometry : angle 0.75649 (32034) hydrogen bonds : bond 0.22197 ( 837) hydrogen bonds : angle 8.21260 ( 2406) Misc. bond : bond 0.00152 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 327 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 490 ILE cc_start: 0.8636 (pt) cc_final: 0.8329 (mt) REVERT: C 167 LEU cc_start: 0.8062 (tp) cc_final: 0.7858 (tp) REVERT: D 490 ILE cc_start: 0.8644 (pt) cc_final: 0.7810 (pt) outliers start: 13 outliers final: 7 residues processed: 339 average time/residue: 0.1776 time to fit residues: 92.6221 Evaluate side-chains 247 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 240 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain E residue 321 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 230 HIS C 230 HIS C 323 GLN D 230 HIS E 230 HIS F 230 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092707 restraints weight = 43346.705| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.02 r_work: 0.3089 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23712 Z= 0.114 Angle : 0.519 5.818 32034 Z= 0.280 Chirality : 0.043 0.175 3558 Planarity : 0.004 0.043 4104 Dihedral : 11.438 89.481 3631 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.81 % Favored : 94.02 % Rotamer: Outliers : 1.46 % Allowed : 6.51 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.15), residues: 2892 helix: 0.46 (0.17), residues: 930 sheet: -1.10 (0.20), residues: 708 loop : -2.45 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 22 TYR 0.010 0.001 TYR D 132 PHE 0.019 0.001 PHE F 279 TRP 0.012 0.002 TRP A 462 HIS 0.005 0.001 HIS F 463 Details of bonding type rmsd covalent geometry : bond 0.00259 (23706) covalent geometry : angle 0.51945 (32034) hydrogen bonds : bond 0.03182 ( 837) hydrogen bonds : angle 5.11397 ( 2406) Misc. bond : bond 0.00124 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 TYR cc_start: 0.8276 (m-10) cc_final: 0.8071 (m-10) REVERT: B 358 ASP cc_start: 0.8795 (m-30) cc_final: 0.8584 (m-30) REVERT: C 257 ARG cc_start: 0.7698 (pmt170) cc_final: 0.7452 (pmt170) REVERT: D 171 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8871 (mm) REVERT: D 319 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7879 (mm-30) REVERT: E 358 ASP cc_start: 0.8786 (m-30) cc_final: 0.8573 (m-30) REVERT: F 420 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7174 (tpt) outliers start: 36 outliers final: 21 residues processed: 283 average time/residue: 0.1739 time to fit residues: 74.1352 Evaluate side-chains 252 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 235 optimal weight: 0.0070 chunk 93 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 overall best weight: 3.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.088633 restraints weight = 43779.276| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.99 r_work: 0.3025 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23712 Z= 0.159 Angle : 0.524 5.355 32034 Z= 0.285 Chirality : 0.043 0.166 3558 Planarity : 0.003 0.040 4104 Dihedral : 10.806 89.173 3606 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.71 % Favored : 93.12 % Rotamer: Outliers : 1.58 % Allowed : 10.07 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.16), residues: 2892 helix: 0.97 (0.18), residues: 930 sheet: -1.00 (0.20), residues: 714 loop : -2.33 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 321 TYR 0.023 0.001 TYR F 132 PHE 0.013 0.001 PHE C 279 TRP 0.012 0.002 TRP E 92 HIS 0.005 0.001 HIS F 463 Details of bonding type rmsd covalent geometry : bond 0.00375 (23706) covalent geometry : angle 0.52438 (32034) hydrogen bonds : bond 0.03406 ( 837) hydrogen bonds : angle 4.83728 ( 2406) Misc. bond : bond 0.00165 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLU cc_start: 0.7795 (tt0) cc_final: 0.7473 (mt-10) REVERT: B 132 TYR cc_start: 0.8336 (m-10) cc_final: 0.8088 (m-10) REVERT: D 171 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8891 (mm) REVERT: D 319 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7970 (mm-30) REVERT: D 490 ILE cc_start: 0.8757 (pt) cc_final: 0.8353 (pt) REVERT: E 358 ASP cc_start: 0.8827 (m-30) cc_final: 0.8614 (m-30) REVERT: E 488 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7029 (mtp85) outliers start: 39 outliers final: 23 residues processed: 231 average time/residue: 0.1685 time to fit residues: 60.0796 Evaluate side-chains 214 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 427 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 116 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 153 optimal weight: 0.2980 chunk 95 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 279 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN C 152 GLN E 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.087042 restraints weight = 44132.634| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.97 r_work: 0.2998 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23712 Z= 0.194 Angle : 0.545 5.744 32034 Z= 0.296 Chirality : 0.044 0.165 3558 Planarity : 0.003 0.040 4104 Dihedral : 10.633 87.070 3606 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.05 % Favored : 92.81 % Rotamer: Outliers : 2.51 % Allowed : 11.45 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2892 helix: 1.12 (0.18), residues: 930 sheet: -1.01 (0.20), residues: 720 loop : -2.29 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 321 TYR 0.027 0.001 TYR F 132 PHE 0.014 0.002 PHE B 237 TRP 0.012 0.002 TRP B 92 HIS 0.005 0.001 HIS F 463 Details of bonding type rmsd covalent geometry : bond 0.00459 (23706) covalent geometry : angle 0.54526 (32034) hydrogen bonds : bond 0.03465 ( 837) hydrogen bonds : angle 4.84582 ( 2406) Misc. bond : bond 0.00167 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8323 (m-10) cc_final: 0.8114 (m-10) REVERT: A 262 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6236 (mtp85) REVERT: B 132 TYR cc_start: 0.8399 (m-10) cc_final: 0.8150 (m-10) REVERT: B 152 GLN cc_start: 0.7438 (pp30) cc_final: 0.7039 (pp30) REVERT: B 262 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6284 (mtp85) REVERT: B 420 MET cc_start: 0.8781 (tpt) cc_final: 0.8160 (tpt) REVERT: B 432 GLU cc_start: 0.8198 (tp30) cc_final: 0.7989 (tp30) REVERT: B 444 GLU cc_start: 0.7080 (mp0) cc_final: 0.6848 (mp0) REVERT: C 420 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7593 (mmm) REVERT: D 171 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8880 (mm) REVERT: D 262 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6241 (mtp85) REVERT: D 319 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8011 (mm-30) REVERT: D 444 GLU cc_start: 0.8048 (tt0) cc_final: 0.7841 (mt-10) REVERT: E 262 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6311 (mtp85) REVERT: E 488 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7195 (mtp85) REVERT: F 319 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8357 (mm-30) outliers start: 62 outliers final: 41 residues processed: 246 average time/residue: 0.1857 time to fit residues: 69.5732 Evaluate side-chains 237 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 126 optimal weight: 0.0060 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.0040 chunk 279 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 115 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 overall best weight: 1.6014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.090388 restraints weight = 43334.201| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.97 r_work: 0.3050 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23712 Z= 0.105 Angle : 0.478 4.827 32034 Z= 0.260 Chirality : 0.042 0.156 3558 Planarity : 0.003 0.040 4104 Dihedral : 10.044 84.911 3606 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.91 % Favored : 93.95 % Rotamer: Outliers : 2.02 % Allowed : 12.70 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2892 helix: 1.37 (0.18), residues: 930 sheet: -0.72 (0.20), residues: 696 loop : -2.22 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 321 TYR 0.017 0.001 TYR C 132 PHE 0.015 0.001 PHE E 151 TRP 0.009 0.001 TRP C 462 HIS 0.005 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00241 (23706) covalent geometry : angle 0.47808 (32034) hydrogen bonds : bond 0.02645 ( 837) hydrogen bonds : angle 4.55162 ( 2406) Misc. bond : bond 0.00129 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8308 (m-10) cc_final: 0.8080 (m-10) REVERT: A 262 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6195 (mtp85) REVERT: A 444 GLU cc_start: 0.7674 (tt0) cc_final: 0.7404 (mt-10) REVERT: A 488 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7345 (mtm-85) REVERT: B 152 GLN cc_start: 0.7337 (pp30) cc_final: 0.7106 (pp30) REVERT: B 262 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6254 (mtp85) REVERT: B 432 GLU cc_start: 0.8246 (tp30) cc_final: 0.8041 (tp30) REVERT: C 319 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8196 (mm-30) REVERT: D 132 TYR cc_start: 0.8235 (m-10) cc_final: 0.8034 (m-10) REVERT: D 152 GLN cc_start: 0.7575 (pp30) cc_final: 0.7156 (pp30) REVERT: D 171 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8871 (mm) REVERT: D 262 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6191 (mtp85) REVERT: D 319 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7973 (mm-30) REVERT: E 262 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6275 (mtp85) REVERT: E 488 ARG cc_start: 0.7576 (mtm-85) cc_final: 0.7044 (mtp85) REVERT: F 319 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8162 (mm-30) outliers start: 50 outliers final: 33 residues processed: 248 average time/residue: 0.1902 time to fit residues: 71.0790 Evaluate side-chains 232 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 185 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN C 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.089959 restraints weight = 43708.864| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.00 r_work: 0.3047 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23712 Z= 0.113 Angle : 0.474 4.631 32034 Z= 0.258 Chirality : 0.042 0.156 3558 Planarity : 0.003 0.039 4104 Dihedral : 9.840 83.170 3606 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.53 % Rotamer: Outliers : 2.02 % Allowed : 13.47 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2892 helix: 1.50 (0.18), residues: 930 sheet: -0.62 (0.20), residues: 696 loop : -2.15 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.027 0.001 TYR F 132 PHE 0.013 0.001 PHE D 151 TRP 0.009 0.001 TRP F 92 HIS 0.005 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00265 (23706) covalent geometry : angle 0.47382 (32034) hydrogen bonds : bond 0.02685 ( 837) hydrogen bonds : angle 4.51365 ( 2406) Misc. bond : bond 0.00135 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8326 (m-10) cc_final: 0.8085 (m-10) REVERT: A 247 PHE cc_start: 0.8551 (m-80) cc_final: 0.8161 (m-10) REVERT: A 262 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6139 (mtp85) REVERT: A 338 MET cc_start: 0.7312 (mmt) cc_final: 0.7074 (mmp) REVERT: A 444 GLU cc_start: 0.7689 (tt0) cc_final: 0.7470 (mt-10) REVERT: A 488 ARG cc_start: 0.7546 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: B 21 MET cc_start: 0.8193 (ptm) cc_final: 0.7937 (ptm) REVERT: B 245 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8586 (m110) REVERT: B 262 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6258 (mtp85) REVERT: B 432 GLU cc_start: 0.8289 (tp30) cc_final: 0.8087 (tp30) REVERT: B 443 VAL cc_start: 0.8060 (t) cc_final: 0.7613 (m) REVERT: B 488 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7307 (ttm110) REVERT: C 319 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8212 (mm-30) REVERT: C 338 MET cc_start: 0.7635 (mmt) cc_final: 0.7320 (mmt) REVERT: C 420 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7605 (mmt) REVERT: D 132 TYR cc_start: 0.8246 (m-10) cc_final: 0.8018 (m-10) REVERT: D 152 GLN cc_start: 0.7550 (pp30) cc_final: 0.7219 (pp30) REVERT: D 171 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8871 (mm) REVERT: D 262 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6136 (mtp85) REVERT: D 319 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8198 (mm-30) REVERT: E 21 MET cc_start: 0.8187 (ptm) cc_final: 0.7924 (ptm) REVERT: E 257 ARG cc_start: 0.7654 (pmt170) cc_final: 0.7366 (pmt170) REVERT: E 262 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6278 (mtp85) REVERT: E 488 ARG cc_start: 0.7524 (mtm-85) cc_final: 0.6991 (mtp85) REVERT: E 490 ILE cc_start: 0.8272 (pt) cc_final: 0.7991 (pt) REVERT: F 319 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8132 (mm-30) outliers start: 50 outliers final: 36 residues processed: 244 average time/residue: 0.1732 time to fit residues: 64.2061 Evaluate side-chains 238 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 188 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 249 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** 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 = 0.3463 r_free = 0.3463 target = 0.108540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086449 restraints weight = 43940.505| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.98 r_work: 0.2984 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23712 Z= 0.223 Angle : 0.565 8.210 32034 Z= 0.306 Chirality : 0.044 0.163 3558 Planarity : 0.003 0.037 4104 Dihedral : 10.266 86.811 3606 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.09 % Favored : 91.80 % Rotamer: Outliers : 2.14 % Allowed : 14.64 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.16), residues: 2892 helix: 1.35 (0.18), residues: 930 sheet: -0.85 (0.20), residues: 720 loop : -2.14 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 446 TYR 0.024 0.001 TYR E 132 PHE 0.016 0.002 PHE B 237 TRP 0.012 0.002 TRP E 92 HIS 0.006 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00530 (23706) covalent geometry : angle 0.56525 (32034) hydrogen bonds : bond 0.03507 ( 837) hydrogen bonds : angle 4.80678 ( 2406) Misc. bond : bond 0.00181 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8364 (m-10) cc_final: 0.8114 (m-10) REVERT: A 262 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6245 (mtp85) REVERT: A 338 MET cc_start: 0.7154 (mmt) cc_final: 0.6754 (mmt) REVERT: A 488 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7237 (mtp85) REVERT: B 21 MET cc_start: 0.8246 (ptm) cc_final: 0.7998 (ptm) REVERT: B 198 GLU cc_start: 0.7431 (mp0) cc_final: 0.7203 (mp0) REVERT: B 245 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8731 (m110) REVERT: B 249 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8535 (mm) REVERT: B 262 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6280 (mtp85) REVERT: B 432 GLU cc_start: 0.8277 (tp30) cc_final: 0.7988 (tp30) REVERT: C 319 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8180 (mm-30) REVERT: C 338 MET cc_start: 0.7592 (mmt) cc_final: 0.7301 (mmt) REVERT: D 132 TYR cc_start: 0.8356 (m-10) cc_final: 0.8101 (m-10) REVERT: D 152 GLN cc_start: 0.7539 (pp30) cc_final: 0.7219 (pp30) REVERT: D 171 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8918 (mm) REVERT: D 262 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6264 (mtp85) REVERT: D 319 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7963 (mm-30) REVERT: E 21 MET cc_start: 0.8264 (ptm) cc_final: 0.8006 (ptm) REVERT: E 262 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6323 (mtp85) REVERT: E 488 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7216 (mtp85) REVERT: E 490 ILE cc_start: 0.8453 (pt) cc_final: 0.8151 (pt) REVERT: F 319 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8177 (mm-30) REVERT: F 338 MET cc_start: 0.7415 (mmt) cc_final: 0.6859 (mmt) outliers start: 53 outliers final: 38 residues processed: 236 average time/residue: 0.1907 time to fit residues: 68.0667 Evaluate side-chains 224 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 179 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 179 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 152 GLN ** 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 = 0.3444 r_free = 0.3444 target = 0.107078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.085052 restraints weight = 44247.101| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.99 r_work: 0.2963 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 23712 Z= 0.254 Angle : 0.596 8.830 32034 Z= 0.322 Chirality : 0.045 0.165 3558 Planarity : 0.003 0.036 4104 Dihedral : 10.500 87.956 3606 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.33 % Favored : 91.56 % Rotamer: Outliers : 2.31 % Allowed : 14.89 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.16), residues: 2892 helix: 0.98 (0.17), residues: 966 sheet: -0.98 (0.19), residues: 720 loop : -2.17 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 446 TYR 0.027 0.002 TYR E 132 PHE 0.019 0.002 PHE B 419 TRP 0.013 0.002 TRP E 92 HIS 0.006 0.001 HIS F 463 Details of bonding type rmsd covalent geometry : bond 0.00602 (23706) covalent geometry : angle 0.59601 (32034) hydrogen bonds : bond 0.03688 ( 837) hydrogen bonds : angle 4.93403 ( 2406) Misc. bond : bond 0.00168 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8344 (m-10) cc_final: 0.8116 (m-10) REVERT: A 247 PHE cc_start: 0.8654 (m-80) cc_final: 0.8307 (m-10) REVERT: A 262 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6284 (mtp85) REVERT: A 338 MET cc_start: 0.7165 (mmt) cc_final: 0.6895 (mmt) REVERT: A 488 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7280 (mtp85) REVERT: B 21 MET cc_start: 0.8297 (ptm) cc_final: 0.8057 (ptm) REVERT: B 152 GLN cc_start: 0.7860 (pp30) cc_final: 0.7178 (pp30) REVERT: B 196 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7579 (p) REVERT: B 245 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8557 (m-40) REVERT: B 262 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.6271 (mtp85) REVERT: B 338 MET cc_start: 0.7092 (mmt) cc_final: 0.6857 (mmt) REVERT: C 152 GLN cc_start: 0.7641 (pp30) cc_final: 0.7000 (pp30) REVERT: D 132 TYR cc_start: 0.8344 (m-10) cc_final: 0.8109 (m-10) REVERT: D 171 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8920 (mm) REVERT: D 262 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6269 (mtp85) REVERT: D 319 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7999 (mm-30) REVERT: E 21 MET cc_start: 0.8290 (ptm) cc_final: 0.8043 (ptm) REVERT: E 262 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6298 (mtp85) REVERT: E 488 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7304 (mtp85) REVERT: F 319 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8220 (mm-30) REVERT: F 488 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7071 (mtp85) outliers start: 57 outliers final: 41 residues processed: 245 average time/residue: 0.1718 time to fit residues: 63.9782 Evaluate side-chains 236 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 24 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** 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 = 0.107134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.085305 restraints weight = 44180.569| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.97 r_work: 0.2968 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 23712 Z= 0.237 Angle : 0.596 8.482 32034 Z= 0.321 Chirality : 0.045 0.164 3558 Planarity : 0.003 0.037 4104 Dihedral : 10.474 87.671 3606 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.40 % Favored : 91.49 % Rotamer: Outliers : 2.35 % Allowed : 14.85 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.16), residues: 2892 helix: 0.96 (0.17), residues: 966 sheet: -1.03 (0.19), residues: 720 loop : -2.15 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 446 TYR 0.029 0.001 TYR E 132 PHE 0.017 0.002 PHE B 419 TRP 0.013 0.002 TRP E 92 HIS 0.006 0.001 HIS F 463 Details of bonding type rmsd covalent geometry : bond 0.00563 (23706) covalent geometry : angle 0.59634 (32034) hydrogen bonds : bond 0.03585 ( 837) hydrogen bonds : angle 4.91580 ( 2406) Misc. bond : bond 0.00160 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 0.901 Fit side-chains REVERT: A 132 TYR cc_start: 0.8320 (m-10) cc_final: 0.8109 (m-10) REVERT: A 152 GLN cc_start: 0.7630 (pp30) cc_final: 0.6978 (pp30) REVERT: A 247 PHE cc_start: 0.8678 (m-80) cc_final: 0.8320 (m-10) REVERT: A 262 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6334 (mtp85) REVERT: A 338 MET cc_start: 0.7088 (mmt) cc_final: 0.6881 (mmt) REVERT: A 488 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7226 (mtp85) REVERT: B 21 MET cc_start: 0.8262 (ptm) cc_final: 0.8012 (ptm) REVERT: B 152 GLN cc_start: 0.7855 (pp30) cc_final: 0.7160 (pp30) REVERT: B 247 PHE cc_start: 0.8708 (m-10) cc_final: 0.8446 (m-10) REVERT: B 262 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6328 (mtp85) REVERT: B 338 MET cc_start: 0.7020 (mmt) cc_final: 0.6706 (mmt) REVERT: C 152 GLN cc_start: 0.7681 (pp30) cc_final: 0.7025 (pp30) REVERT: C 262 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7076 (ptp-170) REVERT: C 319 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8314 (mm-30) REVERT: C 338 MET cc_start: 0.7191 (mmt) cc_final: 0.6909 (mmt) REVERT: D 132 TYR cc_start: 0.8334 (m-10) cc_final: 0.8114 (m-10) REVERT: D 152 GLN cc_start: 0.7682 (pp30) cc_final: 0.6983 (pp30) REVERT: D 171 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8919 (mm) REVERT: D 262 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6321 (mtp85) REVERT: D 319 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7995 (mm-30) REVERT: E 21 MET cc_start: 0.8262 (ptm) cc_final: 0.8029 (ptm) REVERT: E 152 GLN cc_start: 0.7657 (pp30) cc_final: 0.6995 (pp30) REVERT: E 262 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6382 (mtp85) REVERT: E 488 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7237 (mtp85) REVERT: F 319 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8249 (mm-30) REVERT: F 488 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7065 (mtp85) outliers start: 58 outliers final: 44 residues processed: 247 average time/residue: 0.1664 time to fit residues: 63.5307 Evaluate side-chains 246 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 130 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 246 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** 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 = 0.3465 r_free = 0.3465 target = 0.108697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086846 restraints weight = 43959.279| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.99 r_work: 0.2989 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23712 Z= 0.173 Angle : 0.552 8.724 32034 Z= 0.297 Chirality : 0.044 0.159 3558 Planarity : 0.003 0.037 4104 Dihedral : 10.213 85.166 3606 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 2.02 % Allowed : 15.21 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.16), residues: 2892 helix: 1.04 (0.17), residues: 966 sheet: -0.98 (0.20), residues: 720 loop : -2.09 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 446 TYR 0.031 0.001 TYR E 132 PHE 0.017 0.001 PHE B 419 TRP 0.012 0.002 TRP E 92 HIS 0.005 0.001 HIS F 463 Details of bonding type rmsd covalent geometry : bond 0.00412 (23706) covalent geometry : angle 0.55192 (32034) hydrogen bonds : bond 0.03178 ( 837) hydrogen bonds : angle 4.77246 ( 2406) Misc. bond : bond 0.00145 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8313 (m-10) cc_final: 0.8087 (m-10) REVERT: A 152 GLN cc_start: 0.7677 (pp30) cc_final: 0.6993 (pp30) REVERT: A 247 PHE cc_start: 0.8677 (m-80) cc_final: 0.8331 (m-10) REVERT: A 262 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6355 (mtp85) REVERT: A 488 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7200 (mtp85) REVERT: B 21 MET cc_start: 0.8208 (ptm) cc_final: 0.7977 (ptm) REVERT: B 152 GLN cc_start: 0.7791 (pp30) cc_final: 0.7136 (pp30) REVERT: B 247 PHE cc_start: 0.8658 (m-10) cc_final: 0.8362 (m-10) REVERT: B 262 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6282 (mtp85) REVERT: B 338 MET cc_start: 0.6985 (mmt) cc_final: 0.6670 (mmt) REVERT: C 152 GLN cc_start: 0.7666 (pp30) cc_final: 0.7047 (pp30) REVERT: C 262 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7055 (ptp-170) REVERT: C 319 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8275 (mm-30) REVERT: C 338 MET cc_start: 0.7083 (mmt) cc_final: 0.6786 (mmt) REVERT: D 132 TYR cc_start: 0.8306 (m-10) cc_final: 0.8102 (m-10) REVERT: D 152 GLN cc_start: 0.7628 (pp30) cc_final: 0.6974 (pp30) REVERT: D 171 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8911 (mm) REVERT: D 262 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6354 (mtp85) REVERT: D 319 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8003 (mm-30) REVERT: E 21 MET cc_start: 0.8228 (ptm) cc_final: 0.8004 (ptm) REVERT: E 152 GLN cc_start: 0.7578 (pp30) cc_final: 0.6955 (pp30) REVERT: E 262 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6352 (mtp85) REVERT: E 319 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7894 (mm-30) REVERT: E 420 MET cc_start: 0.8681 (tpt) cc_final: 0.8267 (tpt) REVERT: E 488 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7177 (mtp85) REVERT: F 319 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8240 (mm-30) REVERT: F 488 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7014 (mtp85) outliers start: 50 outliers final: 41 residues processed: 250 average time/residue: 0.1668 time to fit residues: 63.7495 Evaluate side-chains 249 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 61 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 285 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** 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 = 0.107327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.085415 restraints weight = 44120.208| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.98 r_work: 0.2967 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23712 Z= 0.229 Angle : 0.598 8.806 32034 Z= 0.321 Chirality : 0.045 0.165 3558 Planarity : 0.003 0.042 4104 Dihedral : 10.460 87.680 3606 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.54 % Favored : 91.36 % Rotamer: Outliers : 1.98 % Allowed : 15.25 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.16), residues: 2892 helix: 0.74 (0.17), residues: 1002 sheet: -1.03 (0.19), residues: 720 loop : -2.11 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 446 TYR 0.031 0.001 TYR E 132 PHE 0.021 0.002 PHE D 419 TRP 0.014 0.002 TRP E 92 HIS 0.006 0.001 HIS F 463 Details of bonding type rmsd covalent geometry : bond 0.00544 (23706) covalent geometry : angle 0.59755 (32034) hydrogen bonds : bond 0.03603 ( 837) hydrogen bonds : angle 4.91089 ( 2406) Misc. bond : bond 0.00174 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4327.76 seconds wall clock time: 75 minutes 15.54 seconds (4515.54 seconds total)