Starting phenix.real_space_refine on Sat Jul 4 12:35:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fob_29344/07_2026/8fob_29344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fob_29344/07_2026/8fob_29344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fob_29344/07_2026/8fob_29344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fob_29344/07_2026/8fob_29344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fob_29344/07_2026/8fob_29344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fob_29344/07_2026/8fob_29344.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fob_29344/07_2026/8fob_29344.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fob_29344/07_2026/8fob_29344.cif" } resolution = 2.71 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= 0.031 sd= 0.128 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 Ca 2 9.91 5 P 8 5.49 5 S 156 5.16 5 C 13436 2.51 5 N 3232 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20390 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "B" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "C" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 320 Unusual residues: {' CA': 2, 'PCW': 1, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'POV:plan-1': 2, 'POV:plan-2': 4, 'POV:plan-3': 4} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 318 Unusual residues: {'PCW': 1, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'POV:plan-1': 2, 'POV:plan-2': 4, 'POV:plan-3': 4} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 353 Unusual residues: {'PCW': 1, 'POV': 7, 'Y01': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'POV:plan-1': 2, 'POV:plan-2': 4, 'POV:plan-3': 4} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 283 Unusual residues: {'PCW': 1, 'POV': 7, 'Y01': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 4, 'POV:plan-3': 4, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 4.27, per 1000 atoms: 0.21 Number of scatterers: 20390 At special positions: 0 Unit cell: (123.48, 125.16, 118.44, 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) Ca 2 19.99 S 156 16.00 P 8 15.00 O 3556 8.00 N 3232 7.00 C 13436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 780.2 milliseconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 62.3% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.515A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.808A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.636A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.519A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.969A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.592A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.671A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.709A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.757A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.950A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.650A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.513A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.780A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 removed outlier: 3.770A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.614A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.518A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.604A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 510 removed outlier: 5.267A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.524A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.183A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.629A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 removed outlier: 3.642A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.515A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.807A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.636A pdb=" N LEU B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.518A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.970A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.591A pdb=" N ILE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.671A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.710A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.757A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.951A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.650A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.512A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.781A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.769A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.614A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 4.519A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.605A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 510 removed outlier: 5.267A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.523A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.183A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.629A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 removed outlier: 3.643A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.515A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.807A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.636A pdb=" N LEU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.518A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.968A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.591A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.670A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.711A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.757A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.951A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.650A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.513A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.780A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 removed outlier: 3.769A pdb=" N VAL C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.614A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 removed outlier: 4.519A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 472 removed outlier: 3.605A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 510 removed outlier: 5.267A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.524A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.183A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 588 removed outlier: 3.629A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 removed outlier: 3.642A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.515A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.807A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.635A pdb=" N LEU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.518A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.970A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.591A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.672A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.710A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.757A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.951A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.650A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.512A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.781A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 removed outlier: 3.770A pdb=" N VAL D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.614A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 4.519A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.605A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 510 removed outlier: 5.268A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.523A pdb=" N PHE D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.183A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 588 removed outlier: 3.629A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 3.642A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.499A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 353 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 268 removed outlier: 6.498A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 353 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.498A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 353 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 268 removed outlier: 6.499A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 353 949 hydrogen bonds defined for protein. 2739 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.29: 3144 1.29 - 1.45: 5428 1.45 - 1.60: 11832 1.60 - 1.76: 76 1.76 - 1.91: 288 Bond restraints: 20768 Sorted by residual: bond pdb=" CAV Y01 B 804 " pdb=" CAZ Y01 B 804 " ideal model delta sigma weight residual 1.507 1.912 -0.405 2.00e-02 2.50e+03 4.11e+02 bond pdb=" CAV Y01 D 805 " pdb=" CAZ Y01 D 805 " ideal model delta sigma weight residual 1.507 1.912 -0.405 2.00e-02 2.50e+03 4.10e+02 bond pdb=" CAV Y01 C 804 " pdb=" CAZ Y01 C 804 " ideal model delta sigma weight residual 1.507 1.911 -0.404 2.00e-02 2.50e+03 4.07e+02 bond pdb=" CAV Y01 A 801 " pdb=" CAZ Y01 A 801 " ideal model delta sigma weight residual 1.507 1.910 -0.403 2.00e-02 2.50e+03 4.06e+02 bond pdb=" CAV Y01 B 803 " pdb=" CAZ Y01 B 803 " ideal model delta sigma weight residual 1.507 1.910 -0.403 2.00e-02 2.50e+03 4.05e+02 ... (remaining 20763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 26798 3.26 - 6.52: 902 6.52 - 9.78: 205 9.78 - 13.04: 80 13.04 - 16.30: 15 Bond angle restraints: 28000 Sorted by residual: angle pdb=" C SER D 175 " pdb=" N GLU D 176 " pdb=" CA GLU D 176 " ideal model delta sigma weight residual 120.82 129.18 -8.36 1.50e+00 4.44e-01 3.11e+01 angle pdb=" C SER A 175 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 120.82 129.17 -8.35 1.50e+00 4.44e-01 3.10e+01 angle pdb=" C SER B 175 " pdb=" N GLU B 176 " pdb=" CA GLU B 176 " ideal model delta sigma weight residual 120.82 129.14 -8.32 1.50e+00 4.44e-01 3.08e+01 angle pdb=" C SER C 175 " pdb=" N GLU C 176 " pdb=" CA GLU C 176 " ideal model delta sigma weight residual 120.82 129.13 -8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" C28 POV D 810 " pdb=" C29 POV D 810 " pdb="C210 POV D 810 " ideal model delta sigma weight residual 127.79 111.49 16.30 3.00e+00 1.11e-01 2.95e+01 ... (remaining 27995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 11950 32.69 - 65.39: 424 65.39 - 98.08: 50 98.08 - 130.77: 8 130.77 - 163.46: 16 Dihedral angle restraints: 12448 sinusoidal: 5484 harmonic: 6964 Sorted by residual: dihedral pdb=" CA GLU C 519 " pdb=" C GLU C 519 " pdb=" N LEU C 520 " pdb=" CA LEU C 520 " ideal model delta harmonic sigma weight residual -180.00 -146.74 -33.26 0 5.00e+00 4.00e-02 4.42e+01 dihedral pdb=" CA GLU A 519 " pdb=" C GLU A 519 " pdb=" N LEU A 520 " pdb=" CA LEU A 520 " ideal model delta harmonic sigma weight residual 180.00 -146.80 -33.20 0 5.00e+00 4.00e-02 4.41e+01 dihedral pdb=" CA GLU B 519 " pdb=" C GLU B 519 " pdb=" N LEU B 520 " pdb=" CA LEU B 520 " ideal model delta harmonic sigma weight residual -180.00 -146.82 -33.18 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 12445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.992: 3068 0.992 - 1.984: 0 1.984 - 2.976: 0 2.976 - 3.968: 4 3.968 - 4.959: 44 Chirality restraints: 3116 Sorted by residual: chirality pdb=" CBC Y01 D 804 " pdb=" CAR Y01 D 804 " pdb=" CAV Y01 D 804 " pdb=" OAW Y01 D 804 " both_signs ideal model delta sigma weight residual False -2.54 2.42 -4.96 2.00e-01 2.50e+01 6.15e+02 chirality pdb=" CBC Y01 C 803 " pdb=" CAR Y01 C 803 " pdb=" CAV Y01 C 803 " pdb=" OAW Y01 C 803 " both_signs ideal model delta sigma weight residual False -2.54 2.36 -4.91 2.00e-01 2.50e+01 6.02e+02 chirality pdb=" CBC Y01 A 801 " pdb=" CAR Y01 A 801 " pdb=" CAV Y01 A 801 " pdb=" OAW Y01 A 801 " both_signs ideal model delta sigma weight residual False -2.54 2.35 -4.89 2.00e-01 2.50e+01 5.99e+02 ... (remaining 3113 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 810 " 0.324 2.00e-02 2.50e+03 3.21e-01 1.03e+03 pdb=" C29 POV C 810 " -0.329 2.00e-02 2.50e+03 pdb="C210 POV C 810 " -0.314 2.00e-02 2.50e+03 pdb="C211 POV C 810 " 0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 807 " 0.314 2.00e-02 2.50e+03 3.13e-01 9.78e+02 pdb=" C29 POV A 807 " -0.317 2.00e-02 2.50e+03 pdb="C210 POV A 807 " -0.309 2.00e-02 2.50e+03 pdb="C211 POV A 807 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 810 " 0.278 2.00e-02 2.50e+03 2.81e-01 7.89e+02 pdb=" C29 POV D 810 " -0.271 2.00e-02 2.50e+03 pdb="C210 POV D 810 " -0.291 2.00e-02 2.50e+03 pdb="C211 POV D 810 " 0.283 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 310 2.64 - 3.20: 17165 3.20 - 3.77: 30968 3.77 - 4.33: 44446 4.33 - 4.90: 70428 Nonbonded interactions: 163317 Sorted by model distance: nonbonded pdb="CA CA A 812 " pdb="CA CA A 813 " model vdw 2.073 1.980 nonbonded pdb=" OH TYR C 547 " pdb=" O HOH C 901 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR C 524 " pdb=" O TYR D 547 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 547 " pdb=" O HOH A 901 " model vdw 2.232 3.040 nonbonded pdb=" O PRO D 544 " pdb=" O HOH D 901 " model vdw 2.237 3.040 ... (remaining 163312 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or (resid 808 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)) or (resid 809 and (name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216)))) selection = (chain 'B' and (resid 28 through 637 or (resid 808 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)) or (resid 809 and (name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216)))) selection = (chain 'C' and (resid 28 through 637 or (resid 808 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)) or (resid 809 and (name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216)))) selection = (chain 'D' and (resid 28 through 637 or (resid 808 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)) or (resid 809 and (name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216)))) } 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=0.45 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.590 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.030 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:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.024 0.405 20768 Z= 1.169 Angle : 1.572 16.303 28000 Z= 0.769 Chirality : 0.539 4.959 3116 Planarity : 0.013 0.321 3416 Dihedral : 17.438 163.463 7944 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.39 % Allowed : 5.81 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -5.44 (0.13), residues: 2360 helix: -3.77 (0.08), residues: 1448 sheet: -3.07 (0.59), residues: 68 loop : -2.96 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 470 TYR 0.044 0.003 TYR B 547 PHE 0.023 0.003 PHE D 508 TRP 0.027 0.003 TRP B 629 HIS 0.014 0.003 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.02353 / 1.17 (20768) covalent geometry : angle 1.57219 / 0.77 (28000) hydrogen bonds : bond 0.30699 / 20.45 ( 949) hydrogen bonds : angle 9.09959 / 6.34 ( 2739) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 470 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.5577 (m-10) cc_final: 0.5356 (m-10) REVERT: A 99 MET cc_start: 0.6952 (mtt) cc_final: 0.6704 (mtt) REVERT: A 110 MET cc_start: 0.7046 (ttm) cc_final: 0.6766 (ttt) REVERT: A 222 TYR cc_start: 0.7335 (m-10) cc_final: 0.7045 (m-80) REVERT: A 497 MET cc_start: 0.7186 (mtt) cc_final: 0.6982 (mtt) REVERT: A 637 GLN cc_start: 0.7186 (mp-120) cc_final: 0.6632 (mm-40) REVERT: B 96 MET cc_start: 0.7863 (mtm) cc_final: 0.7578 (mmm) REVERT: B 110 MET cc_start: 0.6970 (ttm) cc_final: 0.6289 (ttt) REVERT: B 222 TYR cc_start: 0.7153 (m-10) cc_final: 0.6831 (m-80) REVERT: B 294 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7380 (mt-10) REVERT: B 497 MET cc_start: 0.7220 (mtt) cc_final: 0.6998 (mtt) REVERT: B 637 GLN cc_start: 0.7235 (mp-120) cc_final: 0.6742 (mm-40) REVERT: C 96 MET cc_start: 0.7839 (mtm) cc_final: 0.7530 (mmp) REVERT: C 110 MET cc_start: 0.6982 (ttm) cc_final: 0.6434 (ttt) REVERT: C 222 TYR cc_start: 0.7152 (m-10) cc_final: 0.6934 (m-80) REVERT: C 637 GLN cc_start: 0.7060 (mp-120) cc_final: 0.6281 (mm-40) REVERT: D 96 MET cc_start: 0.7786 (mtm) cc_final: 0.7488 (mmp) REVERT: D 110 MET cc_start: 0.6960 (ttm) cc_final: 0.6405 (ttt) REVERT: D 114 LEU cc_start: 0.7232 (tt) cc_final: 0.6934 (tp) REVERT: D 116 GLU cc_start: 0.7771 (tt0) cc_final: 0.7145 (pm20) REVERT: D 222 TYR cc_start: 0.7136 (m-10) cc_final: 0.6879 (m-80) REVERT: D 294 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7426 (mt-10) REVERT: D 637 GLN cc_start: 0.7229 (mp-120) cc_final: 0.6713 (mm-40) outliers start: 8 outliers final: 1 residues processed: 474 average time/residue: 0.5901 time to fit residues: 317.1508 Evaluate side-chains 265 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 127 ASN A 174 ASN A 206 GLN A 217 ASN A 252 ASN A 257 GLN A 258 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 174 ASN B 206 GLN B 217 ASN B 257 GLN B 258 HIS B 267 GLN ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 174 ASN C 206 GLN C 217 ASN C 257 GLN C 258 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 174 ASN D 206 GLN D 217 ASN D 257 GLN D 258 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.206911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.173682 restraints weight = 28618.551| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.64 r_work: 0.3843 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20768 Z= 0.235 Angle : 0.785 7.245 28000 Z= 0.398 Chirality : 0.048 0.390 3116 Planarity : 0.007 0.054 3416 Dihedral : 17.191 145.165 3357 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.41 % Allowed : 12.65 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.04 (0.16), residues: 2360 helix: -1.53 (0.12), residues: 1400 sheet: -2.66 (0.50), residues: 76 loop : -2.59 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 615 TYR 0.028 0.002 TYR D 547 PHE 0.028 0.003 PHE A 537 TRP 0.024 0.002 TRP A 268 HIS 0.006 0.001 HIS D 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (20768) covalent geometry : angle 0.78481 / 0.40 (28000) hydrogen bonds : bond 0.05998 / 4.04 ( 949) hydrogen bonds : angle 4.49175 / 3.14 ( 2739) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 272 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.5836 (m-10) cc_final: 0.5486 (m-10) REVERT: A 99 MET cc_start: 0.6881 (mtt) cc_final: 0.6593 (ppp) REVERT: A 222 TYR cc_start: 0.7418 (m-10) cc_final: 0.7145 (m-80) REVERT: A 263 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7174 (mtt90) REVERT: A 309 ASP cc_start: 0.8350 (p0) cc_final: 0.8102 (p0) REVERT: B 45 TRP cc_start: 0.6248 (m-10) cc_final: 0.6045 (m-10) REVERT: B 96 MET cc_start: 0.7975 (mtm) cc_final: 0.7610 (mmp) REVERT: B 99 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6219 (ppp) REVERT: B 110 MET cc_start: 0.6287 (ttm) cc_final: 0.5649 (ttt) REVERT: B 222 TYR cc_start: 0.7367 (m-10) cc_final: 0.7139 (m-80) REVERT: B 294 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8176 (mt-10) REVERT: B 485 MET cc_start: 0.8897 (mtt) cc_final: 0.8550 (mtt) REVERT: C 33 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.5610 (ttt-90) REVERT: C 74 GLN cc_start: 0.6148 (tp-100) cc_final: 0.5371 (pm20) REVERT: C 110 MET cc_start: 0.6321 (ttm) cc_final: 0.5697 (ttt) REVERT: C 263 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7271 (mtt90) REVERT: D 96 MET cc_start: 0.7860 (mtm) cc_final: 0.7166 (mtp) REVERT: D 110 MET cc_start: 0.6231 (ttm) cc_final: 0.5844 (ttt) REVERT: D 115 TYR cc_start: 0.5959 (m-10) cc_final: 0.5667 (m-80) REVERT: D 294 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8235 (mt-10) REVERT: D 309 ASP cc_start: 0.8511 (p0) cc_final: 0.8180 (p0) REVERT: D 550 ASP cc_start: 0.6543 (m-30) cc_final: 0.6255 (t0) outliers start: 91 outliers final: 25 residues processed: 338 average time/residue: 0.5485 time to fit residues: 213.5661 Evaluate side-chains 273 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 ARG Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 99 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 267 GLN B 217 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN C 217 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.210388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177230 restraints weight = 28705.057| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.69 r_work: 0.3890 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20768 Z= 0.127 Angle : 0.624 8.961 28000 Z= 0.316 Chirality : 0.041 0.280 3116 Planarity : 0.005 0.046 3416 Dihedral : 14.813 117.818 3357 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.00 % Allowed : 15.55 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 2360 helix: -0.54 (0.13), residues: 1468 sheet: -2.64 (0.47), residues: 84 loop : -2.35 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 134 TYR 0.016 0.001 TYR A 547 PHE 0.015 0.002 PHE B 456 TRP 0.017 0.001 TRP A 268 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (20768) covalent geometry : angle 0.62445 / 0.32 (28000) hydrogen bonds : bond 0.04726 / 3.16 ( 949) hydrogen bonds : angle 3.96247 / 2.77 ( 2739) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6838 (mp) REVERT: A 45 TRP cc_start: 0.5846 (m-10) cc_final: 0.5497 (m-10) REVERT: A 99 MET cc_start: 0.7002 (mtt) cc_final: 0.6578 (ppp) REVERT: A 215 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7999 (mtt) REVERT: A 222 TYR cc_start: 0.7319 (m-10) cc_final: 0.7095 (m-80) REVERT: A 263 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7107 (mtt90) REVERT: B 51 LEU cc_start: 0.7358 (tm) cc_final: 0.6527 (mp) REVERT: B 96 MET cc_start: 0.7915 (mtm) cc_final: 0.7480 (mmp) REVERT: B 99 MET cc_start: 0.7181 (mmt) cc_final: 0.6267 (ppp) REVERT: B 110 MET cc_start: 0.6411 (ttm) cc_final: 0.5931 (ttt) REVERT: B 222 TYR cc_start: 0.7377 (m-10) cc_final: 0.7154 (m-80) REVERT: B 294 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8155 (mt-10) REVERT: B 435 MET cc_start: 0.6494 (mmm) cc_final: 0.6113 (mmm) REVERT: C 33 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.5549 (ttt-90) REVERT: C 99 MET cc_start: 0.6431 (mmt) cc_final: 0.6102 (mmt) REVERT: C 110 MET cc_start: 0.6531 (ttm) cc_final: 0.6104 (ttt) REVERT: C 115 TYR cc_start: 0.5681 (m-10) cc_final: 0.5242 (m-80) REVERT: C 215 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8327 (mtt) REVERT: C 435 MET cc_start: 0.6713 (mmm) cc_final: 0.5913 (mmm) REVERT: C 634 GLU cc_start: 0.7343 (tt0) cc_final: 0.7125 (tt0) REVERT: D 38 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6620 (mp) REVERT: D 96 MET cc_start: 0.7832 (mtm) cc_final: 0.7577 (mmp) REVERT: D 99 MET cc_start: 0.6370 (mmt) cc_final: 0.6135 (mmt) REVERT: D 100 GLU cc_start: 0.7761 (mp0) cc_final: 0.7181 (pt0) REVERT: D 110 MET cc_start: 0.6356 (ttm) cc_final: 0.6046 (ttt) REVERT: D 115 TYR cc_start: 0.5976 (m-10) cc_final: 0.5749 (m-80) REVERT: D 215 MET cc_start: 0.8445 (mtp) cc_final: 0.8238 (mtt) REVERT: D 294 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8211 (mt-10) REVERT: D 634 GLU cc_start: 0.7308 (tt0) cc_final: 0.6959 (tt0) outliers start: 62 outliers final: 21 residues processed: 328 average time/residue: 0.5536 time to fit residues: 207.9491 Evaluate side-chains 286 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 65 optimal weight: 20.0000 chunk 217 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 25 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN D 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.206992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.173364 restraints weight = 28875.519| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.75 r_work: 0.3844 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20768 Z= 0.186 Angle : 0.668 9.353 28000 Z= 0.336 Chirality : 0.044 0.326 3116 Planarity : 0.005 0.050 3416 Dihedral : 14.466 112.561 3357 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.22 % Allowed : 15.84 % Favored : 79.94 % 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: -1.66 (0.17), residues: 2360 helix: -0.33 (0.14), residues: 1440 sheet: -2.51 (0.48), residues: 84 loop : -2.22 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 615 TYR 0.022 0.002 TYR A 547 PHE 0.018 0.002 PHE A 537 TRP 0.013 0.001 TRP A 268 HIS 0.004 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (20768) covalent geometry : angle 0.66756 / 0.34 (28000) hydrogen bonds : bond 0.05014 / 3.35 ( 949) hydrogen bonds : angle 4.06257 / 2.84 ( 2739) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 252 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6752 (mp) REVERT: A 45 TRP cc_start: 0.5834 (m-10) cc_final: 0.5590 (m-10) REVERT: A 99 MET cc_start: 0.7019 (mtt) cc_final: 0.6407 (ppp) REVERT: A 110 MET cc_start: 0.6769 (ttt) cc_final: 0.6379 (ppp) REVERT: A 222 TYR cc_start: 0.7347 (m-10) cc_final: 0.7117 (m-80) REVERT: A 263 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7227 (mtt90) REVERT: B 38 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6806 (mp) REVERT: B 51 LEU cc_start: 0.7382 (tm) cc_final: 0.6529 (mp) REVERT: B 96 MET cc_start: 0.7883 (mtm) cc_final: 0.7678 (mmp) REVERT: B 99 MET cc_start: 0.7261 (mmt) cc_final: 0.6212 (ppp) REVERT: B 100 GLU cc_start: 0.7896 (mp0) cc_final: 0.7551 (pt0) REVERT: B 110 MET cc_start: 0.6412 (ttm) cc_final: 0.5978 (ttt) REVERT: B 115 TYR cc_start: 0.5949 (m-10) cc_final: 0.5734 (m-80) REVERT: B 222 TYR cc_start: 0.7298 (m-10) cc_final: 0.7063 (m-80) REVERT: B 435 MET cc_start: 0.6438 (mmm) cc_final: 0.6192 (mmm) REVERT: B 555 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.6317 (t80) REVERT: C 33 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.5651 (ttt-90) REVERT: C 51 LEU cc_start: 0.7444 (tm) cc_final: 0.6582 (mp) REVERT: C 99 MET cc_start: 0.6463 (mmt) cc_final: 0.6193 (mmt) REVERT: C 100 GLU cc_start: 0.7805 (mp0) cc_final: 0.7264 (pt0) REVERT: C 110 MET cc_start: 0.6543 (ttm) cc_final: 0.6199 (ttt) REVERT: C 115 TYR cc_start: 0.5705 (m-10) cc_final: 0.5429 (m-80) REVERT: C 215 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8289 (mtt) REVERT: C 294 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: C 555 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.6392 (t80) REVERT: D 99 MET cc_start: 0.6394 (mmt) cc_final: 0.6109 (mtt) REVERT: D 100 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: D 110 MET cc_start: 0.6373 (ttm) cc_final: 0.5864 (ttt) REVERT: D 625 LEU cc_start: 0.6577 (pp) cc_final: 0.6216 (mm) REVERT: D 636 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7064 (ttp-170) outliers start: 87 outliers final: 31 residues processed: 309 average time/residue: 0.5080 time to fit residues: 182.7362 Evaluate side-chains 275 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 636 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 94 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 129 optimal weight: 40.0000 chunk 229 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN C 118 GLN C 217 ASN C 267 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.210234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.177343 restraints weight = 28582.589| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.63 r_work: 0.3891 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20768 Z= 0.117 Angle : 0.588 7.221 28000 Z= 0.296 Chirality : 0.041 0.259 3116 Planarity : 0.004 0.046 3416 Dihedral : 13.269 92.327 3357 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.73 % Allowed : 17.34 % Favored : 78.92 % 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: -0.89 (0.18), residues: 2360 helix: 0.27 (0.14), residues: 1428 sheet: -2.41 (0.52), residues: 76 loop : -1.83 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 615 TYR 0.014 0.001 TYR B 524 PHE 0.015 0.001 PHE B 456 TRP 0.014 0.001 TRP A 268 HIS 0.002 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (20768) covalent geometry : angle 0.58799 / 0.30 (28000) hydrogen bonds : bond 0.04174 / 2.79 ( 949) hydrogen bonds : angle 3.74814 / 2.62 ( 2739) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 257 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6762 (mp) REVERT: A 45 TRP cc_start: 0.5789 (m-10) cc_final: 0.5566 (m-10) REVERT: A 99 MET cc_start: 0.7270 (mtt) cc_final: 0.6316 (tmm) REVERT: A 110 MET cc_start: 0.6907 (ttt) cc_final: 0.6686 (ptm) REVERT: A 222 TYR cc_start: 0.7218 (m-10) cc_final: 0.6964 (m-80) REVERT: A 263 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7120 (mtt90) REVERT: A 634 GLU cc_start: 0.7336 (tt0) cc_final: 0.7013 (tt0) REVERT: B 38 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6738 (mp) REVERT: B 51 LEU cc_start: 0.7431 (tm) cc_final: 0.6608 (mp) REVERT: B 96 MET cc_start: 0.7846 (mtm) cc_final: 0.7540 (mmp) REVERT: B 99 MET cc_start: 0.7196 (mmt) cc_final: 0.6066 (ppp) REVERT: B 110 MET cc_start: 0.6446 (ttm) cc_final: 0.6055 (ttt) REVERT: B 435 MET cc_start: 0.6426 (mmm) cc_final: 0.6129 (mmm) REVERT: B 555 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.6229 (t80) REVERT: C 51 LEU cc_start: 0.7485 (tm) cc_final: 0.6610 (mp) REVERT: C 96 MET cc_start: 0.7326 (mtp) cc_final: 0.7109 (mmm) REVERT: C 100 GLU cc_start: 0.7881 (mp0) cc_final: 0.7285 (pt0) REVERT: C 215 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: C 229 LEU cc_start: 0.7982 (mt) cc_final: 0.7583 (pp) REVERT: C 255 MET cc_start: 0.8277 (mmt) cc_final: 0.8031 (mpt) REVERT: C 555 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.6293 (t80) REVERT: D 45 TRP cc_start: 0.6121 (m-10) cc_final: 0.5860 (m100) REVERT: D 99 MET cc_start: 0.6439 (mmt) cc_final: 0.6180 (mtt) REVERT: D 100 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7248 (pt0) REVERT: D 110 MET cc_start: 0.6441 (ttm) cc_final: 0.6182 (ttm) REVERT: D 215 MET cc_start: 0.8515 (mtp) cc_final: 0.8058 (ttm) REVERT: D 229 LEU cc_start: 0.8057 (mt) cc_final: 0.7619 (pp) REVERT: D 555 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.6128 (t80) REVERT: D 625 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6284 (mm) REVERT: D 634 GLU cc_start: 0.7364 (tt0) cc_final: 0.7047 (tt0) outliers start: 77 outliers final: 33 residues processed: 307 average time/residue: 0.4706 time to fit residues: 168.2210 Evaluate side-chains 283 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 202 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.206023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.172696 restraints weight = 28473.235| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.59 r_work: 0.3840 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20768 Z= 0.216 Angle : 0.695 8.384 28000 Z= 0.346 Chirality : 0.047 0.346 3116 Planarity : 0.005 0.051 3416 Dihedral : 13.643 105.922 3357 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.75 % Allowed : 16.62 % Favored : 78.63 % 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: -1.30 (0.18), residues: 2360 helix: -0.08 (0.14), residues: 1440 sheet: -2.42 (0.52), residues: 76 loop : -1.98 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 615 TYR 0.018 0.002 TYR B 547 PHE 0.018 0.002 PHE A 537 TRP 0.010 0.002 TRP B 268 HIS 0.004 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (20768) covalent geometry : angle 0.69498 / 0.35 (28000) hydrogen bonds : bond 0.05049 / 3.37 ( 949) hydrogen bonds : angle 4.07578 / 2.86 ( 2739) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 238 time to evaluate : 0.748 Fit side-chains REVERT: A 38 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6775 (mp) REVERT: A 99 MET cc_start: 0.7358 (mtt) cc_final: 0.6931 (mtt) REVERT: A 222 TYR cc_start: 0.7246 (m-10) cc_final: 0.7008 (m-80) REVERT: A 263 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7307 (mtt90) REVERT: A 309 ASP cc_start: 0.8412 (p0) cc_final: 0.8119 (p0) REVERT: A 555 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.6524 (t80) REVERT: B 38 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6774 (mp) REVERT: B 51 LEU cc_start: 0.7405 (tm) cc_final: 0.6564 (mp) REVERT: B 99 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6782 (mmt) REVERT: B 294 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8332 (mt-10) REVERT: B 555 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.6299 (t80) REVERT: C 51 LEU cc_start: 0.7418 (tm) cc_final: 0.6544 (mp) REVERT: C 99 MET cc_start: 0.6061 (mtt) cc_final: 0.5322 (tpp) REVERT: C 100 GLU cc_start: 0.7894 (mp0) cc_final: 0.7436 (pt0) REVERT: C 215 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8294 (mtt) REVERT: C 229 LEU cc_start: 0.7997 (mt) cc_final: 0.7616 (pp) REVERT: C 294 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: C 555 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6357 (t80) REVERT: D 99 MET cc_start: 0.6392 (mmt) cc_final: 0.6109 (mtt) REVERT: D 100 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: D 215 MET cc_start: 0.8452 (mtp) cc_final: 0.8220 (mtt) REVERT: D 229 LEU cc_start: 0.8036 (mt) cc_final: 0.7608 (pp) REVERT: D 294 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8327 (mt-10) outliers start: 98 outliers final: 41 residues processed: 299 average time/residue: 0.4394 time to fit residues: 153.7412 Evaluate side-chains 283 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** 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 = 0.4503 r_free = 0.4503 target = 0.209162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.176569 restraints weight = 28513.645| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.65 r_work: 0.3874 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20768 Z= 0.130 Angle : 0.616 11.964 28000 Z= 0.306 Chirality : 0.042 0.280 3116 Planarity : 0.005 0.047 3416 Dihedral : 12.875 90.317 3357 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.54 % Allowed : 18.27 % Favored : 78.20 % 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: -0.87 (0.18), residues: 2360 helix: 0.24 (0.14), residues: 1432 sheet: -2.34 (0.53), residues: 76 loop : -1.75 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 385 TYR 0.012 0.001 TYR C 524 PHE 0.012 0.001 PHE B 537 TRP 0.013 0.001 TRP A 268 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (20768) covalent geometry : angle 0.61574 / 0.31 (28000) hydrogen bonds : bond 0.04281 / 2.86 ( 949) hydrogen bonds : angle 3.80840 / 2.67 ( 2739) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 254 time to evaluate : 0.767 Fit side-chains REVERT: A 38 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6791 (mp) REVERT: A 99 MET cc_start: 0.7290 (mtt) cc_final: 0.6882 (mtt) REVERT: A 110 MET cc_start: 0.6743 (ttt) cc_final: 0.6498 (ptm) REVERT: A 222 TYR cc_start: 0.7223 (m-10) cc_final: 0.6985 (m-80) REVERT: A 263 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7212 (mtt90) REVERT: A 309 ASP cc_start: 0.8371 (p0) cc_final: 0.8076 (p0) REVERT: A 555 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6500 (t80) REVERT: A 634 GLU cc_start: 0.7330 (tt0) cc_final: 0.7024 (tt0) REVERT: B 29 TRP cc_start: 0.5947 (OUTLIER) cc_final: 0.5654 (m-90) REVERT: B 38 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6831 (mp) REVERT: B 96 MET cc_start: 0.7568 (mtp) cc_final: 0.7237 (mtp) REVERT: B 99 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.5925 (ppp) REVERT: B 229 LEU cc_start: 0.7943 (mt) cc_final: 0.7578 (pp) REVERT: B 294 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8309 (mt-10) REVERT: B 555 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6308 (t80) REVERT: C 99 MET cc_start: 0.6233 (mtt) cc_final: 0.5440 (tpp) REVERT: C 100 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7429 (pt0) REVERT: C 215 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8323 (mtt) REVERT: C 229 LEU cc_start: 0.7966 (mt) cc_final: 0.7636 (pp) REVERT: C 255 MET cc_start: 0.8296 (mmt) cc_final: 0.8041 (mpt) REVERT: C 555 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.6323 (t80) REVERT: D 29 TRP cc_start: 0.6003 (OUTLIER) cc_final: 0.5618 (m-90) REVERT: D 38 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6510 (mp) REVERT: D 45 TRP cc_start: 0.6149 (m-10) cc_final: 0.5851 (m100) REVERT: D 99 MET cc_start: 0.6459 (mmt) cc_final: 0.6158 (mtt) REVERT: D 100 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: D 229 LEU cc_start: 0.8020 (mt) cc_final: 0.7692 (pp) REVERT: D 294 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: D 555 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.6128 (t80) REVERT: D 634 GLU cc_start: 0.7364 (tt0) cc_final: 0.7030 (tt0) outliers start: 73 outliers final: 40 residues processed: 298 average time/residue: 0.4732 time to fit residues: 164.4679 Evaluate side-chains 296 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 241 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 63 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 chunk 174 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 157 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.211526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.178880 restraints weight = 28557.309| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.60 r_work: 0.3903 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20768 Z= 0.114 Angle : 0.605 12.985 28000 Z= 0.298 Chirality : 0.041 0.319 3116 Planarity : 0.004 0.046 3416 Dihedral : 12.166 86.090 3357 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.34 % Allowed : 19.19 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2360 helix: 0.57 (0.14), residues: 1424 sheet: -2.15 (0.53), residues: 76 loop : -1.49 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 385 TYR 0.014 0.001 TYR B 524 PHE 0.014 0.001 PHE B 434 TRP 0.013 0.001 TRP A 268 HIS 0.002 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (20768) covalent geometry : angle 0.60484 / 0.30 (28000) hydrogen bonds : bond 0.03962 / 2.65 ( 949) hydrogen bonds : angle 3.68147 / 2.57 ( 2739) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 276 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7314 (mtt) cc_final: 0.6855 (ttt) REVERT: A 229 LEU cc_start: 0.7954 (mt) cc_final: 0.7591 (pp) REVERT: A 555 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.6487 (t80) REVERT: A 569 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7691 (mp) REVERT: A 634 GLU cc_start: 0.7363 (tt0) cc_final: 0.7126 (tt0) REVERT: B 38 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6792 (mp) REVERT: B 99 MET cc_start: 0.7259 (mmt) cc_final: 0.6933 (mmt) REVERT: B 229 LEU cc_start: 0.7928 (mt) cc_final: 0.7614 (pp) REVERT: B 294 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: B 309 ASP cc_start: 0.8336 (p0) cc_final: 0.7742 (t0) REVERT: B 428 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7129 (mp) REVERT: B 555 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.6295 (t80) REVERT: B 634 GLU cc_start: 0.7314 (tt0) cc_final: 0.7084 (tt0) REVERT: C 51 LEU cc_start: 0.7353 (tm) cc_final: 0.6518 (mp) REVERT: C 99 MET cc_start: 0.6178 (mtt) cc_final: 0.5422 (tpp) REVERT: C 100 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7380 (pt0) REVERT: C 215 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8316 (mtt) REVERT: C 229 LEU cc_start: 0.7932 (mt) cc_final: 0.7675 (pp) REVERT: C 255 MET cc_start: 0.8304 (mmt) cc_final: 0.8045 (mpt) REVERT: C 428 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7157 (mp) REVERT: C 555 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.6342 (t80) REVERT: C 569 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7757 (mp) REVERT: D 29 TRP cc_start: 0.6022 (OUTLIER) cc_final: 0.5517 (m-90) REVERT: D 45 TRP cc_start: 0.6166 (m-10) cc_final: 0.5663 (m100) REVERT: D 99 MET cc_start: 0.6539 (mmt) cc_final: 0.6225 (mtt) REVERT: D 100 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: D 229 LEU cc_start: 0.7990 (mt) cc_final: 0.7693 (pp) REVERT: D 294 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: D 309 ASP cc_start: 0.8322 (p0) cc_final: 0.7757 (t0) REVERT: D 428 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7127 (mp) REVERT: D 555 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6128 (t80) REVERT: D 634 GLU cc_start: 0.7402 (tt0) cc_final: 0.7107 (tt0) outliers start: 69 outliers final: 35 residues processed: 324 average time/residue: 0.4897 time to fit residues: 185.4342 Evaluate side-chains 302 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 174 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.210770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.177571 restraints weight = 28434.141| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.56 r_work: 0.3889 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20768 Z= 0.129 Angle : 0.625 9.592 28000 Z= 0.308 Chirality : 0.043 0.278 3116 Planarity : 0.004 0.046 3416 Dihedral : 12.087 88.429 3357 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.57 % Allowed : 20.64 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2360 helix: 0.54 (0.14), residues: 1424 sheet: -2.06 (0.53), residues: 76 loop : -1.40 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 385 TYR 0.014 0.001 TYR B 524 PHE 0.013 0.001 PHE D 434 TRP 0.010 0.001 TRP A 268 HIS 0.003 0.001 HIS D 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (20768) covalent geometry : angle 0.62492 / 0.31 (28000) hydrogen bonds : bond 0.04150 / 2.77 ( 949) hydrogen bonds : angle 3.71786 / 2.60 ( 2739) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7379 (mtt) cc_final: 0.6896 (ttt) REVERT: A 215 MET cc_start: 0.8370 (mtt) cc_final: 0.7959 (mtp) REVERT: A 229 LEU cc_start: 0.7948 (mt) cc_final: 0.7644 (pp) REVERT: A 555 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6454 (t80) REVERT: A 634 GLU cc_start: 0.7348 (tt0) cc_final: 0.7067 (tt0) REVERT: B 38 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6794 (mp) REVERT: B 45 TRP cc_start: 0.6247 (m-10) cc_final: 0.5761 (m100) REVERT: B 99 MET cc_start: 0.7315 (mmt) cc_final: 0.6823 (mmt) REVERT: B 215 MET cc_start: 0.8376 (mtt) cc_final: 0.8094 (mtp) REVERT: B 229 LEU cc_start: 0.7924 (mt) cc_final: 0.7628 (pp) REVERT: B 294 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8321 (mt-10) REVERT: B 309 ASP cc_start: 0.8351 (p0) cc_final: 0.7757 (t0) REVERT: B 555 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.6276 (t80) REVERT: C 51 LEU cc_start: 0.7412 (tm) cc_final: 0.6587 (mp) REVERT: C 99 MET cc_start: 0.6150 (mtt) cc_final: 0.5386 (tpp) REVERT: C 100 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7375 (pt0) REVERT: C 110 MET cc_start: 0.7077 (ttt) cc_final: 0.6851 (ptm) REVERT: C 215 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8286 (mtt) REVERT: C 229 LEU cc_start: 0.7952 (mt) cc_final: 0.7697 (pp) REVERT: C 255 MET cc_start: 0.8336 (mmt) cc_final: 0.8084 (mpt) REVERT: C 428 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7173 (mp) REVERT: C 555 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6362 (t80) REVERT: D 45 TRP cc_start: 0.6182 (m-10) cc_final: 0.5869 (m100) REVERT: D 99 MET cc_start: 0.6642 (mmt) cc_final: 0.6349 (mtt) REVERT: D 100 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7228 (pt0) REVERT: D 229 LEU cc_start: 0.7977 (mt) cc_final: 0.7696 (pp) REVERT: D 294 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8316 (mt-10) REVERT: D 309 ASP cc_start: 0.8367 (p0) cc_final: 0.7779 (t0) REVERT: D 428 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7182 (mp) REVERT: D 555 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.6153 (t80) REVERT: D 634 GLU cc_start: 0.7397 (tt0) cc_final: 0.7073 (tt0) outliers start: 53 outliers final: 39 residues processed: 296 average time/residue: 0.4885 time to fit residues: 168.7726 Evaluate side-chains 301 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 196 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 chunk 63 optimal weight: 0.0070 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** 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 = 0.4514 r_free = 0.4514 target = 0.211528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.179251 restraints weight = 28823.884| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 3.32 r_work: 0.3888 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20768 Z= 0.130 Angle : 0.638 10.753 28000 Z= 0.311 Chirality : 0.043 0.314 3116 Planarity : 0.005 0.046 3416 Dihedral : 12.020 88.816 3357 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.37 % Allowed : 20.83 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2360 helix: 0.55 (0.14), residues: 1432 sheet: -2.03 (0.53), residues: 76 loop : -1.48 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.017 0.001 TYR A 349 PHE 0.015 0.001 PHE C 434 TRP 0.010 0.001 TRP A 268 HIS 0.003 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (20768) covalent geometry : angle 0.63766 / 0.31 (28000) hydrogen bonds : bond 0.04134 / 2.76 ( 949) hydrogen bonds : angle 3.74041 / 2.62 ( 2739) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7400 (mtt) cc_final: 0.6979 (mtt) REVERT: A 215 MET cc_start: 0.8434 (mtt) cc_final: 0.8024 (mtp) REVERT: A 229 LEU cc_start: 0.7946 (mt) cc_final: 0.7637 (pp) REVERT: A 260 MET cc_start: 0.7587 (tpp) cc_final: 0.7126 (tpp) REVERT: A 456 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6448 (t80) REVERT: A 555 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.6578 (t80) REVERT: A 569 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 634 GLU cc_start: 0.7387 (tt0) cc_final: 0.7097 (tt0) REVERT: B 38 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6779 (mp) REVERT: B 45 TRP cc_start: 0.6278 (m-10) cc_final: 0.5803 (m100) REVERT: B 99 MET cc_start: 0.7250 (mmt) cc_final: 0.6808 (mmt) REVERT: B 215 MET cc_start: 0.8415 (mtt) cc_final: 0.8115 (mtp) REVERT: B 229 LEU cc_start: 0.8014 (mt) cc_final: 0.7703 (pp) REVERT: B 294 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: B 309 ASP cc_start: 0.8416 (p0) cc_final: 0.7800 (t0) REVERT: B 428 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7144 (mp) REVERT: B 555 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6399 (t80) REVERT: C 45 TRP cc_start: 0.6143 (m-10) cc_final: 0.5793 (m100) REVERT: C 51 LEU cc_start: 0.7434 (tm) cc_final: 0.6645 (mp) REVERT: C 99 MET cc_start: 0.6225 (mtt) cc_final: 0.5503 (tpp) REVERT: C 100 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7384 (pt0) REVERT: C 215 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8335 (mtt) REVERT: C 229 LEU cc_start: 0.7959 (mt) cc_final: 0.7658 (pp) REVERT: C 255 MET cc_start: 0.8321 (mmt) cc_final: 0.8052 (mpt) REVERT: C 260 MET cc_start: 0.7631 (tpp) cc_final: 0.7281 (tpp) REVERT: C 428 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7125 (mp) REVERT: C 456 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6489 (t80) REVERT: C 555 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.6468 (t80) REVERT: D 45 TRP cc_start: 0.6179 (m-10) cc_final: 0.5647 (m100) REVERT: D 99 MET cc_start: 0.6624 (mmt) cc_final: 0.6373 (mtt) REVERT: D 100 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7256 (pt0) REVERT: D 229 LEU cc_start: 0.7964 (mt) cc_final: 0.7676 (pp) REVERT: D 260 MET cc_start: 0.7625 (tpp) cc_final: 0.7181 (tpp) REVERT: D 294 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: D 309 ASP cc_start: 0.8439 (p0) cc_final: 0.7812 (t0) REVERT: D 428 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7203 (mp) REVERT: D 555 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6182 (t80) REVERT: D 634 GLU cc_start: 0.7397 (tt0) cc_final: 0.7056 (tt0) outliers start: 49 outliers final: 34 residues processed: 289 average time/residue: 0.4736 time to fit residues: 160.2137 Evaluate side-chains 296 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 149 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 227 optimal weight: 0.3980 chunk 22 optimal weight: 7.9990 chunk 203 optimal weight: 0.0060 chunk 187 optimal weight: 7.9990 chunk 217 optimal weight: 0.0030 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** 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 = 0.4552 r_free = 0.4552 target = 0.214656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.183072 restraints weight = 28755.318| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.89 r_work: 0.3919 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20768 Z= 0.113 Angle : 0.621 15.791 28000 Z= 0.301 Chirality : 0.041 0.307 3116 Planarity : 0.004 0.046 3416 Dihedral : 11.465 89.649 3357 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.13 % Allowed : 21.41 % Favored : 76.45 % 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: -0.07 (0.18), residues: 2360 helix: 0.80 (0.14), residues: 1428 sheet: -1.78 (0.51), residues: 84 loop : -1.26 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.021 0.001 TYR C 349 PHE 0.012 0.001 PHE A 434 TRP 0.013 0.001 TRP A 268 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (20768) covalent geometry : angle 0.62086 / 0.30 (28000) hydrogen bonds : bond 0.03786 / 2.52 ( 949) hydrogen bonds : angle 3.63337 / 2.54 ( 2739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6996.39 seconds wall clock time: 119 minutes 54.52 seconds (7194.52 seconds total)