Starting phenix.real_space_refine on Sun Aug 24 15:13:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fob_29344/08_2025/8fob_29344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fob_29344/08_2025/8fob_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fob_29344/08_2025/8fob_29344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fob_29344/08_2025/8fob_29344.map" model { file = "/net/cci-nas-00/data/ceres_data/8fob_29344/08_2025/8fob_29344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fob_29344/08_2025/8fob_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 185 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: 185 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: 185 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: 185 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: 3.72, per 1000 atoms: 0.18 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: 1.28 Conformation dependent library (CDL) restraints added in 754.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.52 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: 3.15 Time building geometry restraints manager: 1.73 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: 12342 32.69 - 65.39: 661 65.39 - 98.08: 132 98.08 - 130.77: 49 130.77 - 163.46: 16 Dihedral angle restraints: 13200 sinusoidal: 6236 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 13197 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.070 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 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 : 21.836 163.463 8696 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 aren 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 covalent geometry : bond 0.02353 (20768) covalent geometry : angle 1.57219 (28000) hydrogen bonds : bond 0.30699 ( 949) hydrogen bonds : angle 9.09959 ( 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 : 0.671 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: 0.5071 time to fit residues: 271.5049 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 : 0.718 ------------------------------------------------------------------------------- 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: 1.9990 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: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 174 ASN B 206 GLN B 217 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 258 HIS B 267 GLN ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 174 ASN D 206 GLN D 217 ASN D 257 GLN D 258 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.207150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.173909 restraints weight = 28617.810| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.86 r_work: 0.3835 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20768 Z= 0.231 Angle : 0.780 7.233 28000 Z= 0.397 Chirality : 0.047 0.371 3116 Planarity : 0.007 0.054 3416 Dihedral : 17.052 146.440 4109 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.26 % Allowed : 12.60 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.16), residues: 2360 helix: -1.67 (0.12), residues: 1444 sheet: -2.86 (0.46), residues: 84 loop : -2.66 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 615 TYR 0.028 0.002 TYR D 547 PHE 0.028 0.002 PHE A 537 TRP 0.023 0.002 TRP A 268 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00526 (20768) covalent geometry : angle 0.78024 (28000) hydrogen bonds : bond 0.06403 ( 949) hydrogen bonds : angle 4.52211 ( 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: 88 poor density : 275 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.5842 (m-10) cc_final: 0.5467 (m-10) REVERT: A 99 MET cc_start: 0.6865 (mtt) cc_final: 0.6610 (ppp) REVERT: A 222 TYR cc_start: 0.7431 (m-10) cc_final: 0.7166 (m-80) REVERT: A 263 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7185 (mtt90) REVERT: A 309 ASP cc_start: 0.8367 (p0) cc_final: 0.8112 (p0) REVERT: B 96 MET cc_start: 0.7967 (mtm) cc_final: 0.7664 (mmp) REVERT: B 110 MET cc_start: 0.6348 (ttm) cc_final: 0.5696 (ttt) REVERT: B 222 TYR cc_start: 0.7380 (m-10) cc_final: 0.7169 (m-80) REVERT: B 294 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 485 MET cc_start: 0.8908 (mtt) cc_final: 0.8612 (mtt) REVERT: C 33 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5648 (ttt-90) REVERT: C 74 GLN cc_start: 0.6129 (tp-100) cc_final: 0.5371 (pm20) REVERT: C 110 MET cc_start: 0.6377 (ttm) cc_final: 0.5752 (ttt) REVERT: C 222 TYR cc_start: 0.7195 (m-10) cc_final: 0.6992 (m-80) REVERT: C 263 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7236 (mtt90) REVERT: D 96 MET cc_start: 0.7851 (mtm) cc_final: 0.7558 (mtp) REVERT: D 110 MET cc_start: 0.6329 (ttm) cc_final: 0.6126 (ttt) REVERT: D 294 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8240 (mt-10) REVERT: D 309 ASP cc_start: 0.8530 (p0) cc_final: 0.8199 (p0) REVERT: D 550 ASP cc_start: 0.6544 (m-30) cc_final: 0.6256 (t0) outliers start: 88 outliers final: 24 residues processed: 337 average time/residue: 0.4539 time to fit residues: 176.4759 Evaluate side-chains 275 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 177 GLU 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 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 203 LEU 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 Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 99 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 80 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.210249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.176826 restraints weight = 28620.005| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.66 r_work: 0.3890 rms_B_bonded: 3.38 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 = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20768 Z= 0.130 Angle : 0.627 9.449 28000 Z= 0.317 Chirality : 0.042 0.298 3116 Planarity : 0.005 0.047 3416 Dihedral : 14.707 116.563 4109 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.05 % Allowed : 15.70 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.17), residues: 2360 helix: -0.51 (0.13), residues: 1468 sheet: -2.66 (0.47), residues: 84 loop : -2.33 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 615 TYR 0.017 0.001 TYR A 547 PHE 0.016 0.002 PHE D 456 TRP 0.017 0.001 TRP A 268 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00279 (20768) covalent geometry : angle 0.62701 (28000) hydrogen bonds : bond 0.04775 ( 949) hydrogen bonds : angle 3.96334 ( 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: 63 poor density : 288 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6829 (mp) REVERT: A 45 TRP cc_start: 0.5854 (m-10) cc_final: 0.5510 (m-10) REVERT: A 99 MET cc_start: 0.6995 (mtt) cc_final: 0.6574 (ppp) REVERT: A 215 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8055 (mtt) REVERT: A 222 TYR cc_start: 0.7311 (m-10) cc_final: 0.7083 (m-80) REVERT: A 263 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7102 (mtt90) REVERT: A 435 MET cc_start: 0.6713 (mmm) cc_final: 0.6030 (mmm) REVERT: B 51 LEU cc_start: 0.7366 (tm) cc_final: 0.6536 (mp) REVERT: B 96 MET cc_start: 0.7918 (mtm) cc_final: 0.7581 (mmp) REVERT: B 99 MET cc_start: 0.7271 (mmt) cc_final: 0.6135 (ppp) REVERT: B 110 MET cc_start: 0.6454 (ttm) cc_final: 0.5964 (ttt) REVERT: B 215 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8212 (mtt) REVERT: B 222 TYR cc_start: 0.7336 (m-10) cc_final: 0.7105 (m-80) REVERT: B 294 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8155 (mt-10) REVERT: B 435 MET cc_start: 0.7092 (tpp) cc_final: 0.6095 (mmm) REVERT: C 33 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.5545 (ttt-90) REVERT: C 99 MET cc_start: 0.6471 (mmt) cc_final: 0.6138 (mmt) REVERT: C 110 MET cc_start: 0.6519 (ttm) cc_final: 0.6081 (ttt) REVERT: C 115 TYR cc_start: 0.5665 (m-10) cc_final: 0.5405 (m-80) REVERT: C 215 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8348 (mtt) REVERT: C 222 TYR cc_start: 0.7221 (m-10) cc_final: 0.6933 (m-80) REVERT: C 634 GLU cc_start: 0.7297 (tt0) cc_final: 0.7051 (tt0) REVERT: D 38 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6617 (mp) REVERT: D 96 MET cc_start: 0.7869 (mtm) cc_final: 0.7611 (mmp) REVERT: D 99 MET cc_start: 0.6198 (mmt) cc_final: 0.5980 (mmt) REVERT: D 100 GLU cc_start: 0.7801 (mp0) cc_final: 0.7226 (pt0) REVERT: D 294 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8206 (mt-10) REVERT: D 435 MET cc_start: 0.6519 (mmm) cc_final: 0.6257 (mmm) REVERT: D 634 GLU cc_start: 0.7310 (tt0) cc_final: 0.6959 (tt0) outliers start: 63 outliers final: 20 residues processed: 327 average time/residue: 0.4802 time to fit residues: 179.7983 Evaluate side-chains 274 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain B residue 215 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 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 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 D residue 38 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 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: 0.7980 chunk 17 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 181 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.205238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.171164 restraints weight = 28845.468| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.86 r_work: 0.3817 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20768 Z= 0.264 Angle : 0.756 10.159 28000 Z= 0.379 Chirality : 0.049 0.376 3116 Planarity : 0.006 0.055 3416 Dihedral : 15.118 126.521 4109 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 5.18 % Allowed : 15.26 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.17), residues: 2360 helix: -0.51 (0.14), residues: 1416 sheet: -2.54 (0.49), residues: 84 loop : -2.39 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 615 TYR 0.022 0.002 TYR C 547 PHE 0.022 0.002 PHE A 537 TRP 0.013 0.002 TRP A 268 HIS 0.005 0.002 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00612 (20768) covalent geometry : angle 0.75631 (28000) hydrogen bonds : bond 0.05599 ( 949) hydrogen bonds : angle 4.34709 ( 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 356 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 249 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6717 (mp) REVERT: A 45 TRP cc_start: 0.5876 (m-10) cc_final: 0.5639 (m-10) REVERT: A 99 MET cc_start: 0.7115 (mtt) cc_final: 0.6456 (ppp) REVERT: A 110 MET cc_start: 0.6406 (ttt) cc_final: 0.6156 (ttt) REVERT: A 222 TYR cc_start: 0.7335 (m-10) cc_final: 0.7114 (m-80) REVERT: A 263 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7290 (mtt90) REVERT: B 38 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6917 (mp) REVERT: B 51 LEU cc_start: 0.7365 (tm) cc_final: 0.6491 (mp) REVERT: B 96 MET cc_start: 0.7868 (mtm) cc_final: 0.7515 (mmp) REVERT: B 99 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6243 (ppp) REVERT: B 110 MET cc_start: 0.6335 (ttm) cc_final: 0.5918 (ttt) REVERT: B 115 TYR cc_start: 0.6013 (m-10) cc_final: 0.5797 (m-80) REVERT: B 222 TYR cc_start: 0.7297 (m-10) cc_final: 0.7075 (m-80) REVERT: B 435 MET cc_start: 0.7108 (tpp) cc_final: 0.6217 (mmm) REVERT: B 555 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.6360 (t80) REVERT: C 33 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5726 (ttt-90) REVERT: C 51 LEU cc_start: 0.7494 (tm) cc_final: 0.6577 (mp) REVERT: C 99 MET cc_start: 0.6495 (mmt) cc_final: 0.6218 (mmt) REVERT: C 100 GLU cc_start: 0.7843 (mp0) cc_final: 0.7330 (pt0) REVERT: C 110 MET cc_start: 0.6417 (ttm) cc_final: 0.5981 (ttt) REVERT: C 115 TYR cc_start: 0.5758 (m-10) cc_final: 0.5542 (m-80) REVERT: C 215 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8365 (mtt) REVERT: C 294 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8489 (mt-10) REVERT: C 555 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6380 (t80) REVERT: D 96 MET cc_start: 0.7880 (mtm) cc_final: 0.7600 (mtp) REVERT: D 99 MET cc_start: 0.6265 (mmt) cc_final: 0.6011 (mmt) REVERT: D 625 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6195 (mm) REVERT: D 636 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7075 (ttp-170) outliers start: 107 outliers final: 38 residues processed: 320 average time/residue: 0.5548 time to fit residues: 205.5018 Evaluate side-chains 276 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 360 THR 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 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 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 506 SER 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 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 322 LYS 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 506 SER Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 591 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 625 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: 5.9990 chunk 91 optimal weight: 0.0000 chunk 88 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 129 optimal weight: 40.0000 chunk 229 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 217 ASN A 267 GLN C 267 GLN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.208142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.175032 restraints weight = 28548.833| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.67 r_work: 0.3862 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3864 r_free = 0.3864 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3864 r_free = 0.3864 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20768 Z= 0.141 Angle : 0.624 7.080 28000 Z= 0.314 Chirality : 0.042 0.293 3116 Planarity : 0.005 0.049 3416 Dihedral : 14.116 108.676 4109 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.12 % Allowed : 17.15 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.17), residues: 2360 helix: -0.10 (0.14), residues: 1444 sheet: -2.41 (0.50), residues: 84 loop : -2.08 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 385 TYR 0.016 0.001 TYR C 524 PHE 0.015 0.001 PHE C 456 TRP 0.015 0.001 TRP A 268 HIS 0.003 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00319 (20768) covalent geometry : angle 0.62398 (28000) hydrogen bonds : bond 0.04550 ( 949) hydrogen bonds : angle 3.92963 ( 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 328 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 243 time to evaluate : 0.840 Fit side-chains REVERT: A 38 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6779 (mp) REVERT: A 45 TRP cc_start: 0.5855 (m-10) cc_final: 0.5622 (m-10) REVERT: A 99 MET cc_start: 0.7256 (mtt) cc_final: 0.6308 (tmm) REVERT: A 222 TYR cc_start: 0.7236 (m-10) cc_final: 0.6978 (m-80) REVERT: A 263 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7252 (mtt90) REVERT: A 435 MET cc_start: 0.6438 (mmm) cc_final: 0.6127 (mmm) REVERT: B 38 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6682 (mp) REVERT: B 51 LEU cc_start: 0.7367 (tm) cc_final: 0.6521 (mp) REVERT: B 96 MET cc_start: 0.7870 (mtm) cc_final: 0.7511 (mmp) REVERT: B 99 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6187 (ppp) REVERT: B 110 MET cc_start: 0.6370 (ttm) cc_final: 0.6075 (ttt) REVERT: B 215 MET cc_start: 0.8455 (mtp) cc_final: 0.8249 (mtt) REVERT: B 222 TYR cc_start: 0.7268 (m-10) cc_final: 0.7049 (m-80) REVERT: B 294 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: B 435 MET cc_start: 0.6959 (tpp) cc_final: 0.6171 (mmm) REVERT: B 555 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.6280 (t80) REVERT: C 51 LEU cc_start: 0.7453 (tm) cc_final: 0.6609 (mp) REVERT: C 100 GLU cc_start: 0.7830 (mp0) cc_final: 0.7269 (pt0) REVERT: C 110 MET cc_start: 0.6556 (ttm) cc_final: 0.6187 (ttt) REVERT: C 215 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8355 (mtt) REVERT: C 229 LEU cc_start: 0.8053 (mt) cc_final: 0.7630 (pp) REVERT: C 555 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.6285 (t80) REVERT: D 99 MET cc_start: 0.6263 (mmt) cc_final: 0.5999 (mmt) REVERT: D 229 LEU cc_start: 0.8059 (mt) cc_final: 0.7604 (pp) REVERT: D 294 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: D 435 MET cc_start: 0.6474 (mmm) cc_final: 0.6201 (mmm) REVERT: D 625 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6277 (mm) outliers start: 85 outliers final: 35 residues processed: 303 average time/residue: 0.5593 time to fit residues: 196.3211 Evaluate side-chains 274 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 360 THR 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 99 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU 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 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 322 LYS 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 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU 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 625 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 202 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 229 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 21 optimal weight: 0.0030 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 GLN ** C 365 ASN ** 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 = 0.209021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.175784 restraints weight = 28464.034| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.59 r_work: 0.3871 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 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 = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3935 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= 0.128 Angle : 0.605 8.653 28000 Z= 0.303 Chirality : 0.042 0.279 3116 Planarity : 0.004 0.048 3416 Dihedral : 13.444 94.533 4109 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.92 % Allowed : 17.54 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.18), residues: 2360 helix: 0.24 (0.14), residues: 1436 sheet: -2.42 (0.52), residues: 76 loop : -1.84 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 615 TYR 0.013 0.001 TYR B 547 PHE 0.014 0.001 PHE A 456 TRP 0.013 0.001 TRP A 268 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00285 (20768) covalent geometry : angle 0.60512 (28000) hydrogen bonds : bond 0.04258 ( 949) hydrogen bonds : angle 3.76874 ( 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 320 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 239 time to evaluate : 0.920 Fit side-chains REVERT: A 38 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6792 (mp) REVERT: A 99 MET cc_start: 0.7233 (mtt) cc_final: 0.6864 (mtt) REVERT: A 222 TYR cc_start: 0.7235 (m-10) cc_final: 0.6975 (m-80) REVERT: A 263 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7198 (mtt90) REVERT: A 555 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.6258 (t80) REVERT: B 38 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6716 (mp) REVERT: B 51 LEU cc_start: 0.7412 (tm) cc_final: 0.6574 (mp) REVERT: B 96 MET cc_start: 0.7826 (mtm) cc_final: 0.7533 (mmt) REVERT: B 99 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6074 (ppp) REVERT: B 229 LEU cc_start: 0.7957 (mt) cc_final: 0.7568 (pp) REVERT: B 294 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: B 435 MET cc_start: 0.6902 (tpp) cc_final: 0.5954 (mmm) REVERT: B 555 TYR cc_start: 0.6680 (OUTLIER) cc_final: 0.6303 (t80) REVERT: C 51 LEU cc_start: 0.7442 (tm) cc_final: 0.6573 (mp) REVERT: C 99 MET cc_start: 0.6213 (mtt) cc_final: 0.5440 (tpp) REVERT: C 100 GLU cc_start: 0.7896 (mp0) cc_final: 0.7429 (pt0) REVERT: C 110 MET cc_start: 0.6585 (ttm) cc_final: 0.6356 (ttt) REVERT: C 215 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8352 (mtt) REVERT: C 229 LEU cc_start: 0.7965 (mt) cc_final: 0.7611 (pp) REVERT: C 294 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: C 555 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.6336 (t80) REVERT: D 38 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6613 (mp) REVERT: D 45 TRP cc_start: 0.6148 (m-10) cc_final: 0.5850 (m100) REVERT: D 99 MET cc_start: 0.6470 (mmt) cc_final: 0.6269 (mtt) REVERT: D 100 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7150 (pt0) REVERT: D 229 LEU cc_start: 0.8021 (mt) cc_final: 0.7599 (pp) REVERT: D 435 MET cc_start: 0.6518 (mmm) cc_final: 0.6132 (mmm) REVERT: D 555 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6212 (t80) outliers start: 81 outliers final: 34 residues processed: 298 average time/residue: 0.5394 time to fit residues: 186.7681 Evaluate side-chains 282 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 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 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 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 569 LEU Chi-restraints excluded: chain C residue 591 GLU 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 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 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: 0.7980 chunk 85 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 0.0970 chunk 143 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 365 ASN ** 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 = 0.4524 r_free = 0.4524 target = 0.211250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.178324 restraints weight = 28424.168| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.59 r_work: 0.3899 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3902 r_free = 0.3902 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 = 0.3902 r_free = 0.3902 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20768 Z= 0.111 Angle : 0.585 8.705 28000 Z= 0.291 Chirality : 0.040 0.268 3116 Planarity : 0.004 0.046 3416 Dihedral : 12.776 86.855 4109 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.29 % Allowed : 18.75 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.18), residues: 2360 helix: 0.52 (0.14), residues: 1436 sheet: -2.27 (0.53), residues: 76 loop : -1.64 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 615 TYR 0.016 0.001 TYR C 524 PHE 0.012 0.001 PHE D 523 TRP 0.013 0.001 TRP A 268 HIS 0.002 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00236 (20768) covalent geometry : angle 0.58507 (28000) hydrogen bonds : bond 0.03944 ( 949) hydrogen bonds : angle 3.64014 ( 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 334 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 266 time to evaluate : 0.800 Fit side-chains REVERT: A 38 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6758 (mp) REVERT: A 99 MET cc_start: 0.7286 (mtt) cc_final: 0.6839 (ttt) REVERT: A 110 MET cc_start: 0.6991 (ttt) cc_final: 0.6719 (ptm) REVERT: A 222 TYR cc_start: 0.7219 (m-10) cc_final: 0.6987 (m-80) REVERT: A 263 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7426 (mtt90) REVERT: A 309 ASP cc_start: 0.8331 (p0) cc_final: 0.7703 (t0) REVERT: A 555 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.6259 (t80) REVERT: A 634 GLU cc_start: 0.7285 (tt0) cc_final: 0.6984 (tt0) REVERT: B 38 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6806 (mp) REVERT: B 51 LEU cc_start: 0.7446 (tm) cc_final: 0.6648 (mp) REVERT: B 96 MET cc_start: 0.7827 (mtm) cc_final: 0.7554 (mmt) REVERT: B 99 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.5998 (ppp) REVERT: B 229 LEU cc_start: 0.7947 (mt) cc_final: 0.7594 (pp) REVERT: B 359 ARG cc_start: 0.6134 (OUTLIER) cc_final: 0.5918 (mpt-90) REVERT: B 435 MET cc_start: 0.6944 (tpp) cc_final: 0.5948 (mmm) REVERT: B 555 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6288 (t80) REVERT: C 51 LEU cc_start: 0.7413 (tm) cc_final: 0.6564 (mp) REVERT: C 74 GLN cc_start: 0.6338 (mm-40) cc_final: 0.5569 (pm20) REVERT: C 100 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7387 (pt0) REVERT: C 215 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8315 (mtt) REVERT: C 229 LEU cc_start: 0.7926 (mt) cc_final: 0.7614 (pp) REVERT: C 555 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.6346 (t80) REVERT: D 45 TRP cc_start: 0.6167 (m-10) cc_final: 0.5840 (m100) REVERT: D 99 MET cc_start: 0.6473 (mmt) cc_final: 0.6266 (mtt) REVERT: D 100 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7111 (pt0) REVERT: D 229 LEU cc_start: 0.7989 (mt) cc_final: 0.7687 (pp) REVERT: D 309 ASP cc_start: 0.8329 (p0) cc_final: 0.7775 (t0) REVERT: D 435 MET cc_start: 0.6310 (mmm) cc_final: 0.6019 (mmm) REVERT: D 555 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.6091 (t80) REVERT: D 634 GLU cc_start: 0.7379 (tt0) cc_final: 0.7106 (tt0) outliers start: 68 outliers final: 34 residues processed: 312 average time/residue: 0.5263 time to fit residues: 191.3490 Evaluate side-chains 294 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP 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 397 ILE 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 603 MET 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 311 THR Chi-restraints excluded: chain B residue 359 ARG 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 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 203 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 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain D residue 85 ILE 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 555 TYR Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** C 365 ASN ** 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 = 0.4501 r_free = 0.4501 target = 0.208952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.175323 restraints weight = 28435.827| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.57 r_work: 0.3870 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3871 r_free = 0.3871 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 = 0.3871 r_free = 0.3871 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20768 Z= 0.155 Angle : 0.643 9.775 28000 Z= 0.318 Chirality : 0.044 0.306 3116 Planarity : 0.005 0.048 3416 Dihedral : 12.927 86.571 4109 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.44 % Allowed : 19.19 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.18), residues: 2360 helix: 0.31 (0.14), residues: 1444 sheet: -2.07 (0.51), residues: 84 loop : -1.75 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 385 TYR 0.015 0.002 TYR B 547 PHE 0.016 0.002 PHE A 537 TRP 0.009 0.001 TRP A 268 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00354 (20768) covalent geometry : angle 0.64346 (28000) hydrogen bonds : bond 0.04458 ( 949) hydrogen bonds : angle 3.82002 ( 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 328 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 257 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6767 (mp) REVERT: A 99 MET cc_start: 0.7280 (mtt) cc_final: 0.6840 (ttt) REVERT: A 222 TYR cc_start: 0.7236 (m-10) cc_final: 0.6986 (m-80) REVERT: A 229 LEU cc_start: 0.7960 (mt) cc_final: 0.7580 (pp) REVERT: A 263 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7247 (mtt90) REVERT: A 309 ASP cc_start: 0.8370 (p0) cc_final: 0.7767 (t0) REVERT: A 555 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.6256 (t80) REVERT: B 38 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6816 (mp) REVERT: B 99 MET cc_start: 0.7209 (mmt) cc_final: 0.6655 (mmt) REVERT: B 229 LEU cc_start: 0.7923 (mt) cc_final: 0.7605 (pp) REVERT: B 294 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8360 (mt-10) REVERT: B 555 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.6342 (t80) REVERT: C 100 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7457 (pt0) REVERT: C 215 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8316 (mtt) REVERT: C 229 LEU cc_start: 0.7936 (mt) cc_final: 0.7685 (pp) REVERT: C 294 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: C 555 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.6338 (t80) REVERT: D 99 MET cc_start: 0.6488 (mmt) cc_final: 0.6267 (mtt) REVERT: D 100 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7025 (pt0) REVERT: D 229 LEU cc_start: 0.7957 (mt) cc_final: 0.7707 (pp) REVERT: D 290 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8369 (mm-40) REVERT: D 309 ASP cc_start: 0.8391 (p0) cc_final: 0.7793 (t0) REVERT: D 555 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.6155 (t80) outliers start: 71 outliers final: 34 residues processed: 304 average time/residue: 0.5145 time to fit residues: 182.5431 Evaluate side-chains 292 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 452 VAL 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 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 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 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 235 VAL 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 569 LEU Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 174 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** 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 = 0.4489 r_free = 0.4489 target = 0.208765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.169598 restraints weight = 28498.517| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.46 r_work: 0.3890 rms_B_bonded: 3.24 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 = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20768 Z= 0.160 Angle : 0.663 9.927 28000 Z= 0.324 Chirality : 0.044 0.301 3116 Planarity : 0.005 0.046 3416 Dihedral : 12.876 89.671 4109 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.86 % Allowed : 20.16 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.18), residues: 2360 helix: 0.24 (0.14), residues: 1432 sheet: -2.08 (0.51), residues: 84 loop : -1.67 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 615 TYR 0.015 0.002 TYR B 547 PHE 0.015 0.002 PHE D 537 TRP 0.009 0.001 TRP B 268 HIS 0.003 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00366 (20768) covalent geometry : angle 0.66312 (28000) hydrogen bonds : bond 0.04496 ( 949) hydrogen bonds : angle 3.86487 ( 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 317 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6685 (mp) REVERT: A 99 MET cc_start: 0.7354 (mtt) cc_final: 0.6956 (mtt) REVERT: A 215 MET cc_start: 0.8508 (mtt) cc_final: 0.7830 (ptm) REVERT: A 222 TYR cc_start: 0.7252 (m-10) cc_final: 0.7005 (m-80) REVERT: A 229 LEU cc_start: 0.7942 (mt) cc_final: 0.7573 (pp) REVERT: A 263 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7253 (mtt90) REVERT: A 555 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.6308 (t80) REVERT: B 38 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6730 (mp) REVERT: B 45 TRP cc_start: 0.6277 (m-10) cc_final: 0.5817 (m100) REVERT: B 96 MET cc_start: 0.7265 (mmt) cc_final: 0.7037 (mmm) REVERT: B 99 MET cc_start: 0.7223 (mmt) cc_final: 0.6838 (mmt) REVERT: B 229 LEU cc_start: 0.7953 (mt) cc_final: 0.7637 (pp) REVERT: B 359 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.5938 (mpt-90) REVERT: B 555 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6374 (t80) REVERT: C 45 TRP cc_start: 0.6153 (m-10) cc_final: 0.5825 (m100) REVERT: C 51 LEU cc_start: 0.7423 (tm) cc_final: 0.6638 (mp) REVERT: C 100 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7433 (pt0) REVERT: C 215 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: C 229 LEU cc_start: 0.7969 (mt) cc_final: 0.7687 (pp) REVERT: C 294 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: C 555 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6432 (t80) REVERT: D 45 TRP cc_start: 0.6132 (m-10) cc_final: 0.5636 (m100) REVERT: D 99 MET cc_start: 0.6569 (mmt) cc_final: 0.6342 (mtt) REVERT: D 100 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7074 (pt0) REVERT: D 229 LEU cc_start: 0.8008 (mt) cc_final: 0.7696 (pp) REVERT: D 290 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8213 (mm-40) REVERT: D 309 ASP cc_start: 0.8382 (p0) cc_final: 0.7722 (t0) REVERT: D 555 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.6210 (t80) outliers start: 59 outliers final: 37 residues processed: 297 average time/residue: 0.5177 time to fit residues: 179.1893 Evaluate side-chains 300 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 311 THR Chi-restraints excluded: chain B residue 359 ARG 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 481 MET 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 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 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 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 235 VAL 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 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: 9.9990 chunk 148 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** 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 = 0.4509 r_free = 0.4509 target = 0.210912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.178349 restraints weight = 28713.411| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 3.30 r_work: 0.3888 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 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 = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4442 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= 0.124 Angle : 0.631 9.923 28000 Z= 0.308 Chirality : 0.042 0.269 3116 Planarity : 0.004 0.048 3416 Dihedral : 12.488 86.936 4109 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.42 % Allowed : 20.64 % Favored : 76.94 % 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 aren not related in a simple way. whole: -0.44 (0.18), residues: 2360 helix: 0.53 (0.14), residues: 1424 sheet: -1.96 (0.52), residues: 84 loop : -1.47 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 615 TYR 0.016 0.001 TYR A 349 PHE 0.014 0.001 PHE A 434 TRP 0.012 0.001 TRP A 268 HIS 0.002 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00275 (20768) covalent geometry : angle 0.63141 (28000) hydrogen bonds : bond 0.04115 ( 949) hydrogen bonds : angle 3.71637 ( 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 315 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7372 (mtt) cc_final: 0.6975 (mtt) REVERT: A 229 LEU cc_start: 0.7905 (mt) cc_final: 0.7616 (pp) REVERT: A 555 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6416 (t80) REVERT: A 634 GLU cc_start: 0.7326 (tt0) cc_final: 0.7019 (tt0) REVERT: B 38 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6766 (mp) REVERT: B 45 TRP cc_start: 0.6260 (m-10) cc_final: 0.5893 (m100) REVERT: B 51 LEU cc_start: 0.7340 (tm) cc_final: 0.6550 (mp) REVERT: B 99 MET cc_start: 0.7153 (mmt) cc_final: 0.6882 (mmt) REVERT: B 229 LEU cc_start: 0.7974 (mt) cc_final: 0.7648 (pp) REVERT: B 555 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6409 (t80) REVERT: C 45 TRP cc_start: 0.6152 (m-10) cc_final: 0.5788 (m100) REVERT: C 51 LEU cc_start: 0.7399 (tm) cc_final: 0.6601 (mp) REVERT: C 99 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5773 (mmt) REVERT: C 100 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7398 (pt0) REVERT: C 215 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8387 (mtt) REVERT: C 229 LEU cc_start: 0.7944 (mt) cc_final: 0.7643 (pp) REVERT: C 294 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: C 435 MET cc_start: 0.6630 (ttm) cc_final: 0.6368 (ttm) REVERT: C 555 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6445 (t80) REVERT: D 45 TRP cc_start: 0.6161 (m-10) cc_final: 0.5667 (m100) REVERT: D 99 MET cc_start: 0.6548 (mmt) cc_final: 0.6336 (mtt) REVERT: D 100 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7056 (pt0) REVERT: D 215 MET cc_start: 0.8365 (mtt) cc_final: 0.8142 (mtp) REVERT: D 229 LEU cc_start: 0.7968 (mt) cc_final: 0.7682 (pp) REVERT: D 290 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8196 (mm-40) REVERT: D 309 ASP cc_start: 0.8390 (p0) cc_final: 0.7806 (t0) REVERT: D 555 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.6173 (t80) REVERT: D 634 GLU cc_start: 0.7393 (tt0) cc_final: 0.7077 (tt0) outliers start: 50 outliers final: 32 residues processed: 298 average time/residue: 0.4830 time to fit residues: 166.4426 Evaluate side-chains 293 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 397 ILE 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 235 VAL 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 99 MET 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 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 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 235 VAL 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 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: 0.8980 chunk 82 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 20 optimal weight: 0.0870 chunk 227 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 203 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** 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 84 HIS 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 = 0.212096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.179215 restraints weight = 28701.634| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 3.22 r_work: 0.3901 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 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 = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20768 Z= 0.121 Angle : 0.634 12.461 28000 Z= 0.308 Chirality : 0.042 0.270 3116 Planarity : 0.005 0.046 3416 Dihedral : 12.209 88.533 4109 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.13 % Allowed : 21.27 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.18), residues: 2360 helix: 0.66 (0.14), residues: 1424 sheet: -1.90 (0.52), residues: 84 loop : -1.36 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.018 0.001 TYR B 349 PHE 0.018 0.001 PHE B 434 TRP 0.011 0.001 TRP A 268 HIS 0.002 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00267 (20768) covalent geometry : angle 0.63403 (28000) hydrogen bonds : bond 0.04003 ( 949) hydrogen bonds : angle 3.68924 ( 2739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7140.61 seconds wall clock time: 122 minutes 27.07 seconds (7347.07 seconds total)