Starting phenix.real_space_refine on Wed Jun 18 06:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fob_29344/06_2025/8fob_29344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fob_29344/06_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_29344/06_2025/8fob_29344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fob_29344/06_2025/8fob_29344.map" model { file = "/net/cci-nas-00/data/ceres_data/8fob_29344/06_2025/8fob_29344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fob_29344/06_2025/8fob_29344.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} 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: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} 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: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} 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-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, '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: 12.40, per 1000 atoms: 0.61 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: 4.73 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.19 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: 6.50 Time building geometry restraints manager: 5.67 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 45.030 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.003 TRP B 629 HIS 0.014 0.003 HIS C 426 PHE 0.023 0.003 PHE D 508 TYR 0.044 0.003 TYR B 547 ARG 0.011 0.001 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.30699 ( 949) hydrogen bonds : angle 9.09959 ( 2739) covalent geometry : bond 0.02353 (20768) covalent geometry : angle 1.57219 (28000) *********************** 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 : 2.067 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: 1.3229 time to fit residues: 709.2388 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 : 2.339 ------------------------------------------------------------------------------- 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 199 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 174 ASN A 206 GLN A 217 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 37 ASN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 174 ASN C 206 GLN C 217 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 258 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.207641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.174376 restraints weight = 28562.701| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.60 r_work: 0.3857 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20768 Z= 0.211 Angle : 0.766 7.173 28000 Z= 0.391 Chirality : 0.047 0.308 3116 Planarity : 0.006 0.052 3416 Dihedral : 17.294 148.027 4109 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.22 % Allowed : 12.45 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.16), residues: 2360 helix: -1.60 (0.12), residues: 1444 sheet: -2.63 (0.55), residues: 68 loop : -2.67 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 268 HIS 0.004 0.001 HIS B 426 PHE 0.026 0.002 PHE A 537 TYR 0.027 0.002 TYR D 547 ARG 0.007 0.001 ARG B 615 Details of bonding type rmsd hydrogen bonds : bond 0.06555 ( 949) hydrogen bonds : angle 4.54363 ( 2739) covalent geometry : bond 0.00477 (20768) covalent geometry : angle 0.76562 (28000) *********************** 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 365 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 278 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.5855 (m-10) cc_final: 0.5474 (m-10) REVERT: A 99 MET cc_start: 0.6874 (mtt) cc_final: 0.6619 (ppp) REVERT: A 215 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7892 (ttm) REVERT: A 222 TYR cc_start: 0.7457 (m-10) cc_final: 0.7203 (m-80) REVERT: A 263 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7152 (mtt90) REVERT: B 96 MET cc_start: 0.7958 (mtm) cc_final: 0.7670 (mmp) REVERT: B 110 MET cc_start: 0.6420 (ttm) cc_final: 0.5808 (ttt) REVERT: B 215 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7955 (ttm) REVERT: B 222 TYR cc_start: 0.7377 (m-10) cc_final: 0.7129 (m-80) REVERT: B 294 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8154 (mt-10) REVERT: B 485 MET cc_start: 0.8898 (mtt) cc_final: 0.8602 (mtt) REVERT: C 74 GLN cc_start: 0.6128 (tp-100) cc_final: 0.5388 (pm20) REVERT: C 110 MET cc_start: 0.6429 (ttm) cc_final: 0.5791 (ttt) REVERT: C 263 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7233 (mtt90) REVERT: D 74 GLN cc_start: 0.6222 (tp-100) cc_final: 0.5659 (pm20) REVERT: D 96 MET cc_start: 0.7864 (mtm) cc_final: 0.7578 (mtp) REVERT: D 110 MET cc_start: 0.6373 (ttm) cc_final: 0.5941 (ttt) REVERT: D 115 TYR cc_start: 0.5843 (m-10) cc_final: 0.5617 (m-80) REVERT: D 222 TYR cc_start: 0.7315 (m-10) cc_final: 0.7106 (m-80) REVERT: D 263 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7068 (mtt90) REVERT: D 294 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8191 (mt-10) REVERT: D 309 ASP cc_start: 0.8504 (p0) cc_final: 0.8165 (p0) REVERT: D 345 MET cc_start: 0.6491 (tpp) cc_final: 0.6281 (mmt) REVERT: D 550 ASP cc_start: 0.6443 (m-30) cc_final: 0.6212 (t0) outliers start: 87 outliers final: 24 residues processed: 341 average time/residue: 1.0904 time to fit residues: 429.1354 Evaluate side-chains 279 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL 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 506 SER 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 506 SER Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 130 MET 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 C residue 591 GLU 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 263 ARG 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 94 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN C 217 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.210216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.177522 restraints weight = 28402.186| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.65 r_work: 0.3891 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20768 Z= 0.133 Angle : 0.630 8.588 28000 Z= 0.318 Chirality : 0.041 0.297 3116 Planarity : 0.005 0.047 3416 Dihedral : 14.858 117.569 4109 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.10 % Allowed : 15.21 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.17), residues: 2360 helix: -0.59 (0.13), residues: 1484 sheet: -2.65 (0.48), residues: 84 loop : -2.40 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 268 HIS 0.003 0.001 HIS A 122 PHE 0.015 0.002 PHE D 456 TYR 0.017 0.001 TYR A 547 ARG 0.006 0.000 ARG A 615 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 949) hydrogen bonds : angle 3.97702 ( 2739) covalent geometry : bond 0.00287 (20768) covalent geometry : angle 0.62986 (28000) *********************** 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: 64 poor density : 287 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6860 (mp) REVERT: A 45 TRP cc_start: 0.5761 (m-10) cc_final: 0.5381 (m-10) REVERT: A 99 MET cc_start: 0.6950 (mtt) cc_final: 0.6614 (ppp) REVERT: A 215 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7951 (ttm) REVERT: A 222 TYR cc_start: 0.7362 (m-10) cc_final: 0.7131 (m-80) REVERT: A 263 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7140 (mtt90) REVERT: A 435 MET cc_start: 0.7059 (tpp) cc_final: 0.6350 (mmm) REVERT: B 51 LEU cc_start: 0.7348 (tm) cc_final: 0.6511 (mp) REVERT: B 96 MET cc_start: 0.7951 (mtm) cc_final: 0.7646 (mmp) REVERT: B 110 MET cc_start: 0.6482 (ttm) cc_final: 0.6011 (ttt) REVERT: B 222 TYR cc_start: 0.7343 (m-10) cc_final: 0.7123 (m-80) REVERT: B 294 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8172 (mt-10) REVERT: B 435 MET cc_start: 0.7126 (tpp) cc_final: 0.6122 (mmm) REVERT: C 99 MET cc_start: 0.7144 (mmt) cc_final: 0.6764 (mtt) REVERT: C 110 MET cc_start: 0.6555 (ttm) cc_final: 0.6118 (ttt) REVERT: C 115 TYR cc_start: 0.5601 (m-10) cc_final: 0.5375 (m-80) REVERT: C 215 MET cc_start: 0.8558 (mtp) cc_final: 0.8322 (mtt) REVERT: C 263 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7111 (mtt90) REVERT: C 309 ASP cc_start: 0.8355 (p0) cc_final: 0.8113 (p0) REVERT: C 435 MET cc_start: 0.6806 (mmm) cc_final: 0.5995 (mmm) REVERT: C 634 GLU cc_start: 0.7302 (tt0) cc_final: 0.7040 (tt0) REVERT: D 38 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6617 (mp) REVERT: D 96 MET cc_start: 0.7842 (mtm) cc_final: 0.7599 (mmp) REVERT: D 100 GLU cc_start: 0.7807 (mp0) cc_final: 0.7224 (pt0) REVERT: D 110 MET cc_start: 0.6396 (ttm) cc_final: 0.6047 (ttt) REVERT: D 215 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8160 (mtt) REVERT: D 222 TYR cc_start: 0.7266 (m-10) cc_final: 0.7043 (m-80) REVERT: D 634 GLU cc_start: 0.7283 (tt0) cc_final: 0.6964 (tt0) outliers start: 64 outliers final: 20 residues processed: 325 average time/residue: 1.1461 time to fit residues: 428.4473 Evaluate side-chains 275 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 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 235 VAL Chi-restraints excluded: chain C residue 263 ARG Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 25 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 267 GLN C 267 GLN D 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.209173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.175804 restraints weight = 28751.557| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.75 r_work: 0.3870 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 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 = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20768 Z= 0.142 Angle : 0.616 6.747 28000 Z= 0.311 Chirality : 0.042 0.280 3116 Planarity : 0.005 0.048 3416 Dihedral : 13.972 104.074 4109 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.92 % Allowed : 16.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2360 helix: -0.06 (0.14), residues: 1444 sheet: -2.53 (0.48), residues: 84 loop : -2.16 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 268 HIS 0.004 0.001 HIS B 582 PHE 0.017 0.002 PHE B 537 TYR 0.018 0.001 TYR B 547 ARG 0.005 0.000 ARG A 615 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 949) hydrogen bonds : angle 3.87006 ( 2739) covalent geometry : bond 0.00318 (20768) covalent geometry : angle 0.61553 (28000) *********************** 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 333 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 252 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6756 (mp) REVERT: A 45 TRP cc_start: 0.5774 (m-10) cc_final: 0.5534 (m-10) REVERT: A 99 MET cc_start: 0.7086 (mtt) cc_final: 0.6570 (ppp) REVERT: A 110 MET cc_start: 0.6818 (ttt) cc_final: 0.6467 (ppp) REVERT: A 215 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7988 (ttm) REVERT: A 222 TYR cc_start: 0.7330 (m-10) cc_final: 0.7076 (m-80) REVERT: A 263 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7059 (mtt90) REVERT: A 435 MET cc_start: 0.7103 (tpp) cc_final: 0.6085 (mmm) REVERT: B 38 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6701 (mp) REVERT: B 51 LEU cc_start: 0.7386 (tm) cc_final: 0.6536 (mp) REVERT: B 96 MET cc_start: 0.7896 (mtm) cc_final: 0.7534 (mmp) REVERT: B 99 MET cc_start: 0.7226 (mmt) cc_final: 0.6232 (ppp) REVERT: B 110 MET cc_start: 0.6494 (ttm) cc_final: 0.6038 (ttt) REVERT: B 115 TYR cc_start: 0.5897 (m-10) cc_final: 0.5692 (m-80) REVERT: B 222 TYR cc_start: 0.7293 (m-10) cc_final: 0.7045 (m-80) REVERT: B 435 MET cc_start: 0.6951 (tpp) cc_final: 0.6151 (mmm) REVERT: B 555 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6326 (t80) REVERT: C 51 LEU cc_start: 0.7486 (tm) cc_final: 0.6599 (mp) REVERT: C 99 MET cc_start: 0.7147 (mmt) cc_final: 0.5931 (ppp) REVERT: C 110 MET cc_start: 0.6654 (ttm) cc_final: 0.6281 (ttt) REVERT: C 215 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8322 (mtt) REVERT: C 229 LEU cc_start: 0.8105 (mt) cc_final: 0.7655 (pp) REVERT: C 263 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7209 (mtt90) REVERT: C 309 ASP cc_start: 0.8384 (p0) cc_final: 0.8152 (p0) REVERT: C 555 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.6284 (t80) REVERT: D 96 MET cc_start: 0.7879 (mtm) cc_final: 0.7591 (mmp) REVERT: D 99 MET cc_start: 0.6439 (mmt) cc_final: 0.6182 (mmt) REVERT: D 215 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8216 (mtt) REVERT: D 222 TYR cc_start: 0.7259 (m-10) cc_final: 0.7042 (m-80) REVERT: D 435 MET cc_start: 0.6512 (mmm) cc_final: 0.6175 (mmm) REVERT: D 625 LEU cc_start: 0.6551 (pp) cc_final: 0.6174 (mm) REVERT: D 634 GLU cc_start: 0.7316 (tt0) cc_final: 0.6946 (tt0) outliers start: 81 outliers final: 30 residues processed: 306 average time/residue: 1.0614 time to fit residues: 377.2614 Evaluate side-chains 277 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 159 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 360 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 ARG 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 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET 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 591 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 27 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 229 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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** ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.206678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.173440 restraints weight = 28816.748| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.63 r_work: 0.3843 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20768 Z= 0.191 Angle : 0.674 7.506 28000 Z= 0.337 Chirality : 0.045 0.339 3116 Planarity : 0.005 0.050 3416 Dihedral : 13.956 106.990 4109 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.89 % Allowed : 15.99 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2360 helix: -0.10 (0.14), residues: 1444 sheet: -2.48 (0.49), residues: 84 loop : -2.06 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 268 HIS 0.004 0.001 HIS C 582 PHE 0.018 0.002 PHE D 537 TYR 0.021 0.002 TYR C 547 ARG 0.004 0.001 ARG B 615 Details of bonding type rmsd hydrogen bonds : bond 0.04910 ( 949) hydrogen bonds : angle 4.02062 ( 2739) covalent geometry : bond 0.00436 (20768) covalent geometry : angle 0.67394 (28000) *********************** 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 355 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 254 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6781 (mp) REVERT: A 99 MET cc_start: 0.7214 (mtt) cc_final: 0.6571 (ppp) REVERT: A 215 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8075 (ttm) REVERT: A 222 TYR cc_start: 0.7227 (m-10) cc_final: 0.6963 (m-80) REVERT: A 263 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7288 (mtt90) REVERT: A 309 ASP cc_start: 0.8385 (p0) cc_final: 0.8101 (p0) REVERT: A 435 MET cc_start: 0.7076 (tpp) cc_final: 0.6068 (mmm) REVERT: B 38 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6745 (mp) REVERT: B 51 LEU cc_start: 0.7423 (tm) cc_final: 0.6550 (mp) REVERT: B 96 MET cc_start: 0.7888 (mtm) cc_final: 0.7543 (mmp) REVERT: B 99 MET cc_start: 0.7280 (mmt) cc_final: 0.6231 (ppp) REVERT: B 110 MET cc_start: 0.6438 (ttm) cc_final: 0.6022 (ttt) REVERT: B 222 TYR cc_start: 0.7247 (m-10) cc_final: 0.7029 (m-80) REVERT: B 435 MET cc_start: 0.7074 (tpp) cc_final: 0.6245 (mmm) REVERT: B 555 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6337 (t80) REVERT: C 33 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6479 (ttt180) REVERT: C 51 LEU cc_start: 0.7449 (tm) cc_final: 0.6555 (mp) REVERT: C 96 MET cc_start: 0.7283 (mtp) cc_final: 0.7022 (mmm) REVERT: C 99 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.5835 (ppp) REVERT: C 100 GLU cc_start: 0.7804 (mp0) cc_final: 0.7547 (pt0) REVERT: C 110 MET cc_start: 0.6557 (ttm) cc_final: 0.6141 (ttt) REVERT: C 229 LEU cc_start: 0.8030 (mt) cc_final: 0.7633 (pp) REVERT: C 263 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7285 (mtt90) REVERT: C 294 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8394 (mt-10) REVERT: C 555 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.6337 (t80) REVERT: D 45 TRP cc_start: 0.6125 (m-10) cc_final: 0.5853 (m100) REVERT: D 96 MET cc_start: 0.7862 (mtm) cc_final: 0.7578 (mtp) REVERT: D 99 MET cc_start: 0.6611 (mmt) cc_final: 0.6377 (mmt) REVERT: D 100 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7168 (pt0) REVERT: D 215 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8236 (mtt) REVERT: D 222 TYR cc_start: 0.7241 (m-10) cc_final: 0.7035 (m-80) REVERT: D 229 LEU cc_start: 0.8087 (mt) cc_final: 0.7639 (pp) REVERT: D 294 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8380 (mt-10) outliers start: 101 outliers final: 41 residues processed: 321 average time/residue: 1.0856 time to fit residues: 403.7170 Evaluate side-chains 290 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 2.039 ------------------------------------------------------------------------------- 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 215 MET 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 525 ASP Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU 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 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 ARG 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 525 ASP Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 3 optimal weight: 20.0000 chunk 228 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 224 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN D 122 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.205821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.172290 restraints weight = 28667.138| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.70 r_work: 0.3826 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3865 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= 0.217 Angle : 0.703 8.467 28000 Z= 0.351 Chirality : 0.046 0.350 3116 Planarity : 0.005 0.052 3416 Dihedral : 13.877 110.633 4109 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.80 % Allowed : 16.72 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2360 helix: -0.22 (0.14), residues: 1432 sheet: -2.48 (0.52), residues: 76 loop : -1.91 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 268 HIS 0.004 0.001 HIS C 582 PHE 0.016 0.002 PHE C 537 TYR 0.017 0.002 TYR C 547 ARG 0.005 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.05057 ( 949) hydrogen bonds : angle 4.15950 ( 2739) covalent geometry : bond 0.00501 (20768) covalent geometry : angle 0.70324 (28000) *********************** 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 339 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 240 time to evaluate : 2.068 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6699 (mp) REVERT: A 99 MET cc_start: 0.7346 (mtt) cc_final: 0.6502 (pp-130) REVERT: A 222 TYR cc_start: 0.7193 (m-10) cc_final: 0.6958 (m-80) REVERT: A 263 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7280 (mtt90) REVERT: B 29 TRP cc_start: 0.5939 (OUTLIER) cc_final: 0.5447 (m-90) REVERT: B 38 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6854 (mp) REVERT: B 51 LEU cc_start: 0.7410 (tm) cc_final: 0.6563 (mp) REVERT: B 99 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6220 (ppp) REVERT: B 100 GLU cc_start: 0.7923 (mp0) cc_final: 0.7591 (pt0) REVERT: B 222 TYR cc_start: 0.7252 (m-10) cc_final: 0.7037 (m-80) REVERT: B 229 LEU cc_start: 0.8024 (mt) cc_final: 0.7608 (pp) REVERT: B 435 MET cc_start: 0.7095 (tpp) cc_final: 0.6036 (mmm) REVERT: B 555 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6266 (t80) REVERT: C 33 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6494 (ttt180) REVERT: C 51 LEU cc_start: 0.7387 (tm) cc_final: 0.6497 (mp) REVERT: C 96 MET cc_start: 0.7309 (mtp) cc_final: 0.6986 (mmm) REVERT: C 99 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6533 (mtt) REVERT: C 215 MET cc_start: 0.8435 (mtp) cc_final: 0.8195 (mtt) REVERT: C 229 LEU cc_start: 0.8011 (mt) cc_final: 0.7618 (pp) REVERT: C 294 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: C 555 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.6319 (t80) REVERT: D 99 MET cc_start: 0.6356 (mmt) cc_final: 0.6049 (mmt) REVERT: D 215 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8269 (mtt) REVERT: D 222 TYR cc_start: 0.7190 (m-10) cc_final: 0.6989 (m-80) REVERT: D 229 LEU cc_start: 0.8047 (mt) cc_final: 0.7620 (pp) REVERT: D 636 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7183 (ttp-170) outliers start: 99 outliers final: 45 residues processed: 306 average time/residue: 1.0919 time to fit residues: 387.2417 Evaluate side-chains 287 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 99 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 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 215 MET 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 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 636 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 176 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 217 ASN C 217 ASN C 267 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.208993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.176316 restraints weight = 28674.307| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.69 r_work: 0.3867 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 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 = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20768 Z= 0.127 Angle : 0.617 8.506 28000 Z= 0.307 Chirality : 0.042 0.276 3116 Planarity : 0.005 0.048 3416 Dihedral : 13.074 89.430 4109 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.68 % Allowed : 18.22 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2360 helix: 0.21 (0.14), residues: 1436 sheet: -2.38 (0.53), residues: 76 loop : -1.71 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 268 HIS 0.002 0.001 HIS C 582 PHE 0.013 0.001 PHE C 456 TYR 0.013 0.001 TYR A 524 ARG 0.004 0.000 ARG C 263 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 949) hydrogen bonds : angle 3.84661 ( 2739) covalent geometry : bond 0.00283 (20768) covalent geometry : angle 0.61664 (28000) *********************** 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 328 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 2.279 Fit side-chains REVERT: A 38 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6808 (mp) REVERT: A 99 MET cc_start: 0.7250 (mtt) cc_final: 0.6443 (pp-130) REVERT: A 110 MET cc_start: 0.6794 (ttt) cc_final: 0.6473 (ptm) REVERT: A 215 MET cc_start: 0.8524 (mtp) cc_final: 0.8085 (ttm) REVERT: A 222 TYR cc_start: 0.7244 (m-10) cc_final: 0.7032 (m-80) REVERT: A 555 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6280 (t80) REVERT: A 634 GLU cc_start: 0.7368 (tt0) cc_final: 0.7071 (tt0) REVERT: B 38 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6841 (mp) REVERT: B 51 LEU cc_start: 0.7447 (tm) cc_final: 0.6638 (mp) REVERT: B 99 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6760 (mmt) REVERT: B 229 LEU cc_start: 0.7937 (mt) cc_final: 0.7580 (pp) REVERT: B 309 ASP cc_start: 0.8392 (p0) cc_final: 0.7754 (t0) REVERT: B 359 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5929 (mpt-90) REVERT: B 555 TYR cc_start: 0.6695 (OUTLIER) cc_final: 0.6298 (t80) REVERT: C 33 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6489 (ttt180) REVERT: C 51 LEU cc_start: 0.7383 (tm) cc_final: 0.6509 (mp) REVERT: C 96 MET cc_start: 0.7393 (mtp) cc_final: 0.7058 (mmm) REVERT: C 99 MET cc_start: 0.7009 (mmt) cc_final: 0.6485 (mtt) REVERT: C 215 MET cc_start: 0.8501 (mtp) cc_final: 0.8234 (mtt) REVERT: C 229 LEU cc_start: 0.7945 (mt) cc_final: 0.7619 (pp) REVERT: C 555 TYR cc_start: 0.6687 (OUTLIER) cc_final: 0.6308 (t80) REVERT: D 29 TRP cc_start: 0.6159 (OUTLIER) cc_final: 0.5640 (m-90) REVERT: D 33 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.5401 (ttt-90) REVERT: D 45 TRP cc_start: 0.6192 (m-10) cc_final: 0.5687 (m100) REVERT: D 215 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8258 (mtt) REVERT: D 229 LEU cc_start: 0.8027 (mt) cc_final: 0.7680 (pp) REVERT: D 555 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6092 (t80) outliers start: 76 outliers final: 32 residues processed: 301 average time/residue: 1.0642 time to fit residues: 372.6883 Evaluate side-chains 282 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain 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 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 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 33 ARG 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 452 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 215 MET 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 568 LEU Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 215 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 189 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.207613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.174462 restraints weight = 28702.111| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.65 r_work: 0.3851 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20768 Z= 0.161 Angle : 0.654 11.717 28000 Z= 0.324 Chirality : 0.044 0.308 3116 Planarity : 0.005 0.050 3416 Dihedral : 13.016 88.541 4109 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.49 % Allowed : 19.19 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.18), residues: 2360 helix: 0.14 (0.14), residues: 1436 sheet: -2.36 (0.54), residues: 76 loop : -1.68 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 268 HIS 0.003 0.001 HIS C 582 PHE 0.016 0.002 PHE D 537 TYR 0.017 0.002 TYR A 524 ARG 0.004 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 949) hydrogen bonds : angle 3.93336 ( 2739) covalent geometry : bond 0.00369 (20768) covalent geometry : angle 0.65391 (28000) *********************** 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 320 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 248 time to evaluate : 2.230 Fit side-chains REVERT: A 38 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6827 (mp) REVERT: A 99 MET cc_start: 0.7323 (mtt) cc_final: 0.6468 (pp-130) REVERT: A 215 MET cc_start: 0.8454 (mtp) cc_final: 0.8249 (mtt) REVERT: A 222 TYR cc_start: 0.7232 (m-10) cc_final: 0.7025 (m-80) REVERT: A 229 LEU cc_start: 0.7964 (mt) cc_final: 0.7584 (pp) REVERT: A 555 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.6279 (t80) REVERT: B 38 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6856 (mp) REVERT: B 51 LEU cc_start: 0.7438 (tm) cc_final: 0.6637 (mp) REVERT: B 99 MET cc_start: 0.7361 (mmt) cc_final: 0.6947 (mmt) REVERT: B 229 LEU cc_start: 0.7965 (mt) cc_final: 0.7636 (pp) REVERT: B 359 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5945 (mpt-90) REVERT: B 555 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6262 (t80) REVERT: B 636 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7217 (ttp-170) REVERT: C 33 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6556 (ttt180) REVERT: C 45 TRP cc_start: 0.6107 (m-10) cc_final: 0.5687 (m100) REVERT: C 96 MET cc_start: 0.7363 (mtp) cc_final: 0.7032 (mmm) REVERT: C 99 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6533 (mtt) REVERT: C 110 MET cc_start: 0.7035 (ttt) cc_final: 0.6808 (ptm) REVERT: C 215 MET cc_start: 0.8515 (mtp) cc_final: 0.8235 (mtt) REVERT: C 229 LEU cc_start: 0.7976 (mt) cc_final: 0.7708 (pp) REVERT: C 255 MET cc_start: 0.8332 (mmt) cc_final: 0.8073 (mpt) REVERT: C 294 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: C 555 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.6302 (t80) REVERT: D 29 TRP cc_start: 0.6106 (OUTLIER) cc_final: 0.5585 (m-90) REVERT: D 38 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6670 (mp) REVERT: D 100 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7176 (pt0) REVERT: D 215 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8246 (mtt) REVERT: D 229 LEU cc_start: 0.8018 (mt) cc_final: 0.7747 (pp) REVERT: D 555 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.6096 (t80) outliers start: 72 outliers final: 36 residues processed: 296 average time/residue: 1.1275 time to fit residues: 386.3394 Evaluate side-chains 293 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 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 481 MET Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 372 LEU 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 625 LEU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 99 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 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 215 MET 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 568 LEU 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 38 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 32 optimal weight: 0.0030 chunk 215 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.210684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177586 restraints weight = 28610.526| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.70 r_work: 0.3883 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 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 = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20768 Z= 0.117 Angle : 0.609 10.885 28000 Z= 0.301 Chirality : 0.041 0.257 3116 Planarity : 0.004 0.048 3416 Dihedral : 12.485 86.296 4109 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.86 % Allowed : 20.25 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2360 helix: 0.44 (0.14), residues: 1440 sheet: -2.29 (0.53), residues: 76 loop : -1.52 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 268 HIS 0.002 0.001 HIS B 426 PHE 0.014 0.001 PHE C 434 TYR 0.019 0.001 TYR A 524 ARG 0.003 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 949) hydrogen bonds : angle 3.74575 ( 2739) covalent geometry : bond 0.00257 (20768) covalent geometry : angle 0.60885 (28000) *********************** 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 330 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 2.079 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7250 (mtt) cc_final: 0.6235 (pp-130) REVERT: A 215 MET cc_start: 0.8536 (mtp) cc_final: 0.8313 (mtt) REVERT: A 229 LEU cc_start: 0.7948 (mt) cc_final: 0.7655 (pp) REVERT: A 437 LEU cc_start: 0.6207 (pt) cc_final: 0.5949 (mp) REVERT: A 555 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6319 (t80) REVERT: A 634 GLU cc_start: 0.7286 (tt0) cc_final: 0.7008 (tt0) REVERT: B 38 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6805 (mp) REVERT: B 45 TRP cc_start: 0.6300 (m-10) cc_final: 0.5811 (m100) REVERT: B 96 MET cc_start: 0.7279 (mmt) cc_final: 0.6860 (mmm) REVERT: B 99 MET cc_start: 0.7339 (mmt) cc_final: 0.6184 (ptp) REVERT: B 229 LEU cc_start: 0.7974 (mt) cc_final: 0.7673 (pp) REVERT: B 290 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8251 (mm-40) REVERT: B 555 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.6294 (t80) REVERT: C 33 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6523 (ttt180) REVERT: C 45 TRP cc_start: 0.6152 (m-10) cc_final: 0.5813 (m100) REVERT: C 51 LEU cc_start: 0.7382 (tm) cc_final: 0.6583 (mp) REVERT: C 96 MET cc_start: 0.7366 (mtp) cc_final: 0.7036 (mmm) REVERT: C 99 MET cc_start: 0.6977 (mmt) cc_final: 0.6481 (mtt) REVERT: C 215 MET cc_start: 0.8538 (mtp) cc_final: 0.8265 (mtt) REVERT: C 229 LEU cc_start: 0.7976 (mt) cc_final: 0.7706 (pp) REVERT: C 255 MET cc_start: 0.8328 (mmt) cc_final: 0.8055 (mpt) REVERT: C 555 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.6318 (t80) REVERT: D 29 TRP cc_start: 0.5994 (OUTLIER) cc_final: 0.5390 (m-90) REVERT: D 38 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6631 (mp) REVERT: D 45 TRP cc_start: 0.6168 (m-10) cc_final: 0.5735 (m100) REVERT: D 100 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7160 (pt0) REVERT: D 215 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8258 (mtt) REVERT: D 229 LEU cc_start: 0.7999 (mt) cc_final: 0.7714 (pp) REVERT: D 290 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8214 (mm-40) REVERT: D 309 ASP cc_start: 0.8352 (p0) cc_final: 0.7872 (t0) REVERT: D 555 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.6076 (t80) outliers start: 59 outliers final: 28 residues processed: 311 average time/residue: 1.0933 time to fit residues: 399.8537 Evaluate side-chains 291 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 591 GLU 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 372 LEU 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 C residue 33 ARG 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 C residue 591 GLU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 215 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 182 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 226 optimal weight: 0.0370 chunk 230 optimal weight: 9.9990 chunk 4 optimal weight: 40.0000 chunk 144 optimal weight: 6.9990 chunk 92 optimal weight: 0.0170 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.212546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.180115 restraints weight = 28708.304| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.57 r_work: 0.3911 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20768 Z= 0.113 Angle : 0.620 10.885 28000 Z= 0.304 Chirality : 0.041 0.255 3116 Planarity : 0.004 0.048 3416 Dihedral : 12.168 84.935 4109 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.08 % Allowed : 21.22 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2360 helix: 0.63 (0.14), residues: 1440 sheet: -1.98 (0.52), residues: 84 loop : -1.38 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 268 HIS 0.004 0.001 HIS A 122 PHE 0.020 0.001 PHE B 434 TYR 0.017 0.001 TYR A 524 ARG 0.003 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 949) hydrogen bonds : angle 3.68094 ( 2739) covalent geometry : bond 0.00243 (20768) covalent geometry : angle 0.62018 (28000) ********************** 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 317 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 2.329 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7292 (mtt) cc_final: 0.6272 (pp-130) REVERT: A 215 MET cc_start: 0.8544 (mtp) cc_final: 0.8309 (mtt) REVERT: A 229 LEU cc_start: 0.7923 (mt) cc_final: 0.7650 (pp) REVERT: A 555 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6301 (t80) REVERT: B 38 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6799 (mp) REVERT: B 45 TRP cc_start: 0.6275 (m-10) cc_final: 0.5875 (m100) REVERT: B 51 LEU cc_start: 0.7354 (tm) cc_final: 0.6570 (mp) REVERT: B 96 MET cc_start: 0.7214 (mmt) cc_final: 0.6812 (mmm) REVERT: B 99 MET cc_start: 0.7252 (mmt) cc_final: 0.6122 (ptp) REVERT: B 215 MET cc_start: 0.8246 (mtt) cc_final: 0.7641 (ptm) REVERT: B 229 LEU cc_start: 0.7952 (mt) cc_final: 0.7648 (pp) REVERT: B 290 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8257 (mm-40) REVERT: B 309 ASP cc_start: 0.8257 (p0) cc_final: 0.7821 (t0) REVERT: B 456 PHE cc_start: 0.6859 (m-80) cc_final: 0.6596 (m-80) REVERT: B 555 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.6285 (t80) REVERT: C 45 TRP cc_start: 0.6180 (m-10) cc_final: 0.5841 (m100) REVERT: C 51 LEU cc_start: 0.7418 (tm) cc_final: 0.6644 (mp) REVERT: C 96 MET cc_start: 0.7299 (mtp) cc_final: 0.7011 (mmm) REVERT: C 99 MET cc_start: 0.6960 (mmt) cc_final: 0.6457 (mtt) REVERT: C 215 MET cc_start: 0.8513 (mtp) cc_final: 0.8252 (mtt) REVERT: C 229 LEU cc_start: 0.7964 (mt) cc_final: 0.7694 (pp) REVERT: C 255 MET cc_start: 0.8307 (mmt) cc_final: 0.8067 (mpt) REVERT: C 260 MET cc_start: 0.7670 (tpp) cc_final: 0.7379 (tpp) REVERT: C 555 TYR cc_start: 0.6581 (OUTLIER) cc_final: 0.6273 (t80) REVERT: D 29 TRP cc_start: 0.5992 (OUTLIER) cc_final: 0.5309 (m-90) REVERT: D 45 TRP cc_start: 0.6127 (m-10) cc_final: 0.5701 (m100) REVERT: D 100 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7127 (pt0) REVERT: D 215 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8251 (mtt) REVERT: D 229 LEU cc_start: 0.7956 (mt) cc_final: 0.7683 (pp) REVERT: D 290 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8261 (mm-40) REVERT: D 309 ASP cc_start: 0.8317 (p0) cc_final: 0.7898 (t0) REVERT: D 555 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.6075 (t80) REVERT: D 634 GLU cc_start: 0.7396 (tt0) cc_final: 0.7065 (tt0) outliers start: 43 outliers final: 33 residues processed: 302 average time/residue: 1.0960 time to fit residues: 383.5993 Evaluate side-chains 294 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 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 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 625 LEU 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 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 215 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 0.8980 chunk 220 optimal weight: 0.5980 chunk 206 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.212636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.180394 restraints weight = 28662.428| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.25 r_work: 0.3903 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- 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: 0.7225 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20768 Z= 0.120 Angle : 0.623 9.524 28000 Z= 0.305 Chirality : 0.042 0.384 3116 Planarity : 0.005 0.047 3416 Dihedral : 12.084 81.952 4109 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.03 % Allowed : 21.80 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2360 helix: 0.71 (0.14), residues: 1440 sheet: -1.84 (0.52), residues: 84 loop : -1.27 (0.24), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 268 HIS 0.004 0.001 HIS B 122 PHE 0.017 0.001 PHE D 434 TYR 0.021 0.001 TYR C 349 ARG 0.003 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 949) hydrogen bonds : angle 3.70362 ( 2739) covalent geometry : bond 0.00265 (20768) covalent geometry : angle 0.62279 (28000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15042.50 seconds wall clock time: 256 minutes 56.09 seconds (15416.09 seconds total)