Starting phenix.real_space_refine on Wed May 21 03:04:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fob_29344/05_2025/8fob_29344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fob_29344/05_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_29344/05_2025/8fob_29344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fob_29344/05_2025/8fob_29344.map" model { file = "/net/cci-nas-00/data/ceres_data/8fob_29344/05_2025/8fob_29344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fob_29344/05_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-5687/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: 12.28, per 1000 atoms: 0.60 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: 5.45 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: 2.29 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: 6.56 Time building geometry restraints manager: 6.18 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 45.640 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.090 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.830 ------------------------------------------------------------------------------- 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 : 2.661 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: 1.2607 time to fit residues: 678.1845 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 : 2.333 ------------------------------------------------------------------------------- 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: 3.40 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 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 = 0.09 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 : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.5851 (m-10) cc_final: 0.5470 (m-10) REVERT: A 99 MET cc_start: 0.6871 (mtt) cc_final: 0.6618 (ppp) REVERT: A 215 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7891 (ttm) REVERT: A 222 TYR cc_start: 0.7455 (m-10) cc_final: 0.7201 (m-80) REVERT: A 263 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7151 (mtt90) REVERT: B 96 MET cc_start: 0.7957 (mtm) cc_final: 0.7670 (mmp) REVERT: B 110 MET cc_start: 0.6430 (ttm) cc_final: 0.5818 (ttt) REVERT: B 215 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7954 (ttm) REVERT: B 222 TYR cc_start: 0.7375 (m-10) cc_final: 0.7126 (m-80) REVERT: B 294 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 485 MET cc_start: 0.8896 (mtt) cc_final: 0.8601 (mtt) REVERT: C 74 GLN cc_start: 0.6129 (tp-100) cc_final: 0.5390 (pm20) REVERT: C 110 MET cc_start: 0.6438 (ttm) cc_final: 0.5799 (ttt) REVERT: C 263 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7232 (mtt90) REVERT: D 74 GLN cc_start: 0.6221 (tp-100) cc_final: 0.5660 (pm20) REVERT: D 96 MET cc_start: 0.7863 (mtm) cc_final: 0.7578 (mtp) REVERT: D 110 MET cc_start: 0.6382 (ttm) cc_final: 0.5949 (ttt) REVERT: D 115 TYR cc_start: 0.5844 (m-10) cc_final: 0.5620 (m-80) REVERT: D 222 TYR cc_start: 0.7314 (m-10) cc_final: 0.7105 (m-80) REVERT: D 263 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7066 (mtt90) REVERT: D 294 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8192 (mt-10) REVERT: D 309 ASP cc_start: 0.8506 (p0) cc_final: 0.8167 (p0) REVERT: D 345 MET cc_start: 0.6490 (tpp) cc_final: 0.6280 (mmt) REVERT: D 550 ASP cc_start: 0.6445 (m-30) cc_final: 0.6214 (t0) outliers start: 87 outliers final: 24 residues processed: 341 average time/residue: 1.0761 time to fit residues: 424.5951 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 : 2.063 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.209786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.176412 restraints weight = 28358.536| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.65 r_work: 0.3883 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20768 Z= 0.136 Angle : 0.637 9.085 28000 Z= 0.321 Chirality : 0.042 0.296 3116 Planarity : 0.005 0.047 3416 Dihedral : 15.008 119.571 4109 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.25 % Allowed : 15.07 % 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: -2.01 (0.17), residues: 2360 helix: -0.62 (0.13), residues: 1484 sheet: -2.63 (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 C 582 PHE 0.015 0.002 PHE D 456 TYR 0.018 0.001 TYR A 547 ARG 0.006 0.000 ARG A 615 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 949) hydrogen bonds : angle 4.01050 ( 2739) covalent geometry : bond 0.00296 (20768) covalent geometry : angle 0.63683 (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 349 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 282 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6850 (mp) REVERT: A 45 TRP cc_start: 0.5782 (m-10) cc_final: 0.5431 (m-10) REVERT: A 99 MET cc_start: 0.6955 (mtt) cc_final: 0.6617 (ppp) REVERT: A 215 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7955 (ttm) REVERT: A 222 TYR cc_start: 0.7336 (m-10) cc_final: 0.7104 (m-80) REVERT: A 263 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7124 (mtt90) REVERT: A 435 MET cc_start: 0.7076 (tpp) cc_final: 0.6134 (mmm) REVERT: B 51 LEU cc_start: 0.7354 (tm) cc_final: 0.6528 (mp) REVERT: B 96 MET cc_start: 0.7951 (mtm) cc_final: 0.7647 (mmp) REVERT: B 110 MET cc_start: 0.6425 (ttm) cc_final: 0.5956 (ttt) REVERT: B 222 TYR cc_start: 0.7349 (m-10) cc_final: 0.7134 (m-80) REVERT: B 435 MET cc_start: 0.7096 (tpp) cc_final: 0.6077 (mmm) REVERT: C 96 MET cc_start: 0.7412 (mtp) cc_final: 0.7119 (mtp) REVERT: C 99 MET cc_start: 0.7149 (mmt) cc_final: 0.6016 (ppp) REVERT: C 110 MET cc_start: 0.6490 (ttm) cc_final: 0.6057 (ttt) REVERT: C 115 TYR cc_start: 0.5646 (m-10) cc_final: 0.5425 (m-80) REVERT: C 215 MET cc_start: 0.8597 (mtp) cc_final: 0.8370 (mtt) REVERT: C 263 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7127 (mtt90) REVERT: C 309 ASP cc_start: 0.8357 (p0) cc_final: 0.8114 (p0) REVERT: C 435 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5969 (mmm) REVERT: D 96 MET cc_start: 0.7836 (mtm) cc_final: 0.7588 (mmp) REVERT: D 100 GLU cc_start: 0.7825 (mp0) cc_final: 0.7239 (pt0) REVERT: D 110 MET cc_start: 0.6315 (ttm) cc_final: 0.5965 (ttt) REVERT: D 115 TYR cc_start: 0.5845 (m-10) cc_final: 0.5644 (m-80) REVERT: D 215 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8228 (mtt) REVERT: D 435 MET cc_start: 0.6532 (mmm) cc_final: 0.6207 (mmm) REVERT: D 634 GLU cc_start: 0.7274 (tt0) cc_final: 0.6906 (tt0) outliers start: 67 outliers final: 22 residues processed: 320 average time/residue: 1.0969 time to fit residues: 405.2598 Evaluate side-chains 275 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 2.067 ------------------------------------------------------------------------------- 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 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 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 435 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 625 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: 3.9990 chunk 140 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** 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 = 0.4498 r_free = 0.4498 target = 0.208298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.174534 restraints weight = 28470.975| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.69 r_work: 0.3862 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 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 = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20768 Z= 0.161 Angle : 0.639 6.695 28000 Z= 0.322 Chirality : 0.043 0.290 3116 Planarity : 0.005 0.049 3416 Dihedral : 14.233 108.658 4109 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.60 % Allowed : 15.60 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.17), residues: 2360 helix: -0.17 (0.14), residues: 1440 sheet: -2.59 (0.51), residues: 76 loop : -2.17 (0.21), residues: 844 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 0.018 0.002 PHE A 537 TYR 0.020 0.002 TYR A 547 ARG 0.005 0.001 ARG B 615 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 949) hydrogen bonds : angle 3.96268 ( 2739) covalent geometry : bond 0.00365 (20768) covalent geometry : angle 0.63851 (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 352 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 257 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6798 (mp) REVERT: A 45 TRP cc_start: 0.5760 (m-10) cc_final: 0.5510 (m-10) REVERT: A 99 MET cc_start: 0.7093 (mtt) cc_final: 0.6644 (ppp) REVERT: A 215 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7954 (ttm) REVERT: A 222 TYR cc_start: 0.7322 (m-10) cc_final: 0.7060 (m-80) REVERT: A 263 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7252 (mtt90) REVERT: A 435 MET cc_start: 0.7130 (tpp) cc_final: 0.6207 (mmm) REVERT: B 38 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6838 (mp) REVERT: B 51 LEU cc_start: 0.7394 (tm) cc_final: 0.6537 (mp) REVERT: B 96 MET cc_start: 0.7872 (mtm) cc_final: 0.7523 (mmp) REVERT: B 99 MET cc_start: 0.7216 (mmt) cc_final: 0.6262 (ppp) REVERT: B 110 MET cc_start: 0.6536 (ttm) cc_final: 0.6099 (ttt) REVERT: B 222 TYR cc_start: 0.7291 (m-10) cc_final: 0.7071 (m-80) REVERT: B 435 MET cc_start: 0.6996 (tpp) cc_final: 0.6175 (mmm) REVERT: B 555 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.6317 (t80) REVERT: C 51 LEU cc_start: 0.7460 (tm) cc_final: 0.6577 (mp) REVERT: C 99 MET cc_start: 0.7161 (mmt) cc_final: 0.6760 (mtt) REVERT: C 110 MET cc_start: 0.6665 (ttm) cc_final: 0.6321 (ttt) REVERT: C 215 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8306 (mtt) REVERT: C 263 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7215 (mtt90) REVERT: C 294 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8437 (mt-10) REVERT: C 309 ASP cc_start: 0.8395 (p0) cc_final: 0.8152 (p0) REVERT: C 555 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.6327 (t80) REVERT: D 96 MET cc_start: 0.7869 (mtm) cc_final: 0.7591 (mmp) REVERT: D 99 MET cc_start: 0.6417 (mmt) cc_final: 0.6163 (mmt) REVERT: D 110 MET cc_start: 0.6438 (ttm) cc_final: 0.5932 (ttt) REVERT: D 215 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8203 (mtt) REVERT: D 385 ARG cc_start: 0.7301 (tmm-80) cc_final: 0.7087 (tmm-80) REVERT: D 625 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6150 (mm) REVERT: D 634 GLU cc_start: 0.7295 (tt0) cc_final: 0.6895 (tt0) outliers start: 95 outliers final: 29 residues processed: 317 average time/residue: 1.0325 time to fit residues: 381.3516 Evaluate side-chains 272 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 2.254 ------------------------------------------------------------------------------- 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 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 625 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 294 GLU 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 625 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 506 SER Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 625 LEU 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: 0.8980 chunk 201 optimal weight: 0.0060 chunk 180 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 overall best weight: 3.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.206634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.173110 restraints weight = 28682.637| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.63 r_work: 0.3842 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20768 Z= 0.188 Angle : 0.672 8.608 28000 Z= 0.335 Chirality : 0.045 0.323 3116 Planarity : 0.005 0.050 3416 Dihedral : 14.079 108.965 4109 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.04 % Allowed : 16.18 % Favored : 78.78 % 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 (0.17), residues: 2360 helix: -0.15 (0.14), residues: 1440 sheet: -2.51 (0.53), residues: 76 loop : -2.07 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 268 HIS 0.004 0.001 HIS C 582 PHE 0.018 0.002 PHE B 537 TYR 0.019 0.002 TYR C 547 ARG 0.004 0.001 ARG C 615 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 949) hydrogen bonds : angle 4.04846 ( 2739) covalent geometry : bond 0.00433 (20768) covalent geometry : angle 0.67210 (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 351 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 247 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6774 (mp) REVERT: A 99 MET cc_start: 0.7204 (mtt) cc_final: 0.6561 (ppp) REVERT: A 215 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8044 (ttm) REVERT: A 222 TYR cc_start: 0.7244 (m-10) cc_final: 0.7008 (m-80) REVERT: A 263 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7340 (mtt90) REVERT: A 309 ASP cc_start: 0.8387 (p0) cc_final: 0.8097 (p0) REVERT: A 435 MET cc_start: 0.7072 (tpp) cc_final: 0.6179 (mmm) REVERT: B 38 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6760 (mp) REVERT: B 51 LEU cc_start: 0.7386 (tm) cc_final: 0.6513 (mp) REVERT: B 96 MET cc_start: 0.7885 (mtm) cc_final: 0.7538 (mmp) REVERT: B 99 MET cc_start: 0.7285 (mmt) cc_final: 0.6201 (ppp) REVERT: B 222 TYR cc_start: 0.7270 (m-10) cc_final: 0.7052 (m-80) REVERT: B 294 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: B 435 MET cc_start: 0.7074 (tpp) cc_final: 0.6253 (mmm) REVERT: B 555 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6346 (t80) REVERT: C 33 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6474 (ttt180) REVERT: C 51 LEU cc_start: 0.7437 (tm) cc_final: 0.6535 (mp) REVERT: C 99 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.5857 (ppp) REVERT: C 100 GLU cc_start: 0.7825 (mp0) cc_final: 0.7566 (pt0) REVERT: C 229 LEU cc_start: 0.8067 (mt) cc_final: 0.7657 (pp) REVERT: C 263 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7290 (mtt90) REVERT: C 294 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: C 555 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6355 (t80) REVERT: D 38 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6676 (mp) REVERT: D 45 TRP cc_start: 0.6141 (m-10) cc_final: 0.5860 (m100) REVERT: D 96 MET cc_start: 0.7869 (mtm) cc_final: 0.7618 (mtp) REVERT: D 99 MET cc_start: 0.6577 (mmt) cc_final: 0.6352 (mmt) REVERT: D 110 MET cc_start: 0.6407 (ttm) cc_final: 0.5939 (ttt) REVERT: D 115 TYR cc_start: 0.6129 (m-10) cc_final: 0.5893 (m-80) REVERT: D 215 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8240 (mtt) REVERT: D 229 LEU cc_start: 0.8067 (mt) cc_final: 0.7609 (pp) REVERT: D 294 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8386 (mt-10) outliers start: 104 outliers final: 43 residues processed: 319 average time/residue: 1.0189 time to fit residues: 378.3508 Evaluate side-chains 295 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 428 LEU 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 294 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 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 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 C residue 625 LEU 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 294 GLU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 3 optimal weight: 8.9990 chunk 228 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 64 optimal weight: 30.0000 chunk 224 optimal weight: 7.9990 chunk 184 optimal weight: 40.0000 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 ASN C 217 ASN C 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.207206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.173895 restraints weight = 28586.217| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.71 r_work: 0.3845 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 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 = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20768 Z= 0.162 Angle : 0.645 9.155 28000 Z= 0.321 Chirality : 0.044 0.311 3116 Planarity : 0.005 0.050 3416 Dihedral : 13.586 100.368 4109 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.31 % Allowed : 16.86 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.17 (0.18), residues: 2360 helix: 0.00 (0.14), residues: 1436 sheet: -2.46 (0.53), residues: 76 loop : -1.88 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 268 HIS 0.003 0.001 HIS C 582 PHE 0.015 0.002 PHE B 537 TYR 0.016 0.002 TYR B 547 ARG 0.004 0.000 ARG C 615 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 949) hydrogen bonds : angle 3.94759 ( 2739) covalent geometry : bond 0.00372 (20768) covalent geometry : angle 0.64537 (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 328 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 239 time to evaluate : 2.358 Fit side-chains REVERT: A 38 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6727 (mp) REVERT: A 99 MET cc_start: 0.7257 (mtt) cc_final: 0.6476 (pp-130) REVERT: A 110 MET cc_start: 0.6969 (ttt) cc_final: 0.6663 (ptm) REVERT: A 222 TYR cc_start: 0.7225 (m-10) cc_final: 0.6993 (m-80) REVERT: A 263 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7320 (mtt90) REVERT: A 309 ASP cc_start: 0.8393 (p0) cc_final: 0.8106 (p0) REVERT: A 435 MET cc_start: 0.6984 (tpp) cc_final: 0.6000 (mmm) REVERT: A 555 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6329 (t80) REVERT: B 38 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6782 (mp) REVERT: B 51 LEU cc_start: 0.7415 (tm) cc_final: 0.6560 (mp) REVERT: B 96 MET cc_start: 0.7845 (mtm) cc_final: 0.7491 (mmp) REVERT: B 99 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6097 (ppp) REVERT: B 222 TYR cc_start: 0.7270 (m-10) cc_final: 0.7027 (m-80) REVERT: B 229 LEU cc_start: 0.7992 (mt) cc_final: 0.7589 (pp) REVERT: B 294 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: B 435 MET cc_start: 0.7035 (tpp) cc_final: 0.6006 (mmm) REVERT: B 555 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.6257 (t80) REVERT: C 33 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6497 (ttt180) REVERT: C 51 LEU cc_start: 0.7442 (tm) cc_final: 0.6563 (mp) REVERT: C 99 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6525 (mtt) REVERT: C 215 MET cc_start: 0.8553 (mtp) cc_final: 0.8343 (mtt) REVERT: C 229 LEU cc_start: 0.7996 (mt) cc_final: 0.7616 (pp) REVERT: C 294 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: C 555 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6321 (t80) REVERT: D 99 MET cc_start: 0.6554 (mmt) cc_final: 0.6226 (mmt) REVERT: D 110 MET cc_start: 0.6424 (ttm) cc_final: 0.6191 (ttm) REVERT: D 215 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8214 (mtt) REVERT: D 229 LEU cc_start: 0.8038 (mt) cc_final: 0.7610 (pp) REVERT: D 294 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: D 555 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.6139 (t80) outliers start: 89 outliers final: 43 residues processed: 298 average time/residue: 1.0629 time to fit residues: 367.9067 Evaluate side-chains 289 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 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 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 99 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU 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 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 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 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 625 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 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 176 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 59 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN C 267 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.209988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.177299 restraints weight = 28531.919| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.61 r_work: 0.3883 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 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 = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20768 Z= 0.115 Angle : 0.599 9.978 28000 Z= 0.297 Chirality : 0.041 0.259 3116 Planarity : 0.004 0.047 3416 Dihedral : 12.845 89.991 4109 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.29 % Allowed : 18.85 % Favored : 77.86 % 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: -0.68 (0.18), residues: 2360 helix: 0.41 (0.14), residues: 1436 sheet: -2.34 (0.53), residues: 76 loop : -1.71 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 268 HIS 0.002 0.001 HIS D 426 PHE 0.014 0.001 PHE B 456 TYR 0.013 0.001 TYR A 524 ARG 0.004 0.000 ARG B 385 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 949) hydrogen bonds : angle 3.73522 ( 2739) covalent geometry : bond 0.00249 (20768) covalent geometry : angle 0.59887 (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 327 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 2.185 Fit side-chains REVERT: A 38 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6770 (mp) REVERT: A 45 TRP cc_start: 0.6230 (m100) cc_final: 0.5745 (m-10) REVERT: A 99 MET cc_start: 0.7210 (mtt) cc_final: 0.6465 (pp-130) REVERT: A 222 TYR cc_start: 0.7229 (m-10) cc_final: 0.6994 (m-80) REVERT: A 435 MET cc_start: 0.6987 (tpp) cc_final: 0.6011 (mmm) REVERT: A 555 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.6273 (t80) REVERT: A 634 GLU cc_start: 0.7348 (tt0) cc_final: 0.7060 (tt0) REVERT: B 38 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6773 (mp) REVERT: B 51 LEU cc_start: 0.7445 (tm) cc_final: 0.6645 (mp) REVERT: B 99 MET cc_start: 0.7279 (mmt) cc_final: 0.6834 (mmt) REVERT: B 229 LEU cc_start: 0.7931 (mt) cc_final: 0.7567 (pp) REVERT: B 359 ARG cc_start: 0.6100 (OUTLIER) cc_final: 0.5875 (mpt-90) REVERT: B 435 MET cc_start: 0.6955 (tpp) cc_final: 0.5974 (mmm) REVERT: B 555 TYR cc_start: 0.6690 (OUTLIER) cc_final: 0.6298 (t80) REVERT: C 33 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6501 (ttt180) REVERT: C 51 LEU cc_start: 0.7416 (tm) cc_final: 0.6564 (mp) REVERT: C 99 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6598 (mtt) REVERT: C 215 MET cc_start: 0.8549 (mtp) cc_final: 0.8335 (mtt) REVERT: C 229 LEU cc_start: 0.7953 (mt) cc_final: 0.7631 (pp) REVERT: C 309 ASP cc_start: 0.8354 (p0) cc_final: 0.7742 (t0) REVERT: C 555 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.6309 (t80) REVERT: D 29 TRP cc_start: 0.6088 (OUTLIER) cc_final: 0.5511 (m-90) REVERT: D 45 TRP cc_start: 0.6190 (m-10) cc_final: 0.5706 (m100) REVERT: D 100 GLU cc_start: 0.7852 (mp0) cc_final: 0.7290 (pt0) REVERT: D 110 MET cc_start: 0.6369 (ttm) cc_final: 0.6161 (ttm) REVERT: D 215 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8263 (mtt) REVERT: D 229 LEU cc_start: 0.7999 (mt) cc_final: 0.7641 (pp) REVERT: D 555 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.6150 (t80) REVERT: D 634 GLU cc_start: 0.7379 (tt0) cc_final: 0.7085 (tt0) outliers start: 68 outliers final: 36 residues processed: 303 average time/residue: 1.0176 time to fit residues: 358.5215 Evaluate side-chains 287 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 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 525 ASP Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU 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 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU 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 311 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 591 GLU 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: 2.9990 chunk 213 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 131 optimal weight: 0.0980 chunk 207 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN C 267 GLN D 31 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.209087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.175573 restraints weight = 28585.911| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.68 r_work: 0.3864 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 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 = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4122 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= 0.139 Angle : 0.622 8.295 28000 Z= 0.308 Chirality : 0.043 0.301 3116 Planarity : 0.005 0.048 3416 Dihedral : 12.768 85.988 4109 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.49 % Allowed : 19.48 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.68 (0.18), residues: 2360 helix: 0.40 (0.14), residues: 1436 sheet: -2.21 (0.54), residues: 76 loop : -1.71 (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 D 582 PHE 0.014 0.002 PHE A 537 TYR 0.015 0.001 TYR B 524 ARG 0.004 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 949) hydrogen bonds : angle 3.78508 ( 2739) covalent geometry : bond 0.00313 (20768) covalent geometry : angle 0.62171 (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 : 2.085 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6724 (mp) REVERT: A 99 MET cc_start: 0.7270 (mtt) cc_final: 0.6467 (pp-130) REVERT: A 118 GLN cc_start: 0.7829 (tt0) cc_final: 0.7078 (tp-100) REVERT: A 222 TYR cc_start: 0.7226 (m-10) cc_final: 0.7007 (m-80) REVERT: A 309 ASP cc_start: 0.8396 (p0) cc_final: 0.8116 (p0) REVERT: A 555 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.6242 (t80) REVERT: A 634 GLU cc_start: 0.7339 (tt0) cc_final: 0.7020 (tt0) REVERT: B 38 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6769 (mp) REVERT: B 99 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6895 (mmt) REVERT: B 110 MET cc_start: 0.7125 (ttt) cc_final: 0.6882 (ptm) REVERT: B 229 LEU cc_start: 0.7951 (mt) cc_final: 0.7621 (pp) REVERT: B 294 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: B 555 TYR cc_start: 0.6733 (OUTLIER) cc_final: 0.6341 (t80) REVERT: C 99 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6543 (mmt) REVERT: C 215 MET cc_start: 0.8563 (mtp) cc_final: 0.8341 (mtt) REVERT: C 229 LEU cc_start: 0.7954 (mt) cc_final: 0.7687 (pp) REVERT: C 309 ASP cc_start: 0.8406 (p0) cc_final: 0.7783 (t0) REVERT: C 555 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.6340 (t80) REVERT: D 29 TRP cc_start: 0.6082 (OUTLIER) cc_final: 0.5516 (m-90) REVERT: D 45 TRP cc_start: 0.6134 (m-10) cc_final: 0.5884 (m100) REVERT: D 215 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8228 (mtt) REVERT: D 229 LEU cc_start: 0.7998 (mt) cc_final: 0.7710 (pp) REVERT: D 294 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8387 (mt-10) REVERT: D 555 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6122 (t80) outliers start: 72 outliers final: 39 residues processed: 297 average time/residue: 1.0225 time to fit residues: 352.8933 Evaluate side-chains 294 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 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 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2518 > 50: distance: 1 - 27: 37.135 distance: 11 - 33: 26.097 distance: 17 - 41: 28.846 distance: 23 - 27: 34.918 distance: 27 - 28: 8.609 distance: 28 - 29: 10.956 distance: 28 - 31: 48.033 distance: 29 - 30: 15.363 distance: 29 - 33: 37.588 distance: 31 - 32: 8.916 distance: 33 - 34: 47.315 distance: 34 - 35: 38.583 distance: 35 - 36: 46.767 distance: 35 - 41: 58.710 distance: 37 - 38: 20.369 distance: 37 - 39: 20.187 distance: 38 - 40: 18.283 distance: 41 - 42: 45.643 distance: 42 - 43: 52.643 distance: 42 - 45: 34.467 distance: 43 - 44: 33.130 distance: 43 - 53: 45.553 distance: 45 - 46: 28.765 distance: 46 - 47: 43.021 distance: 46 - 48: 19.663 distance: 47 - 49: 6.102 distance: 48 - 50: 41.089 distance: 49 - 51: 14.959 distance: 50 - 51: 26.338 distance: 51 - 52: 45.174 distance: 53 - 54: 34.441 distance: 54 - 55: 44.033 distance: 54 - 57: 40.216 distance: 55 - 56: 25.886 distance: 55 - 64: 42.648 distance: 57 - 58: 41.717 distance: 58 - 59: 12.547 distance: 59 - 60: 58.561 distance: 60 - 61: 19.665 distance: 61 - 62: 42.181 distance: 61 - 63: 56.173 distance: 64 - 65: 10.242 distance: 64 - 70: 42.221 distance: 65 - 66: 5.454 distance: 65 - 68: 5.157 distance: 66 - 67: 45.881 distance: 66 - 71: 21.294 distance: 68 - 69: 46.151 distance: 69 - 70: 41.962 distance: 71 - 72: 4.171 distance: 72 - 73: 12.478 distance: 72 - 75: 56.048 distance: 73 - 74: 27.419 distance: 73 - 79: 36.639 distance: 75 - 76: 5.079 distance: 76 - 77: 61.740 distance: 76 - 78: 22.652 distance: 79 - 80: 28.045 distance: 79 - 161: 33.841 distance: 80 - 81: 3.013 distance: 80 - 83: 53.436 distance: 81 - 82: 5.968 distance: 82 - 158: 31.256 distance: 83 - 84: 3.505 distance: 85 - 86: 23.372 distance: 86 - 87: 16.647 distance: 88 - 89: 10.084 distance: 88 - 94: 43.440 distance: 89 - 90: 46.107 distance: 89 - 92: 50.679 distance: 90 - 91: 15.809 distance: 90 - 95: 31.330 distance: 93 - 94: 16.269 distance: 95 - 96: 40.239 distance: 96 - 99: 48.448 distance: 97 - 98: 40.628 distance: 97 - 106: 41.115 distance: 99 - 100: 19.455 distance: 100 - 101: 33.061 distance: 101 - 102: 14.437 distance: 102 - 103: 6.104 distance: 103 - 104: 31.613 distance: 103 - 105: 42.017 distance: 106 - 107: 39.406 distance: 107 - 108: 9.209 distance: 107 - 110: 59.917 distance: 108 - 109: 7.229 distance: 108 - 113: 30.362 distance: 110 - 111: 28.041 distance: 110 - 112: 55.620