Starting phenix.real_space_refine on Wed Jun 18 11:13:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4a_22662/06_2025/7k4a_22662_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4a_22662/06_2025/7k4a_22662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k4a_22662/06_2025/7k4a_22662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4a_22662/06_2025/7k4a_22662.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4a_22662/06_2025/7k4a_22662_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4a_22662/06_2025/7k4a_22662_neut.cif" } resolution = 3.26 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= 0.019 sd= 0.056 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 1 9.91 5 P 8 5.49 5 S 160 5.16 5 C 13784 2.51 5 N 3324 2.21 5 O 3548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20825 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4868 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 1 Chain: "B" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4868 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 1 Chain: "C" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4868 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 1 Chain: "D" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4868 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 26, 'TRANS': 578} Chain breaks: 1 Chain: "A" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 339 Unusual residues: {' CA': 1, 'PCW': 13, 'Y01': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 568 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PCW:plan-1': 11, 'PCW:plan-2': 3, 'PCW:plan-3': 11, 'PCW:plan-4': 11} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 373 Unusual residues: {'PCW': 13, 'Y01': 4} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 568 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PCW:plan-1': 11, 'PCW:plan-2': 3, 'PCW:plan-3': 11, 'PCW:plan-4': 11} Unresolved non-hydrogen planarities: 123 Chain: "C" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 338 Unusual residues: {'PCW': 13, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 568 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PCW:plan-1': 11, 'PCW:plan-2': 3, 'PCW:plan-3': 11, 'PCW:plan-4': 11} Unresolved non-hydrogen planarities: 123 Chain: "D" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Unusual residues: {'PCW': 13, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 568 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PCW:plan-1': 11, 'PCW:plan-2': 3, 'PCW:plan-3': 11, 'PCW:plan-4': 11} Unresolved non-hydrogen planarities: 123 Time building chain proxies: 15.16, per 1000 atoms: 0.73 Number of scatterers: 20825 At special positions: 0 Unit cell: (142.636, 142.636, 122.38, 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 1 19.99 S 160 16.00 P 8 15.00 O 3548 8.00 N 3324 7.00 C 13784 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: 6.00 Conformation dependent library (CDL) restraints added in 2.9 seconds 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4592 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 52.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 27 through 47 removed outlier: 3.639A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.510A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.229A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.590A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.912A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.518A pdb=" N ARG A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.578A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.935A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.629A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 203' Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.944A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 253 through 261 removed outlier: 4.219A pdb=" N LEU A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.592A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.501A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 310 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 380 through 395 removed outlier: 3.641A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.514A pdb=" N ILE A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 445 removed outlier: 4.016A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.890A pdb=" N ASN A 464 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 499 through 512 removed outlier: 3.558A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.605A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.033A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 578 removed outlier: 3.629A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 588 through 607 removed outlier: 3.519A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.574A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.509A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.229A pdb=" N ILE B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.590A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.912A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.519A pdb=" N ARG B 134 " --> pdb=" O MET B 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.578A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.934A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.631A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 203' Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.944A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 253 through 261 removed outlier: 4.219A pdb=" N LEU B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.592A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.501A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 310 " --> pdb=" O ILE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 380 through 395 removed outlier: 3.641A pdb=" N ARG B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.514A pdb=" N ILE B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 445 removed outlier: 4.016A pdb=" N TYR B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.889A pdb=" N ASN B 464 " --> pdb=" O GLY B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.557A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 539 removed outlier: 3.606A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.033A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 578 removed outlier: 3.629A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 588 through 607 removed outlier: 3.519A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.640A pdb=" N GLN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.510A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.229A pdb=" N ILE C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.590A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.912A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.519A pdb=" N ARG C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.578A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.935A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.630A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 203' Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 210 through 222 removed outlier: 3.943A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.220A pdb=" N LEU C 259 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.593A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.500A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN C 310 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 318 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 339 through 346 Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.642A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 403 through 411 removed outlier: 3.514A pdb=" N ILE C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 445 removed outlier: 4.016A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 removed outlier: 3.890A pdb=" N ASN C 464 " --> pdb=" O GLY C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 499 through 512 removed outlier: 3.557A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 539 removed outlier: 3.606A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.032A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 578 removed outlier: 3.628A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.519A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 47 removed outlier: 3.639A pdb=" N GLN D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.510A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.230A pdb=" N ILE D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.590A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.913A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.518A pdb=" N ARG D 134 " --> pdb=" O MET D 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.578A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.935A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.629A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 203' Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 210 through 222 removed outlier: 3.944A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 253 through 261 removed outlier: 4.220A pdb=" N LEU D 259 " --> pdb=" O MET D 255 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.592A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.786A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN D 310 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 339 through 346 Processing helix chain 'D' and resid 380 through 395 removed outlier: 3.641A pdb=" N ARG D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 403 through 411 removed outlier: 3.514A pdb=" N ILE D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 445 removed outlier: 4.016A pdb=" N TYR D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 465 removed outlier: 3.890A pdb=" N ASN D 464 " --> pdb=" O GLY D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 499 through 512 removed outlier: 3.557A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 539 removed outlier: 3.605A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.032A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.628A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 588 through 607 removed outlier: 3.519A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 617 hydrogen bonds defined for protein. 1776 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: 5.55 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3164 1.31 - 1.44: 5457 1.44 - 1.56: 12227 1.56 - 1.69: 128 1.69 - 1.82: 272 Bond restraints: 21248 Sorted by residual: bond pdb=" C19 PCW C 701 " pdb=" C20 PCW C 701 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C19 PCW D 704 " pdb=" C20 PCW D 704 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C19 PCW A 815 " pdb=" C20 PCW A 815 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C19 PCW B 702 " pdb=" C20 PCW B 702 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C19 PCW A 813 " pdb=" C20 PCW A 813 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.19e+02 ... (remaining 21243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 27732 3.36 - 6.72: 585 6.72 - 10.09: 204 10.09 - 13.45: 39 13.45 - 16.81: 28 Bond angle restraints: 28588 Sorted by residual: angle pdb=" C19 PCW D 703 " pdb=" C20 PCW D 703 " pdb=" C21 PCW D 703 " ideal model delta sigma weight residual 127.82 111.01 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" C19 PCW A 813 " pdb=" C20 PCW A 813 " pdb=" C21 PCW A 813 " ideal model delta sigma weight residual 127.82 111.03 16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" C19 PCW B 717 " pdb=" C20 PCW B 717 " pdb=" C21 PCW B 717 " ideal model delta sigma weight residual 127.82 111.07 16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" C19 PCW C 716 " pdb=" C20 PCW C 716 " pdb=" C21 PCW C 716 " ideal model delta sigma weight residual 127.82 111.11 16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C19 PCW C 707 " pdb=" C20 PCW C 707 " pdb=" C21 PCW C 707 " ideal model delta sigma weight residual 127.82 111.25 16.57 3.00e+00 1.11e-01 3.05e+01 ... (remaining 28583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 12632 24.33 - 48.67: 708 48.67 - 73.00: 152 73.00 - 97.33: 8 97.33 - 121.67: 8 Dihedral angle restraints: 13508 sinusoidal: 6412 harmonic: 7096 Sorted by residual: dihedral pdb=" CA TYR C 67 " pdb=" C TYR C 67 " pdb=" N GLU C 68 " pdb=" CA GLU C 68 " ideal model delta harmonic sigma weight residual 180.00 149.45 30.55 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA TYR A 67 " pdb=" C TYR A 67 " pdb=" N GLU A 68 " pdb=" CA GLU A 68 " ideal model delta harmonic sigma weight residual 180.00 149.46 30.54 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA TYR D 67 " pdb=" C TYR D 67 " pdb=" N GLU D 68 " pdb=" CA GLU D 68 " ideal model delta harmonic sigma weight residual 180.00 149.48 30.52 0 5.00e+00 4.00e-02 3.73e+01 ... (remaining 13505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2345 0.059 - 0.118: 667 0.118 - 0.178: 99 0.178 - 0.237: 41 0.237 - 0.296: 20 Chirality restraints: 3172 Sorted by residual: chirality pdb=" C2 PCW D 708 " pdb=" C1 PCW D 708 " pdb=" C3 PCW D 708 " pdb=" O2 PCW D 708 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2 PCW B 707 " pdb=" C1 PCW B 707 " pdb=" C3 PCW B 707 " pdb=" O2 PCW B 707 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C2 PCW C 706 " pdb=" C1 PCW C 706 " pdb=" C3 PCW C 706 " pdb=" O2 PCW C 706 " both_signs ideal model delta sigma weight residual False -2.32 -2.61 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3169 not shown) Planarity restraints: 3500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW C 701 " -0.167 2.00e-02 2.50e+03 2.43e-01 5.91e+02 pdb=" C19 PCW C 701 " 0.344 2.00e-02 2.50e+03 pdb=" C20 PCW C 701 " -0.281 2.00e-02 2.50e+03 pdb=" C21 PCW C 701 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW D 704 " -0.166 2.00e-02 2.50e+03 2.42e-01 5.87e+02 pdb=" C19 PCW D 704 " 0.342 2.00e-02 2.50e+03 pdb=" C20 PCW D 704 " -0.281 2.00e-02 2.50e+03 pdb=" C21 PCW D 704 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW B 702 " 0.164 2.00e-02 2.50e+03 2.39e-01 5.70e+02 pdb=" C19 PCW B 702 " -0.336 2.00e-02 2.50e+03 pdb=" C20 PCW B 702 " 0.278 2.00e-02 2.50e+03 pdb=" C21 PCW B 702 " -0.106 2.00e-02 2.50e+03 ... (remaining 3497 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4927 2.79 - 3.32: 17146 3.32 - 3.85: 30713 3.85 - 4.37: 38375 4.37 - 4.90: 65716 Nonbonded interactions: 156877 Sorted by model distance: nonbonded pdb=" OD2 ASP A 489 " pdb=" OG1 THR A 581 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP C 489 " pdb=" OG1 THR C 581 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP B 489 " pdb=" OG1 THR B 581 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP D 489 " pdb=" OG1 THR D 581 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.323 3.040 ... (remaining 156872 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 25 through 638 or (resid 808 and (name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 809 and (name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (resid 8 \ 10 and (name C15 or name C16 or name C17 or name C18 or name C19)) or (resid 812 \ through 813 and (name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19)) or (resid 815 and (name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'B' and (resid 25 through 638 or (resid 708 and (name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 709 and (name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (resid 7 \ 10 and (name C15 or name C16 or name C17 or name C18 or name C19)) or (resid 712 \ through 713 and (name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19)) or (resid 715 and (name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'C' and (resid 25 through 638 or (resid 708 and (name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 709 and (name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (resid 7 \ 10 and (name C15 or name C16 or name C17 or name C18 or name C19)) or (resid 712 \ through 713 and (name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19)) or (resid 715 and (name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'D' and (resid 25 through 638 or (resid 708 and (name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 709 and (name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (resid 7 \ 10 and (name C15 or name C16 or name C17 or name C18 or name C19)) or resid 712 \ through 713 or resid 715)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 49.180 Find NCS groups from input model: 1.160 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.013 0.220 21248 Z= 0.641 Angle : 1.438 16.811 28588 Z= 0.681 Chirality : 0.060 0.296 3172 Planarity : 0.014 0.243 3500 Dihedral : 15.267 121.667 8916 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.48 % Favored : 89.35 % Rotamer: Outliers : 0.52 % Allowed : 4.03 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -6.74 (0.11), residues: 2404 helix: -4.58 (0.06), residues: 1332 sheet: -5.14 (0.26), residues: 84 loop : -4.06 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 613 HIS 0.016 0.002 HIS C 522 PHE 0.026 0.003 PHE C 169 TYR 0.034 0.003 TYR D 547 ARG 0.009 0.001 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.34529 ( 617) hydrogen bonds : angle 9.75634 ( 1776) covalent geometry : bond 0.01336 (21248) covalent geometry : angle 1.43797 (28588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 460 time to evaluate : 2.143 Fit side-chains REVERT: A 146 ARG cc_start: 0.7490 (mmt180) cc_final: 0.7134 (mmm-85) REVERT: A 309 ASP cc_start: 0.8788 (t70) cc_final: 0.8418 (t0) REVERT: A 491 MET cc_start: 0.7518 (mmp) cc_final: 0.7248 (mmp) REVERT: A 565 ILE cc_start: 0.8910 (tp) cc_final: 0.8544 (tp) REVERT: A 592 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8028 (mt) REVERT: A 618 ILE cc_start: 0.8386 (mp) cc_final: 0.8044 (tp) REVERT: A 637 GLN cc_start: 0.8230 (mt0) cc_final: 0.8025 (mt0) REVERT: B 146 ARG cc_start: 0.7455 (mmt180) cc_final: 0.7111 (mmm-85) REVERT: B 174 ASN cc_start: 0.8749 (t0) cc_final: 0.8459 (t0) REVERT: B 309 ASP cc_start: 0.8778 (t70) cc_final: 0.8422 (t0) REVERT: B 491 MET cc_start: 0.7514 (mmp) cc_final: 0.7211 (mmp) REVERT: B 565 ILE cc_start: 0.8876 (tp) cc_final: 0.8520 (tp) REVERT: B 618 ILE cc_start: 0.8411 (mp) cc_final: 0.8046 (tp) REVERT: B 637 GLN cc_start: 0.8210 (mt0) cc_final: 0.8005 (mt0) REVERT: C 234 LEU cc_start: 0.7681 (mt) cc_final: 0.7461 (mt) REVERT: C 309 ASP cc_start: 0.8690 (t70) cc_final: 0.8298 (t0) REVERT: C 491 MET cc_start: 0.7334 (mmp) cc_final: 0.6986 (mmp) REVERT: C 565 ILE cc_start: 0.8769 (tp) cc_final: 0.8364 (tp) REVERT: C 578 MET cc_start: 0.8541 (mtt) cc_final: 0.8322 (mtp) REVERT: C 589 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7269 (tpp-160) REVERT: C 618 ILE cc_start: 0.7987 (mp) cc_final: 0.7601 (tp) REVERT: C 629 TRP cc_start: 0.7740 (m100) cc_final: 0.7534 (m100) REVERT: D 146 ARG cc_start: 0.7176 (mmt180) cc_final: 0.6734 (mmm-85) REVERT: D 309 ASP cc_start: 0.8754 (t70) cc_final: 0.8325 (t0) REVERT: D 491 MET cc_start: 0.7298 (mmp) cc_final: 0.6980 (mmp) REVERT: D 565 ILE cc_start: 0.8805 (tp) cc_final: 0.8397 (tp) REVERT: D 578 MET cc_start: 0.8528 (mtt) cc_final: 0.8318 (mtp) REVERT: D 589 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.7261 (tpp-160) REVERT: D 590 ASP cc_start: 0.7475 (m-30) cc_final: 0.7264 (p0) REVERT: D 618 ILE cc_start: 0.7845 (mp) cc_final: 0.7475 (tp) REVERT: D 637 GLN cc_start: 0.8108 (mt0) cc_final: 0.7822 (mt0) outliers start: 11 outliers final: 8 residues processed: 471 average time/residue: 0.3732 time to fit residues: 255.2210 Evaluate side-chains 284 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 275 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 0.0970 chunk 217 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 37 ASN A 73 HIS A 165 HIS A 174 ASN A 206 GLN A 217 ASN A 237 ASN A 238 HIS A 265 HIS A 426 HIS A 522 HIS B 31 GLN B 37 ASN B 73 HIS B 165 HIS B 206 GLN B 217 ASN B 237 ASN B 238 HIS B 265 HIS B 290 GLN B 426 HIS B 522 HIS C 31 GLN C 37 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 217 ASN C 237 ASN C 238 HIS C 265 HIS C 290 GLN C 426 HIS C 522 HIS D 31 GLN D 37 ASN D 165 HIS D 174 ASN D 206 GLN D 217 ASN D 237 ASN D 238 HIS D 265 HIS D 290 GLN D 426 HIS D 522 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.181340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132954 restraints weight = 23745.635| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.71 r_work: 0.3321 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21248 Z= 0.114 Angle : 0.649 9.242 28588 Z= 0.326 Chirality : 0.040 0.182 3172 Planarity : 0.005 0.052 3500 Dihedral : 14.066 89.679 4222 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.51 % Allowed : 7.64 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.19 (0.14), residues: 2404 helix: -3.07 (0.11), residues: 1304 sheet: -4.95 (0.30), residues: 84 loop : -3.73 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 613 HIS 0.006 0.001 HIS A 73 PHE 0.012 0.001 PHE B 434 TYR 0.011 0.001 TYR B 216 ARG 0.009 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 617) hydrogen bonds : angle 4.70953 ( 1776) covalent geometry : bond 0.00245 (21248) covalent geometry : angle 0.64933 (28588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 322 time to evaluate : 2.192 Fit side-chains REVERT: A 306 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: A 309 ASP cc_start: 0.8827 (t70) cc_final: 0.8625 (t0) REVERT: A 337 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8360 (tp) REVERT: A 466 MET cc_start: 0.8851 (mtm) cc_final: 0.8636 (mtp) REVERT: A 491 MET cc_start: 0.8396 (mmp) cc_final: 0.8192 (mmp) REVERT: B 96 MET cc_start: 0.8231 (mmm) cc_final: 0.8021 (mmp) REVERT: B 306 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: B 337 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8339 (tp) REVERT: B 466 MET cc_start: 0.8867 (mtm) cc_final: 0.8656 (mtp) REVERT: B 491 MET cc_start: 0.8389 (mmp) cc_final: 0.8185 (mmp) REVERT: B 621 ARG cc_start: 0.7726 (mtp-110) cc_final: 0.7414 (mtp-110) REVERT: C 233 ASP cc_start: 0.7716 (p0) cc_final: 0.7495 (p0) REVERT: C 306 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: C 309 ASP cc_start: 0.8828 (t70) cc_final: 0.8621 (t0) REVERT: C 337 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8360 (tp) REVERT: C 466 MET cc_start: 0.8874 (mtm) cc_final: 0.8671 (mtp) REVERT: C 629 TRP cc_start: 0.8464 (m100) cc_final: 0.8225 (m100) REVERT: D 306 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: D 309 ASP cc_start: 0.8930 (t70) cc_final: 0.8695 (t0) REVERT: D 337 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8495 (tm) REVERT: D 491 MET cc_start: 0.8417 (mmp) cc_final: 0.8216 (mmp) outliers start: 53 outliers final: 10 residues processed: 354 average time/residue: 0.2794 time to fit residues: 160.6115 Evaluate side-chains 271 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 0 optimal weight: 30.0000 chunk 234 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 132 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 118 GLN A 122 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 118 GLN B 122 HIS B 174 ASN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 118 GLN C 122 HIS ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 118 GLN D 122 HIS D 265 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129549 restraints weight = 23558.369| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.75 r_work: 0.3223 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21248 Z= 0.157 Angle : 0.662 8.949 28588 Z= 0.329 Chirality : 0.042 0.177 3172 Planarity : 0.004 0.045 3500 Dihedral : 13.247 85.346 4217 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.13 % Allowed : 10.44 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.29 (0.15), residues: 2404 helix: -2.14 (0.13), residues: 1300 sheet: -4.45 (0.35), residues: 84 loop : -3.62 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 613 HIS 0.003 0.001 HIS D 265 PHE 0.017 0.002 PHE B 493 TYR 0.014 0.002 TYR D 216 ARG 0.005 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 617) hydrogen bonds : angle 4.30943 ( 1776) covalent geometry : bond 0.00380 (21248) covalent geometry : angle 0.66193 (28588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 2.434 Fit side-chains REVERT: A 219 LEU cc_start: 0.8717 (mt) cc_final: 0.8437 (mp) REVERT: A 306 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: A 319 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8557 (tt) REVERT: A 337 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8486 (tp) REVERT: A 565 ILE cc_start: 0.8987 (tp) cc_final: 0.8678 (tp) REVERT: B 219 LEU cc_start: 0.8711 (mt) cc_final: 0.8408 (mp) REVERT: B 306 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: B 319 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8562 (tt) REVERT: B 337 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8489 (tp) REVERT: B 565 ILE cc_start: 0.9009 (tp) cc_final: 0.8659 (tp) REVERT: B 621 ARG cc_start: 0.7681 (mtp-110) cc_final: 0.7399 (mtp-110) REVERT: C 219 LEU cc_start: 0.8732 (mt) cc_final: 0.8441 (mp) REVERT: C 306 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: C 319 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8558 (tt) REVERT: C 337 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8494 (tp) REVERT: D 306 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: D 319 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8545 (tt) REVERT: D 337 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8492 (tp) REVERT: D 565 ILE cc_start: 0.9023 (tp) cc_final: 0.8675 (tp) outliers start: 45 outliers final: 26 residues processed: 292 average time/residue: 0.2995 time to fit residues: 139.8524 Evaluate side-chains 267 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 0.0040 chunk 109 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 265 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS D 546 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.176272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129693 restraints weight = 23790.188| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.66 r_work: 0.3252 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21248 Z= 0.135 Angle : 0.623 9.168 28588 Z= 0.311 Chirality : 0.041 0.178 3172 Planarity : 0.004 0.044 3500 Dihedral : 12.787 81.515 4217 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.08 % Allowed : 10.58 % Favored : 86.34 % 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: -3.72 (0.16), residues: 2404 helix: -1.57 (0.14), residues: 1304 sheet: -4.09 (0.37), residues: 84 loop : -3.54 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 613 HIS 0.004 0.001 HIS D 265 PHE 0.012 0.001 PHE C 553 TYR 0.011 0.001 TYR A 216 ARG 0.004 0.000 ARG C 305 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 617) hydrogen bonds : angle 4.07532 ( 1776) covalent geometry : bond 0.00323 (21248) covalent geometry : angle 0.62287 (28588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 266 time to evaluate : 2.189 Fit side-chains REVERT: A 160 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8179 (pp) REVERT: A 219 LEU cc_start: 0.8723 (mt) cc_final: 0.8449 (mp) REVERT: A 274 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8842 (p) REVERT: A 306 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: A 319 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8555 (tt) REVERT: A 337 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8464 (tp) REVERT: A 366 THR cc_start: 0.9022 (t) cc_final: 0.8809 (t) REVERT: A 592 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8324 (mt) REVERT: A 637 GLN cc_start: 0.8178 (mp10) cc_final: 0.7874 (mp10) REVERT: B 160 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8219 (pp) REVERT: B 215 MET cc_start: 0.8200 (mmm) cc_final: 0.7964 (mmm) REVERT: B 219 LEU cc_start: 0.8727 (mt) cc_final: 0.8429 (mp) REVERT: B 274 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8849 (p) REVERT: B 306 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: B 319 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8584 (tt) REVERT: B 337 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8468 (tp) REVERT: B 366 THR cc_start: 0.8999 (t) cc_final: 0.8781 (t) REVERT: B 637 GLN cc_start: 0.8165 (mp10) cc_final: 0.7851 (mp10) REVERT: C 160 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8197 (pp) REVERT: C 306 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: C 319 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8561 (tt) REVERT: C 337 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8475 (tp) REVERT: C 366 THR cc_start: 0.9042 (t) cc_final: 0.8822 (t) REVERT: D 160 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8179 (pp) REVERT: D 274 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8873 (p) REVERT: D 319 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8557 (tt) REVERT: D 337 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8464 (tp) REVERT: D 366 THR cc_start: 0.8997 (t) cc_final: 0.8774 (t) REVERT: D 637 GLN cc_start: 0.8134 (mp10) cc_final: 0.7833 (mp10) outliers start: 65 outliers final: 25 residues processed: 319 average time/residue: 0.2823 time to fit residues: 145.6686 Evaluate side-chains 290 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 540 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 119 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS B 546 ASN C 265 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.177573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131237 restraints weight = 23694.966| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.61 r_work: 0.3275 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21248 Z= 0.122 Angle : 0.612 10.034 28588 Z= 0.303 Chirality : 0.040 0.177 3172 Planarity : 0.004 0.045 3500 Dihedral : 12.157 77.997 4209 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.46 % Allowed : 11.62 % Favored : 84.91 % 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: -3.25 (0.16), residues: 2404 helix: -1.16 (0.14), residues: 1320 sheet: -3.88 (0.40), residues: 84 loop : -3.39 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 613 HIS 0.004 0.001 HIS D 265 PHE 0.013 0.001 PHE D 256 TYR 0.011 0.001 TYR B 555 ARG 0.004 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 617) hydrogen bonds : angle 3.90941 ( 1776) covalent geometry : bond 0.00287 (21248) covalent geometry : angle 0.61160 (28588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 267 time to evaluate : 2.263 Fit side-chains REVERT: A 160 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8101 (pp) REVERT: A 274 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8815 (p) REVERT: A 306 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: A 319 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8561 (tt) REVERT: A 337 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8453 (tp) REVERT: A 592 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8228 (mt) REVERT: A 637 GLN cc_start: 0.8191 (mp10) cc_final: 0.7694 (mp10) REVERT: B 160 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8118 (pp) REVERT: B 274 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8831 (p) REVERT: B 306 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: B 319 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8558 (tt) REVERT: B 337 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8467 (tp) REVERT: B 637 GLN cc_start: 0.8162 (mp10) cc_final: 0.7664 (mp10) REVERT: C 160 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8137 (pp) REVERT: C 233 ASP cc_start: 0.7597 (p0) cc_final: 0.7363 (p0) REVERT: C 306 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: C 319 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8523 (tt) REVERT: C 337 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8485 (tp) REVERT: D 160 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8094 (pp) REVERT: D 176 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: D 306 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: D 309 ASP cc_start: 0.8911 (t0) cc_final: 0.8576 (t0) REVERT: D 319 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8540 (tt) REVERT: D 337 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8465 (tp) REVERT: D 366 THR cc_start: 0.9021 (t) cc_final: 0.8818 (t) REVERT: D 429 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8027 (mt) REVERT: D 637 GLN cc_start: 0.8127 (mp10) cc_final: 0.7627 (mp10) outliers start: 73 outliers final: 32 residues processed: 325 average time/residue: 0.2881 time to fit residues: 150.6108 Evaluate side-chains 294 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 540 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 231 optimal weight: 0.0670 chunk 164 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 546 ASN B 265 HIS C 265 HIS C 546 ASN D 265 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.180092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123229 restraints weight = 23534.421| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.62 r_work: 0.3285 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21248 Z= 0.121 Angle : 0.619 9.057 28588 Z= 0.303 Chirality : 0.041 0.185 3172 Planarity : 0.004 0.045 3500 Dihedral : 11.552 80.008 4209 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.51 % Allowed : 12.90 % Favored : 83.59 % 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: -2.90 (0.17), residues: 2404 helix: -0.85 (0.15), residues: 1316 sheet: -3.48 (0.44), residues: 84 loop : -3.30 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 613 HIS 0.005 0.001 HIS D 265 PHE 0.014 0.001 PHE D 553 TYR 0.012 0.001 TYR D 216 ARG 0.006 0.000 ARG B 621 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 617) hydrogen bonds : angle 3.81705 ( 1776) covalent geometry : bond 0.00285 (21248) covalent geometry : angle 0.61907 (28588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 270 time to evaluate : 2.398 Fit side-chains REVERT: A 160 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8011 (pp) REVERT: A 233 ASP cc_start: 0.7615 (p0) cc_final: 0.7356 (p0) REVERT: A 274 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 306 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: A 319 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8561 (tt) REVERT: A 337 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8452 (tp) REVERT: A 592 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8183 (mt) REVERT: A 637 GLN cc_start: 0.8193 (mp10) cc_final: 0.7655 (mp10) REVERT: B 160 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8086 (pp) REVERT: B 233 ASP cc_start: 0.7599 (p0) cc_final: 0.7368 (p0) REVERT: B 274 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8774 (p) REVERT: B 319 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8542 (tt) REVERT: B 337 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8446 (tp) REVERT: B 637 GLN cc_start: 0.8187 (mp10) cc_final: 0.7644 (mp10) REVERT: C 160 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8060 (pp) REVERT: C 319 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8532 (tt) REVERT: C 337 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8478 (tp) REVERT: D 160 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8048 (pp) REVERT: D 219 LEU cc_start: 0.8219 (mp) cc_final: 0.7945 (mp) REVERT: D 233 ASP cc_start: 0.7642 (p0) cc_final: 0.7436 (p0) REVERT: D 255 MET cc_start: 0.8597 (mmm) cc_final: 0.8314 (tpt) REVERT: D 306 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: D 309 ASP cc_start: 0.8942 (t0) cc_final: 0.8649 (t0) REVERT: D 319 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8579 (tt) REVERT: D 337 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8452 (tp) REVERT: D 366 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8817 (t) REVERT: D 429 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7977 (mt) REVERT: D 637 GLN cc_start: 0.8091 (mp10) cc_final: 0.7832 (mp10) outliers start: 74 outliers final: 33 residues processed: 326 average time/residue: 0.2849 time to fit residues: 150.7553 Evaluate side-chains 304 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 540 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 89 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 49 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 206 optimal weight: 8.9990 chunk 112 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 265 HIS B 265 HIS C 265 HIS D 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.184292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144112 restraints weight = 23725.963| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.23 r_work: 0.3270 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21248 Z= 0.101 Angle : 0.588 9.358 28588 Z= 0.288 Chirality : 0.040 0.177 3172 Planarity : 0.004 0.045 3500 Dihedral : 10.859 80.559 4209 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.08 % Allowed : 13.52 % Favored : 83.40 % 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: -2.56 (0.17), residues: 2404 helix: -0.55 (0.15), residues: 1320 sheet: -2.99 (0.47), residues: 84 loop : -3.22 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 613 HIS 0.005 0.001 HIS D 265 PHE 0.009 0.001 PHE A 244 TYR 0.010 0.001 TYR B 555 ARG 0.006 0.000 ARG A 621 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 617) hydrogen bonds : angle 3.67157 ( 1776) covalent geometry : bond 0.00225 (21248) covalent geometry : angle 0.58849 (28588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 277 time to evaluate : 2.404 Fit side-chains REVERT: A 160 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 306 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: A 319 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8564 (tt) REVERT: A 337 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8389 (tp) REVERT: A 565 ILE cc_start: 0.8882 (tp) cc_final: 0.8589 (tp) REVERT: A 637 GLN cc_start: 0.8151 (mp10) cc_final: 0.7829 (mp10) REVERT: B 160 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8041 (pp) REVERT: B 319 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8561 (tt) REVERT: B 337 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 437 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8101 (mt) REVERT: B 637 GLN cc_start: 0.8156 (mp10) cc_final: 0.7815 (mp10) REVERT: C 160 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8064 (pp) REVERT: C 169 PHE cc_start: 0.8432 (m-80) cc_final: 0.8066 (m-80) REVERT: C 255 MET cc_start: 0.8402 (mmm) cc_final: 0.8115 (tpt) REVERT: C 306 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: C 319 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8534 (tt) REVERT: C 337 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8421 (tp) REVERT: C 437 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8087 (mt) REVERT: D 96 MET cc_start: 0.8349 (mmp) cc_final: 0.8146 (mtm) REVERT: D 160 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7991 (pp) REVERT: D 255 MET cc_start: 0.8453 (mmm) cc_final: 0.8218 (tpt) REVERT: D 306 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: D 309 ASP cc_start: 0.8855 (t0) cc_final: 0.8547 (t0) REVERT: D 319 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8578 (tt) REVERT: D 337 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8390 (tp) REVERT: D 366 THR cc_start: 0.8978 (t) cc_final: 0.8756 (t) REVERT: D 429 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7925 (mt) REVERT: D 590 ASP cc_start: 0.8189 (t70) cc_final: 0.7696 (m-30) outliers start: 65 outliers final: 27 residues processed: 325 average time/residue: 0.2987 time to fit residues: 157.2722 Evaluate side-chains 290 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 540 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 106 optimal weight: 0.0980 chunk 209 optimal weight: 0.2980 chunk 72 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 197 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 125 optimal weight: 0.0020 chunk 191 optimal weight: 10.0000 chunk 188 optimal weight: 30.0000 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS B 265 HIS C 265 HIS D 118 GLN D 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.185321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132150 restraints weight = 23723.317| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.64 r_work: 0.3429 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21248 Z= 0.100 Angle : 0.596 10.191 28588 Z= 0.287 Chirality : 0.040 0.174 3172 Planarity : 0.004 0.073 3500 Dihedral : 10.454 81.208 4209 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 3.04 % Allowed : 13.95 % Favored : 83.02 % 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: -2.28 (0.17), residues: 2404 helix: -0.27 (0.15), residues: 1324 sheet: -2.53 (0.50), residues: 84 loop : -3.22 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 613 HIS 0.006 0.001 HIS D 265 PHE 0.009 0.001 PHE D 244 TYR 0.011 0.001 TYR D 216 ARG 0.006 0.000 ARG A 621 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 617) hydrogen bonds : angle 3.64751 ( 1776) covalent geometry : bond 0.00222 (21248) covalent geometry : angle 0.59607 (28588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8418 (mmp) cc_final: 0.8181 (mtm) REVERT: A 160 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7977 (pp) REVERT: A 306 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: A 309 ASP cc_start: 0.8773 (t0) cc_final: 0.8488 (t0) REVERT: A 337 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8356 (tp) REVERT: A 437 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8080 (mt) REVERT: A 565 ILE cc_start: 0.8869 (tp) cc_final: 0.8624 (tp) REVERT: A 637 GLN cc_start: 0.8176 (mp10) cc_final: 0.7908 (mp10) REVERT: B 160 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8032 (pp) REVERT: B 306 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: B 309 ASP cc_start: 0.8807 (t0) cc_final: 0.8521 (t0) REVERT: B 319 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8553 (tt) REVERT: B 337 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8388 (tp) REVERT: B 437 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8129 (mt) REVERT: B 637 GLN cc_start: 0.8138 (mp10) cc_final: 0.7863 (mp10) REVERT: C 160 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8049 (pp) REVERT: C 169 PHE cc_start: 0.8361 (m-80) cc_final: 0.8000 (m-80) REVERT: C 255 MET cc_start: 0.8328 (mmm) cc_final: 0.8065 (tpt) REVERT: C 306 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: C 309 ASP cc_start: 0.8745 (t0) cc_final: 0.8482 (t0) REVERT: C 319 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8522 (tt) REVERT: C 337 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8405 (tp) REVERT: C 437 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8114 (mt) REVERT: D 160 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7970 (pp) REVERT: D 255 MET cc_start: 0.8363 (mmm) cc_final: 0.8158 (tpt) REVERT: D 306 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: D 309 ASP cc_start: 0.8817 (t0) cc_final: 0.8504 (t0) REVERT: D 319 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8522 (tt) REVERT: D 337 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8353 (tp) REVERT: D 366 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8784 (t) REVERT: D 437 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8074 (mt) REVERT: D 637 GLN cc_start: 0.8033 (mp10) cc_final: 0.7776 (mp10) outliers start: 64 outliers final: 27 residues processed: 314 average time/residue: 0.2941 time to fit residues: 148.2987 Evaluate side-chains 294 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 540 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 160 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 265 HIS B 265 HIS C 265 HIS D 118 GLN D 265 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.176644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127344 restraints weight = 23690.132| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.45 r_work: 0.3285 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21248 Z= 0.202 Angle : 0.711 11.056 28588 Z= 0.343 Chirality : 0.045 0.182 3172 Planarity : 0.005 0.077 3500 Dihedral : 11.378 86.092 4209 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 2.85 % Allowed : 14.37 % Favored : 82.78 % 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: -2.42 (0.17), residues: 2404 helix: -0.44 (0.15), residues: 1340 sheet: -2.42 (0.52), residues: 84 loop : -3.25 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 613 HIS 0.016 0.001 HIS D 265 PHE 0.013 0.002 PHE D 256 TYR 0.021 0.002 TYR B 328 ARG 0.007 0.000 ARG C 621 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 617) hydrogen bonds : angle 4.11045 ( 1776) covalent geometry : bond 0.00500 (21248) covalent geometry : angle 0.71073 (28588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 258 time to evaluate : 2.476 Fit side-chains REVERT: A 160 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8081 (pp) REVERT: A 215 MET cc_start: 0.7576 (mmm) cc_final: 0.7256 (mmm) REVERT: A 219 LEU cc_start: 0.8566 (mt) cc_final: 0.8236 (mp) REVERT: A 306 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: A 309 ASP cc_start: 0.8814 (t0) cc_final: 0.8553 (t0) REVERT: A 337 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 437 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8243 (mt) REVERT: A 565 ILE cc_start: 0.8892 (tp) cc_final: 0.8611 (tp) REVERT: A 592 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8161 (mt) REVERT: A 637 GLN cc_start: 0.8190 (mp10) cc_final: 0.7785 (mp10) REVERT: B 160 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8102 (pp) REVERT: B 309 ASP cc_start: 0.8812 (t0) cc_final: 0.8562 (t0) REVERT: B 319 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8517 (tt) REVERT: B 337 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8501 (tp) REVERT: B 437 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8239 (mt) REVERT: B 565 ILE cc_start: 0.8943 (tp) cc_final: 0.8608 (tp) REVERT: B 637 GLN cc_start: 0.8179 (mp10) cc_final: 0.7777 (mp10) REVERT: C 160 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8113 (pp) REVERT: C 309 ASP cc_start: 0.8766 (t0) cc_final: 0.8534 (t0) REVERT: C 319 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8531 (tt) REVERT: C 337 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8501 (tp) REVERT: C 437 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8236 (mt) REVERT: C 565 ILE cc_start: 0.8942 (tp) cc_final: 0.8613 (tp) REVERT: D 160 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8088 (pp) REVERT: D 306 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: D 309 ASP cc_start: 0.8871 (t0) cc_final: 0.8559 (t0) REVERT: D 319 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8525 (tt) REVERT: D 337 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8526 (tp) REVERT: D 437 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8300 (mt) REVERT: D 565 ILE cc_start: 0.8953 (tp) cc_final: 0.8611 (tp) outliers start: 60 outliers final: 25 residues processed: 307 average time/residue: 0.3556 time to fit residues: 175.7322 Evaluate side-chains 283 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 540 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 50 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 GLN D 265 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.177694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126275 restraints weight = 23693.980| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.42 r_work: 0.3299 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21248 Z= 0.155 Angle : 0.675 12.525 28588 Z= 0.323 Chirality : 0.043 0.177 3172 Planarity : 0.005 0.071 3500 Dihedral : 11.243 87.334 4209 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 2.56 % Allowed : 15.61 % Favored : 81.83 % 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: -2.38 (0.17), residues: 2404 helix: -0.41 (0.15), residues: 1348 sheet: -2.32 (0.54), residues: 84 loop : -3.27 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 613 HIS 0.005 0.001 HIS B 265 PHE 0.013 0.001 PHE B 456 TYR 0.024 0.001 TYR A 328 ARG 0.007 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 617) hydrogen bonds : angle 3.96169 ( 1776) covalent geometry : bond 0.00380 (21248) covalent geometry : angle 0.67540 (28588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 2.369 Fit side-chains REVERT: A 160 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8018 (pp) REVERT: A 215 MET cc_start: 0.7493 (mmm) cc_final: 0.7224 (mmm) REVERT: A 219 LEU cc_start: 0.8530 (mt) cc_final: 0.8226 (mp) REVERT: A 309 ASP cc_start: 0.8769 (t0) cc_final: 0.8502 (t0) REVERT: A 337 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8470 (tp) REVERT: A 437 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8306 (mt) REVERT: A 565 ILE cc_start: 0.8903 (tp) cc_final: 0.8669 (tp) REVERT: A 592 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8164 (mt) REVERT: B 160 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8050 (pp) REVERT: B 309 ASP cc_start: 0.8791 (t0) cc_final: 0.8535 (t0) REVERT: B 319 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8545 (tt) REVERT: B 337 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8458 (tp) REVERT: B 437 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8215 (mt) REVERT: C 96 MET cc_start: 0.8366 (mmp) cc_final: 0.8164 (mtm) REVERT: C 160 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8067 (pp) REVERT: C 309 ASP cc_start: 0.8757 (t0) cc_final: 0.8504 (t0) REVERT: C 319 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8511 (tt) REVERT: C 337 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8465 (tp) REVERT: C 437 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8206 (mt) REVERT: D 160 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8020 (pp) REVERT: D 306 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: D 309 ASP cc_start: 0.8881 (t0) cc_final: 0.8566 (t0) REVERT: D 319 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8551 (tt) REVERT: D 337 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8487 (tp) REVERT: D 437 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8328 (mt) outliers start: 54 outliers final: 25 residues processed: 298 average time/residue: 0.2881 time to fit residues: 139.4811 Evaluate side-chains 283 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 540 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 47 optimal weight: 0.6980 chunk 68 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 229 optimal weight: 0.0070 chunk 20 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 234 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.183846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136686 restraints weight = 23802.651| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.45 r_work: 0.3428 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.002 0.031 21248 Z= 0.106 Angle : 0.620 12.870 28588 Z= 0.298 Chirality : 0.040 0.178 3172 Planarity : 0.004 0.067 3500 Dihedral : 10.766 89.134 4209 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.32 % Allowed : 15.84 % Favored : 81.83 % 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: -2.04 (0.17), residues: 2404 helix: -0.11 (0.15), residues: 1348 sheet: -2.13 (0.55), residues: 84 loop : -3.15 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 321 HIS 0.004 0.001 HIS C 265 PHE 0.020 0.001 PHE B 553 TYR 0.014 0.001 TYR C 328 ARG 0.007 0.000 ARG A 621 Details of bonding type rmsd hydrogen bonds : bond 0.02718 ( 617) hydrogen bonds : angle 3.72839 ( 1776) covalent geometry : bond 0.00233 (21248) covalent geometry : angle 0.61979 (28588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12905.80 seconds wall clock time: 223 minutes 3.92 seconds (13383.92 seconds total)