Starting phenix.real_space_refine on Sun Aug 24 16:01:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4a_22662/08_2025/7k4a_22662_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4a_22662/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k4a_22662/08_2025/7k4a_22662_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4a_22662/08_2025/7k4a_22662_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k4a_22662/08_2025/7k4a_22662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4a_22662/08_2025/7k4a_22662.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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-3': 11, 'PCW:plan-4': 11, 'PCW:plan-2': 3} 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-3': 11, 'PCW:plan-4': 11, 'PCW:plan-2': 3} 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-3': 11, 'PCW:plan-4': 11, 'PCW:plan-2': 3} 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-3': 11, 'PCW:plan-4': 11, 'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 123 Time building chain proxies: 4.86, per 1000 atoms: 0.23 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: 1.63 Conformation dependent library (CDL) restraints added in 826.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.67 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: 2.52 Time building geometry restraints manager: 2.23 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 17.720 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.720 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.001 ARG B 146 TYR 0.034 0.003 TYR D 547 PHE 0.026 0.003 PHE C 169 TRP 0.030 0.003 TRP A 613 HIS 0.016 0.002 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.01336 (21248) covalent geometry : angle 1.43797 (28588) hydrogen bonds : bond 0.34529 ( 617) hydrogen bonds : angle 9.75634 ( 1776) *********************** 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 : 0.807 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: 0.1857 time to fit residues: 127.5881 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 : 0.788 ------------------------------------------------------------------------------- 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 216 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 118 GLN 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 ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 37 ASN C 174 ASN C 206 GLN C 217 ASN C 237 ASN C 238 HIS C 265 HIS C 290 GLN C 426 HIS C 522 HIS C 546 ASN D 31 GLN D 37 ASN D 118 GLN 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 D 546 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.176795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128743 restraints weight = 23641.916| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.71 r_work: 0.3233 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21248 Z= 0.145 Angle : 0.688 9.356 28588 Z= 0.344 Chirality : 0.042 0.183 3172 Planarity : 0.005 0.053 3500 Dihedral : 14.315 91.543 4222 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.44 % Favored : 91.39 % Rotamer: Outliers : 2.80 % Allowed : 7.40 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.19 (0.14), residues: 2404 helix: -3.06 (0.11), residues: 1296 sheet: -4.96 (0.29), residues: 84 loop : -3.73 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 305 TYR 0.011 0.001 TYR C 547 PHE 0.014 0.002 PHE B 256 TRP 0.016 0.001 TRP C 613 HIS 0.005 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00343 (21248) covalent geometry : angle 0.68835 (28588) hydrogen bonds : bond 0.04000 ( 617) hydrogen bonds : angle 4.77837 ( 1776) *********************** 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 359 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 0.816 Fit side-chains REVERT: A 96 MET cc_start: 0.8190 (mmm) cc_final: 0.7978 (mmp) REVERT: A 306 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: A 309 ASP cc_start: 0.8864 (t70) cc_final: 0.8657 (t0) REVERT: A 337 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8472 (tp) REVERT: A 592 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8352 (mt) REVERT: B 96 MET cc_start: 0.8215 (mmm) cc_final: 0.8010 (mmp) REVERT: B 306 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: B 337 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8459 (tp) REVERT: B 491 MET cc_start: 0.8424 (mmp) cc_final: 0.8224 (mmp) REVERT: B 592 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8323 (mt) REVERT: B 621 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.7357 (mtp-110) REVERT: C 96 MET cc_start: 0.8225 (mmm) cc_final: 0.8011 (mmp) REVERT: C 233 ASP cc_start: 0.7813 (p0) cc_final: 0.7574 (p0) REVERT: C 306 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: C 309 ASP cc_start: 0.8836 (t70) cc_final: 0.8629 (t0) REVERT: C 337 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8467 (tp) REVERT: D 96 MET cc_start: 0.8172 (mmm) cc_final: 0.7943 (mmp) REVERT: D 306 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: D 309 ASP cc_start: 0.8958 (t70) cc_final: 0.8709 (t0) REVERT: D 337 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8470 (tp) outliers start: 59 outliers final: 11 residues processed: 340 average time/residue: 0.1449 time to fit residues: 79.5292 Evaluate side-chains 257 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 A residue 592 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 B residue 592 LEU Chi-restraints excluded: chain C residue 235 VAL 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 141 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 122 HIS A 265 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 265 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 122 HIS C 174 ASN C 265 HIS ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 122 HIS D 265 HIS ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.176396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128380 restraints weight = 23715.373| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.63 r_work: 0.3254 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21248 Z= 0.145 Angle : 0.651 9.192 28588 Z= 0.324 Chirality : 0.042 0.182 3172 Planarity : 0.004 0.046 3500 Dihedral : 13.504 86.804 4219 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.89 % Allowed : 9.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.32 (0.15), residues: 2404 helix: -2.16 (0.13), residues: 1296 sheet: -4.58 (0.34), residues: 84 loop : -3.63 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 305 TYR 0.014 0.001 TYR C 216 PHE 0.014 0.001 PHE B 256 TRP 0.013 0.001 TRP B 613 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00351 (21248) covalent geometry : angle 0.65072 (28588) hydrogen bonds : bond 0.03627 ( 617) hydrogen bonds : angle 4.28398 ( 1776) *********************** 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 319 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 258 time to evaluate : 0.777 Fit side-chains REVERT: A 160 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8243 (pp) REVERT: A 219 LEU cc_start: 0.8719 (mt) cc_final: 0.8474 (mp) REVERT: A 306 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: A 319 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 337 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 565 ILE cc_start: 0.9002 (tp) cc_final: 0.8652 (tp) REVERT: A 592 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8339 (mt) REVERT: B 160 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8265 (pp) REVERT: B 219 LEU cc_start: 0.8719 (mt) cc_final: 0.8422 (mp) REVERT: B 306 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: B 319 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8546 (tt) REVERT: B 337 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8492 (tp) REVERT: B 592 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8330 (mt) REVERT: B 621 ARG cc_start: 0.7697 (mtp-110) cc_final: 0.7420 (mtp-110) REVERT: C 160 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8257 (pp) REVERT: C 306 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: C 319 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8543 (tt) REVERT: C 337 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8496 (tp) REVERT: D 160 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8221 (pp) REVERT: D 215 MET cc_start: 0.8285 (mmm) cc_final: 0.8069 (mmm) REVERT: D 219 LEU cc_start: 0.8689 (mt) cc_final: 0.8428 (mp) REVERT: D 306 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: D 319 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8549 (tt) REVERT: D 337 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8484 (tp) outliers start: 61 outliers final: 31 residues processed: 305 average time/residue: 0.1441 time to fit residues: 71.2671 Evaluate side-chains 279 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE 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 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 A residue 592 LEU Chi-restraints excluded: chain B residue 160 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 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 520 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 274 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 378 MET 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 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 378 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 134 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 80 optimal weight: 30.0000 chunk 226 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 265 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 265 HIS D 127 ASN D 265 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.173272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.123650 restraints weight = 23901.407| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.59 r_work: 0.3213 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3087 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= 0.190 Angle : 0.681 9.110 28588 Z= 0.339 Chirality : 0.043 0.185 3172 Planarity : 0.005 0.045 3500 Dihedral : 13.221 85.151 4219 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 3.56 % Allowed : 10.34 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.16), residues: 2404 helix: -1.63 (0.14), residues: 1296 sheet: -4.28 (0.37), residues: 84 loop : -3.58 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 621 TYR 0.012 0.002 TYR D 216 PHE 0.014 0.002 PHE D 256 TRP 0.015 0.001 TRP A 613 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00467 (21248) covalent geometry : angle 0.68074 (28588) hydrogen bonds : bond 0.03716 ( 617) hydrogen bonds : angle 4.27639 ( 1776) *********************** 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 329 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 254 time to evaluate : 0.772 Fit side-chains REVERT: A 160 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8128 (pp) REVERT: A 215 MET cc_start: 0.8218 (mmm) cc_final: 0.7806 (tpp) REVERT: A 219 LEU cc_start: 0.8692 (mt) cc_final: 0.8465 (mp) REVERT: A 274 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8705 (p) REVERT: A 306 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: A 319 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8559 (tt) REVERT: A 337 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8448 (tp) REVERT: A 592 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8246 (mt) REVERT: B 160 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8158 (pp) REVERT: B 215 MET cc_start: 0.8198 (mmm) cc_final: 0.7954 (mmm) REVERT: B 219 LEU cc_start: 0.8698 (mt) cc_final: 0.8432 (mp) REVERT: B 274 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8704 (p) REVERT: B 306 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: B 319 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8565 (tt) REVERT: B 337 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8466 (tp) REVERT: B 592 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8230 (mt) REVERT: C 160 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8185 (pp) REVERT: C 274 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8773 (p) REVERT: C 306 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: C 319 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8575 (tt) REVERT: C 337 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8458 (tp) REVERT: D 160 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8151 (pp) REVERT: D 215 MET cc_start: 0.8280 (mmm) cc_final: 0.8058 (mmm) REVERT: D 219 LEU cc_start: 0.8716 (mt) cc_final: 0.8462 (mp) REVERT: D 274 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8841 (p) REVERT: D 319 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8558 (tt) REVERT: D 337 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8479 (tp) REVERT: D 429 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8172 (mt) REVERT: D 637 GLN cc_start: 0.8126 (mp10) cc_final: 0.7772 (mp10) outliers start: 75 outliers final: 32 residues processed: 317 average time/residue: 0.1414 time to fit residues: 72.8650 Evaluate side-chains 291 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 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 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 520 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 274 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 378 MET 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 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 378 MET Chi-restraints excluded: chain D residue 429 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 B 546 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121839 restraints weight = 23703.930| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.91 r_work: 0.3221 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21248 Z= 0.108 Angle : 0.599 9.343 28588 Z= 0.300 Chirality : 0.040 0.197 3172 Planarity : 0.004 0.045 3500 Dihedral : 12.338 82.679 4219 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 3.13 % Allowed : 11.62 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.16), residues: 2404 helix: -1.19 (0.14), residues: 1320 sheet: -3.95 (0.41), residues: 84 loop : -3.39 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 305 TYR 0.011 0.001 TYR C 216 PHE 0.010 0.001 PHE D 244 TRP 0.015 0.001 TRP A 613 HIS 0.005 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00244 (21248) covalent geometry : angle 0.59920 (28588) hydrogen bonds : bond 0.02859 ( 617) hydrogen bonds : angle 3.87513 ( 1776) *********************** 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 348 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 0.828 Fit side-chains REVERT: A 160 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8072 (pp) REVERT: A 274 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8778 (p) REVERT: A 306 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7557 (mp10) REVERT: A 319 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8525 (tt) REVERT: A 337 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8464 (tp) REVERT: B 160 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8039 (pp) REVERT: B 233 ASP cc_start: 0.7582 (p0) cc_final: 0.7376 (p0) REVERT: B 274 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8782 (p) REVERT: B 306 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: B 319 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8502 (tt) REVERT: B 337 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8474 (tp) REVERT: B 592 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8246 (mt) REVERT: C 160 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8039 (pp) REVERT: C 233 ASP cc_start: 0.7593 (p0) cc_final: 0.7369 (p0) REVERT: C 306 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: C 319 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8510 (tt) REVERT: C 337 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8473 (tp) REVERT: C 637 GLN cc_start: 0.8174 (mp10) cc_final: 0.7938 (mp10) REVERT: D 160 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8077 (pp) REVERT: D 215 MET cc_start: 0.8183 (mmm) cc_final: 0.7977 (mmm) REVERT: D 219 LEU cc_start: 0.8630 (mt) cc_final: 0.8374 (mp) REVERT: D 319 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8533 (tt) REVERT: D 337 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8455 (tp) REVERT: D 429 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.8002 (mt) REVERT: D 637 GLN cc_start: 0.8118 (mp10) cc_final: 0.7718 (mp10) outliers start: 66 outliers final: 21 residues processed: 337 average time/residue: 0.1444 time to fit residues: 78.2460 Evaluate side-chains 289 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 520 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 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 B residue 520 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 266 THR 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 520 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 266 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 429 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 170 optimal weight: 0.0170 chunk 94 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 188 optimal weight: 20.0000 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS D 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124973 restraints weight = 23761.036| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.62 r_work: 0.3179 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21248 Z= 0.228 Angle : 0.716 11.930 28588 Z= 0.352 Chirality : 0.046 0.185 3172 Planarity : 0.005 0.053 3500 Dihedral : 12.745 87.202 4217 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.84 % Allowed : 12.05 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.16), residues: 2404 helix: -1.16 (0.14), residues: 1324 sheet: -3.61 (0.44), residues: 84 loop : -3.48 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 621 TYR 0.011 0.002 TYR C 216 PHE 0.020 0.002 PHE D 256 TRP 0.015 0.001 TRP D 613 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00568 (21248) covalent geometry : angle 0.71567 (28588) hydrogen bonds : bond 0.03867 ( 617) hydrogen bonds : angle 4.20166 ( 1776) *********************** 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 350 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 269 time to evaluate : 0.754 Fit side-chains REVERT: A 152 PHE cc_start: 0.8677 (m-80) cc_final: 0.8462 (m-80) REVERT: A 160 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8147 (pp) REVERT: A 233 ASP cc_start: 0.7819 (p0) cc_final: 0.7577 (p0) REVERT: A 274 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8860 (p) REVERT: A 306 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: A 319 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 337 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8492 (tp) REVERT: A 437 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 608 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7604 (tt) REVERT: B 152 PHE cc_start: 0.8739 (m-80) cc_final: 0.8482 (m-80) REVERT: B 160 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8184 (pp) REVERT: B 274 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8859 (p) REVERT: B 319 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8543 (tt) REVERT: B 337 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8497 (tp) REVERT: B 437 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 592 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8276 (mt) REVERT: B 608 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7582 (tt) REVERT: C 160 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8190 (pp) REVERT: C 233 ASP cc_start: 0.7795 (p0) cc_final: 0.7593 (p0) REVERT: C 306 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: C 319 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8562 (tt) REVERT: C 337 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8501 (tp) REVERT: C 437 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8287 (mt) REVERT: C 590 ASP cc_start: 0.8270 (t70) cc_final: 0.8011 (p0) REVERT: C 608 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7571 (tt) REVERT: D 160 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8173 (pp) REVERT: D 215 MET cc_start: 0.8328 (mmm) cc_final: 0.8105 (mmm) REVERT: D 219 LEU cc_start: 0.8804 (mt) cc_final: 0.8542 (mp) REVERT: D 319 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8541 (tt) REVERT: D 337 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8492 (tp) REVERT: D 429 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8190 (mt) REVERT: D 437 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8307 (mt) REVERT: D 608 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7575 (tt) outliers start: 81 outliers final: 41 residues processed: 333 average time/residue: 0.1402 time to fit residues: 75.6085 Evaluate side-chains 313 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET 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 437 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 608 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 365 ASN Chi-restraints excluded: chain B residue 368 LEU 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 520 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 266 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 437 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 265 HIS 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 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 12 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 chunk 82 optimal weight: 5.9990 chunk 124 optimal weight: 0.0060 chunk 110 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 overall best weight: 0.5274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 637 GLN B 265 HIS B 637 GLN C 265 HIS D 464 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.181647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135904 restraints weight = 23737.686| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.69 r_work: 0.3330 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21248 Z= 0.103 Angle : 0.599 9.823 28588 Z= 0.298 Chirality : 0.040 0.181 3172 Planarity : 0.004 0.039 3500 Dihedral : 11.677 87.997 4217 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.89 % Allowed : 13.90 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.17), residues: 2404 helix: -0.72 (0.15), residues: 1316 sheet: -3.37 (0.47), residues: 84 loop : -3.29 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 621 TYR 0.009 0.001 TYR C 216 PHE 0.012 0.001 PHE D 244 TRP 0.008 0.001 TRP D 268 HIS 0.005 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00226 (21248) covalent geometry : angle 0.59868 (28588) hydrogen bonds : bond 0.02665 ( 617) hydrogen bonds : angle 3.70667 ( 1776) *********************** 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 353 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 292 time to evaluate : 0.838 Fit side-chains REVERT: A 160 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8027 (pp) REVERT: A 319 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 337 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8431 (tp) REVERT: A 565 ILE cc_start: 0.8916 (tp) cc_final: 0.8635 (tp) REVERT: B 160 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8075 (pp) REVERT: B 319 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8599 (tt) REVERT: B 337 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8443 (tp) REVERT: B 565 ILE cc_start: 0.8924 (tp) cc_final: 0.8636 (tp) REVERT: B 592 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8283 (mt) REVERT: C 160 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8064 (pp) REVERT: C 319 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8547 (tt) REVERT: C 337 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 565 ILE cc_start: 0.8907 (tp) cc_final: 0.8626 (tp) REVERT: C 590 ASP cc_start: 0.8138 (t70) cc_final: 0.7636 (m-30) REVERT: C 637 GLN cc_start: 0.7988 (mp10) cc_final: 0.7746 (pm20) REVERT: D 160 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8028 (pp) REVERT: D 219 LEU cc_start: 0.8740 (mt) cc_final: 0.8489 (mp) REVERT: D 303 GLU cc_start: 0.7847 (pm20) cc_final: 0.7517 (pm20) REVERT: D 306 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: D 319 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8571 (tt) REVERT: D 337 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 565 ILE cc_start: 0.8936 (tp) cc_final: 0.8653 (tp) outliers start: 61 outliers final: 25 residues processed: 337 average time/residue: 0.1389 time to fit residues: 76.0208 Evaluate side-chains 289 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 266 THR 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 520 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 266 THR 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 520 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 266 THR 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 520 LEU 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 266 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 452 VAL Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 229 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 171)---------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121692 restraints weight = 23706.910| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.54 r_work: 0.3198 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21248 Z= 0.219 Angle : 0.718 10.409 28588 Z= 0.349 Chirality : 0.045 0.184 3172 Planarity : 0.005 0.049 3500 Dihedral : 12.092 88.972 4217 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.18 % Allowed : 13.99 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.17), residues: 2404 helix: -0.81 (0.15), residues: 1324 sheet: -3.22 (0.48), residues: 84 loop : -3.35 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 621 TYR 0.013 0.002 TYR D 216 PHE 0.017 0.002 PHE D 256 TRP 0.011 0.001 TRP B 613 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00547 (21248) covalent geometry : angle 0.71758 (28588) hydrogen bonds : bond 0.03681 ( 617) hydrogen bonds : angle 4.07449 ( 1776) *********************** 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 319 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 0.653 Fit side-chains REVERT: A 152 PHE cc_start: 0.8687 (m-80) cc_final: 0.8471 (m-80) REVERT: A 160 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8102 (pp) REVERT: A 319 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8566 (tt) REVERT: A 337 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8436 (tp) REVERT: A 608 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7543 (tt) REVERT: B 152 PHE cc_start: 0.8729 (m-80) cc_final: 0.8481 (m-80) REVERT: B 160 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8121 (pp) REVERT: B 319 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8566 (tt) REVERT: B 337 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8437 (tp) REVERT: B 592 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8251 (mt) REVERT: B 608 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7542 (tt) REVERT: C 160 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8138 (pp) REVERT: C 319 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8561 (tt) REVERT: C 337 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8443 (tp) REVERT: C 608 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7548 (tt) REVERT: D 160 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8093 (pp) REVERT: D 219 LEU cc_start: 0.8799 (mt) cc_final: 0.8529 (mp) REVERT: D 319 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8541 (tt) REVERT: D 337 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8442 (tp) REVERT: D 429 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8146 (mt) REVERT: D 608 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7536 (tt) outliers start: 67 outliers final: 31 residues processed: 307 average time/residue: 0.1290 time to fit residues: 63.8736 Evaluate side-chains 287 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 266 THR 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 520 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 266 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 365 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 266 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 520 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 631 LEU 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 365 ASN Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 608 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 166 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.179645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130548 restraints weight = 23744.419| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.52 r_work: 0.3319 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21248 Z= 0.115 Angle : 0.631 11.737 28588 Z= 0.308 Chirality : 0.041 0.180 3172 Planarity : 0.004 0.037 3500 Dihedral : 11.490 87.342 4217 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.61 % Allowed : 14.85 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.17), residues: 2404 helix: -0.51 (0.15), residues: 1324 sheet: -2.82 (0.51), residues: 84 loop : -3.24 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 621 TYR 0.012 0.001 TYR A 216 PHE 0.011 0.001 PHE D 244 TRP 0.007 0.001 TRP A 321 HIS 0.013 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00266 (21248) covalent geometry : angle 0.63064 (28588) hydrogen bonds : bond 0.02836 ( 617) hydrogen bonds : angle 3.73740 ( 1776) *********************** 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 325 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8070 (pp) REVERT: A 319 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8596 (tt) REVERT: A 337 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8452 (tp) REVERT: B 160 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8135 (pp) REVERT: B 319 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8585 (tt) REVERT: B 337 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8467 (tp) REVERT: B 592 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8277 (mt) REVERT: C 160 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8110 (pp) REVERT: C 319 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8588 (tt) REVERT: C 337 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8460 (tp) REVERT: C 590 ASP cc_start: 0.8197 (t70) cc_final: 0.7721 (m-30) REVERT: D 78 MET cc_start: 0.6980 (mtm) cc_final: 0.6602 (ptp) REVERT: D 160 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8110 (pp) REVERT: D 215 MET cc_start: 0.7476 (mmm) cc_final: 0.6896 (mmm) REVERT: D 219 LEU cc_start: 0.8757 (mt) cc_final: 0.8471 (mp) REVERT: D 233 ASP cc_start: 0.7742 (p0) cc_final: 0.7531 (p0) REVERT: D 319 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8556 (tt) REVERT: D 337 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8458 (tp) REVERT: D 637 GLN cc_start: 0.8001 (mp10) cc_final: 0.7605 (pm20) outliers start: 55 outliers final: 28 residues processed: 312 average time/residue: 0.1297 time to fit residues: 65.5917 Evaluate side-chains 282 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 265 HIS Chi-restraints excluded: chain A residue 266 THR 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 520 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 266 THR 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 368 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 266 THR 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 520 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 631 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 115 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 170 optimal weight: 0.0470 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 178 optimal weight: 0.4980 chunk 157 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.184073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131169 restraints weight = 23867.694| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.70 r_work: 0.3352 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21248 Z= 0.105 Angle : 0.616 9.983 28588 Z= 0.301 Chirality : 0.040 0.174 3172 Planarity : 0.004 0.039 3500 Dihedral : 10.969 82.291 4217 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.18 % Allowed : 15.42 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.17), residues: 2404 helix: -0.16 (0.15), residues: 1308 sheet: -2.46 (0.52), residues: 84 loop : -3.19 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 621 TYR 0.013 0.001 TYR D 216 PHE 0.020 0.001 PHE D 553 TRP 0.008 0.001 TRP A 268 HIS 0.004 0.000 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00231 (21248) covalent geometry : angle 0.61640 (28588) hydrogen bonds : bond 0.02676 ( 617) hydrogen bonds : angle 3.69005 ( 1776) ********************** 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 310 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7899 (pp) REVERT: A 337 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8370 (tp) REVERT: A 565 ILE cc_start: 0.8907 (tp) cc_final: 0.8614 (tp) REVERT: B 160 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7965 (pp) REVERT: B 319 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8484 (tt) REVERT: B 337 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8397 (tp) REVERT: B 565 ILE cc_start: 0.8921 (tp) cc_final: 0.8577 (tp) REVERT: B 592 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8113 (mt) REVERT: C 160 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7939 (pp) REVERT: C 319 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8488 (tt) REVERT: C 337 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8413 (tp) REVERT: C 565 ILE cc_start: 0.8922 (tp) cc_final: 0.8582 (tp) REVERT: C 590 ASP cc_start: 0.8254 (t70) cc_final: 0.7674 (m-30) REVERT: D 160 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7950 (pp) REVERT: D 215 MET cc_start: 0.7410 (mmm) cc_final: 0.6947 (mmm) REVERT: D 219 LEU cc_start: 0.8516 (mt) cc_final: 0.8225 (mp) REVERT: D 306 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: D 337 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8383 (tp) REVERT: D 637 GLN cc_start: 0.7814 (mp10) cc_final: 0.7468 (pm20) outliers start: 46 outliers final: 19 residues processed: 298 average time/residue: 0.1215 time to fit residues: 59.3719 Evaluate side-chains 286 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 337 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU 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 368 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 266 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 77 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.181883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143828 restraints weight = 23820.746| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.31 r_work: 0.3181 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21248 Z= 0.117 Angle : 0.632 10.262 28588 Z= 0.306 Chirality : 0.041 0.174 3172 Planarity : 0.004 0.038 3500 Dihedral : 10.905 77.724 4217 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.94 % Allowed : 16.03 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.17), residues: 2404 helix: 0.01 (0.15), residues: 1312 sheet: -2.29 (0.54), residues: 84 loop : -3.12 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.012 0.001 TYR A 216 PHE 0.011 0.001 PHE D 256 TRP 0.006 0.001 TRP D 593 HIS 0.004 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00272 (21248) covalent geometry : angle 0.63220 (28588) hydrogen bonds : bond 0.02847 ( 617) hydrogen bonds : angle 3.70010 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6361.49 seconds wall clock time: 109 minutes 15.56 seconds (6555.56 seconds total)