Starting phenix.real_space_refine on Thu Jan 23 22:50:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ftg_50744/01_2025/9ftg_50744.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ftg_50744/01_2025/9ftg_50744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ftg_50744/01_2025/9ftg_50744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ftg_50744/01_2025/9ftg_50744.map" model { file = "/net/cci-nas-00/data/ceres_data/9ftg_50744/01_2025/9ftg_50744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ftg_50744/01_2025/9ftg_50744.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 40 5.16 5 C 13690 2.51 5 N 3535 2.21 5 O 3935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 21205 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4240 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 9.69, per 1000 atoms: 0.46 Number of scatterers: 21205 At special positions: 0 Unit cell: (135.287, 134.425, 152.521, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 40 16.00 O 3935 8.00 N 3535 7.00 C 13690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 371 " - pdb=" SG CYS A 373 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.98 Conformation dependent library (CDL) restraints added in 2.7 seconds 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5190 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 30 sheets defined 27.2% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 88 through 97 removed outlier: 3.778A pdb=" N LEU A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 4.030A pdb=" N GLU A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.880A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.744A pdb=" N SER A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 544 through 563 removed outlier: 3.789A pdb=" N LEU A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 604 removed outlier: 3.761A pdb=" N VAL A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 636 removed outlier: 3.543A pdb=" N VAL A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) Proline residue: A 621 - end of helix removed outlier: 3.764A pdb=" N TYR A 624 " --> pdb=" O TYR A 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 97 removed outlier: 3.778A pdb=" N LEU B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 4.031A pdb=" N GLU B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 514 through 522 removed outlier: 3.880A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 536 removed outlier: 3.744A pdb=" N SER B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 544 through 563 removed outlier: 3.789A pdb=" N LEU B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 561 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 563 " --> pdb=" O PHE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 604 removed outlier: 3.761A pdb=" N VAL B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 592 " --> pdb=" O ALA B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 636 removed outlier: 3.542A pdb=" N VAL B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) Proline residue: B 621 - end of helix removed outlier: 3.763A pdb=" N TYR B 624 " --> pdb=" O TYR B 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 97 removed outlier: 3.778A pdb=" N LEU D 92 " --> pdb=" O PRO D 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 4.030A pdb=" N GLU D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 514 through 522 removed outlier: 3.879A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 removed outlier: 3.744A pdb=" N SER D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 544 through 563 removed outlier: 3.790A pdb=" N LEU D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE D 561 " --> pdb=" O VAL D 557 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR D 562 " --> pdb=" O ALA D 558 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE D 563 " --> pdb=" O PHE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 604 removed outlier: 3.762A pdb=" N VAL D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 636 removed outlier: 3.542A pdb=" N VAL D 618 " --> pdb=" O THR D 614 " (cutoff:3.500A) Proline residue: D 621 - end of helix removed outlier: 3.763A pdb=" N TYR D 624 " --> pdb=" O TYR D 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 97 removed outlier: 3.778A pdb=" N LEU E 92 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 118 removed outlier: 4.031A pdb=" N GLU E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 514 through 522 removed outlier: 3.880A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 536 removed outlier: 3.744A pdb=" N SER E 533 " --> pdb=" O ILE E 529 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 536 " --> pdb=" O VAL E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 544 through 563 removed outlier: 3.789A pdb=" N LEU E 554 " --> pdb=" O SER E 550 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE E 561 " --> pdb=" O VAL E 557 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR E 562 " --> pdb=" O ALA E 558 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE E 563 " --> pdb=" O PHE E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 604 removed outlier: 3.761A pdb=" N VAL E 591 " --> pdb=" O THR E 587 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 592 " --> pdb=" O ALA E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 636 removed outlier: 3.542A pdb=" N VAL E 618 " --> pdb=" O THR E 614 " (cutoff:3.500A) Proline residue: E 621 - end of helix removed outlier: 3.764A pdb=" N TYR E 624 " --> pdb=" O TYR E 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 97 removed outlier: 3.778A pdb=" N LEU C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 118 removed outlier: 4.031A pdb=" N GLU C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 514 through 522 removed outlier: 3.880A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 536 removed outlier: 3.744A pdb=" N SER C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 544 through 563 removed outlier: 3.788A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 561 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE C 563 " --> pdb=" O PHE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 604 removed outlier: 3.762A pdb=" N VAL C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 592 " --> pdb=" O ALA C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 636 removed outlier: 3.544A pdb=" N VAL C 618 " --> pdb=" O THR C 614 " (cutoff:3.500A) Proline residue: C 621 - end of helix removed outlier: 3.764A pdb=" N TYR C 624 " --> pdb=" O TYR C 620 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.648A pdb=" N ASP A 122 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 208 removed outlier: 3.508A pdb=" N VAL A 304 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 301 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 237 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 271 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 222 removed outlier: 8.209A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.519A pdb=" N VAL A 415 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.270A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 486 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS A 512 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL A 484 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 45 Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.648A pdb=" N ASP B 122 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.507A pdb=" N VAL B 304 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 301 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 237 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 271 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 222 removed outlier: 8.210A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.519A pdb=" N VAL B 415 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.270A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 486 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS B 512 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL B 484 " --> pdb=" O LYS B 512 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 43 through 45 Processing sheet with id=AB5, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.649A pdb=" N ASP D 122 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 206 through 208 removed outlier: 3.508A pdb=" N VAL D 304 " --> pdb=" O GLN D 206 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 301 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 237 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 271 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 218 through 222 removed outlier: 8.209A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 376 through 379 removed outlier: 3.519A pdb=" N VAL D 415 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.271A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER D 486 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS D 512 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL D 484 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 43 through 45 Processing sheet with id=AC2, first strand: chain 'E' and resid 79 through 80 removed outlier: 3.648A pdb=" N ASP E 122 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 206 through 208 removed outlier: 3.507A pdb=" N VAL E 304 " --> pdb=" O GLN E 206 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG E 301 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU E 237 " --> pdb=" O ARG E 301 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 271 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 218 through 222 removed outlier: 8.209A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 376 through 379 removed outlier: 3.519A pdb=" N VAL E 415 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 397 through 399 removed outlier: 5.270A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER E 486 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS E 512 " --> pdb=" O VAL E 484 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL E 484 " --> pdb=" O LYS E 512 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 43 through 45 Processing sheet with id=AC8, first strand: chain 'C' and resid 79 through 80 removed outlier: 3.648A pdb=" N ASP C 122 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 206 through 208 removed outlier: 3.507A pdb=" N VAL C 304 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 301 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 237 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 271 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 218 through 222 removed outlier: 8.210A pdb=" N LEU C 247 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE C 259 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU C 249 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.520A pdb=" N VAL C 415 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 341 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 352 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE C 339 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N THR C 354 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP C 337 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LYS C 356 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA C 335 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER C 358 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLY C 333 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N HIS C 360 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N THR C 331 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.269A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER C 486 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS C 512 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL C 484 " --> pdb=" O LYS C 512 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.63 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6910 1.34 - 1.46: 5185 1.46 - 1.58: 9515 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 21660 Sorted by residual: bond pdb=" CG PRO D 442 " pdb=" CD PRO D 442 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 7.69e-01 bond pdb=" CG PRO C 442 " pdb=" CD PRO C 442 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.56e-01 bond pdb=" CG PRO B 442 " pdb=" CD PRO B 442 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.44e-01 bond pdb=" CG PRO E 442 " pdb=" CD PRO E 442 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.38e-01 bond pdb=" CG PRO A 442 " pdb=" CD PRO A 442 " ideal model delta sigma weight residual 1.512 1.490 0.022 2.70e-02 1.37e+03 6.93e-01 ... (remaining 21655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 29075 1.52 - 3.03: 380 3.03 - 4.55: 45 4.55 - 6.06: 20 6.06 - 7.58: 10 Bond angle restraints: 29530 Sorted by residual: angle pdb=" C GLN C 39 " pdb=" N HIS C 40 " pdb=" CA HIS C 40 " ideal model delta sigma weight residual 121.76 126.97 -5.21 2.19e+00 2.09e-01 5.65e+00 angle pdb=" C GLN E 39 " pdb=" N HIS E 40 " pdb=" CA HIS E 40 " ideal model delta sigma weight residual 121.76 126.95 -5.19 2.19e+00 2.09e-01 5.63e+00 angle pdb=" C GLN D 39 " pdb=" N HIS D 40 " pdb=" CA HIS D 40 " ideal model delta sigma weight residual 121.76 126.94 -5.18 2.19e+00 2.09e-01 5.60e+00 angle pdb=" C GLN B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta sigma weight residual 121.76 126.93 -5.17 2.19e+00 2.09e-01 5.57e+00 angle pdb=" C GLN A 39 " pdb=" N HIS A 40 " pdb=" CA HIS A 40 " ideal model delta sigma weight residual 121.76 126.91 -5.15 2.19e+00 2.09e-01 5.53e+00 ... (remaining 29525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 11014 16.67 - 33.34: 1155 33.34 - 50.01: 361 50.01 - 66.68: 61 66.68 - 83.35: 20 Dihedral angle restraints: 12611 sinusoidal: 4566 harmonic: 8045 Sorted by residual: dihedral pdb=" CB CYS A 371 " pdb=" SG CYS A 371 " pdb=" SG CYS A 373 " pdb=" CB CYS A 373 " ideal model delta sinusoidal sigma weight residual -86.00 -119.00 33.00 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CA ARG E 498 " pdb=" C ARG E 498 " pdb=" N GLY E 499 " pdb=" CA GLY E 499 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ARG C 498 " pdb=" C ARG C 498 " pdb=" N GLY C 499 " pdb=" CA GLY C 499 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 12608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2758 0.052 - 0.103: 576 0.103 - 0.155: 96 0.155 - 0.206: 0 0.206 - 0.258: 5 Chirality restraints: 3435 Sorted by residual: chirality pdb=" CB THR E 637 " pdb=" CA THR E 637 " pdb=" OG1 THR E 637 " pdb=" CG2 THR E 637 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB THR B 637 " pdb=" CA THR B 637 " pdb=" OG1 THR B 637 " pdb=" CG2 THR B 637 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR D 637 " pdb=" CA THR D 637 " pdb=" OG1 THR D 637 " pdb=" CG2 THR D 637 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 3432 not shown) Planarity restraints: 3810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 637 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C THR E 637 " 0.024 2.00e-02 2.50e+03 pdb=" O THR E 637 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP E 638 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 637 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C THR D 637 " 0.023 2.00e-02 2.50e+03 pdb=" O THR D 637 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP D 638 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 637 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C THR B 637 " -0.023 2.00e-02 2.50e+03 pdb=" O THR B 637 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP B 638 " 0.008 2.00e-02 2.50e+03 ... (remaining 3807 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 63 2.61 - 3.18: 16644 3.18 - 3.75: 28778 3.75 - 4.33: 39817 4.33 - 4.90: 70309 Nonbonded interactions: 155611 Sorted by model distance: nonbonded pdb=" SG CYS E 371 " pdb=" SG CYS E 373 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS B 371 " pdb=" SG CYS B 373 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 371 " pdb=" SG CYS D 373 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS C 371 " pdb=" SG CYS C 373 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS B 275 " pdb=" SG CYS B 280 " model vdw 2.035 3.760 ... (remaining 155606 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 42.050 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 : 0.003 0.025 21660 Z= 0.208 Angle : 0.480 7.577 29530 Z= 0.241 Chirality : 0.043 0.258 3435 Planarity : 0.003 0.040 3810 Dihedral : 15.404 83.349 7415 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 21.16 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2725 helix: 0.77 (0.19), residues: 625 sheet: 0.48 (0.19), residues: 795 loop : -1.50 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 482 HIS 0.002 0.000 HIS D 360 PHE 0.020 0.001 PHE B 414 TYR 0.010 0.001 TYR C 441 ARG 0.003 0.000 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 2.475 Fit side-chains REVERT: B 605 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7592 (ptpp) REVERT: B 608 VAL cc_start: 0.8773 (t) cc_final: 0.8451 (p) REVERT: C 158 LYS cc_start: 0.8263 (pttp) cc_final: 0.8046 (pttt) REVERT: C 272 ASN cc_start: 0.7916 (m-40) cc_final: 0.7320 (p0) REVERT: C 469 PHE cc_start: 0.8938 (p90) cc_final: 0.8541 (p90) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3077 time to fit residues: 96.6330 Evaluate side-chains 184 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 115 optimal weight: 40.0000 chunk 71 optimal weight: 7.9990 chunk 140 optimal weight: 0.0070 chunk 111 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 206 GLN A 272 ASN A 307 ASN A 410 ASN B 206 GLN B 272 ASN B 307 ASN B 410 ASN D 206 GLN D 272 ASN D 307 ASN D 410 ASN E 206 GLN E 272 ASN E 307 ASN E 410 ASN C 160 GLN C 206 GLN C 272 ASN C 307 ASN C 410 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.199044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119996 restraints weight = 22375.424| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.40 r_work: 0.2860 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 21660 Z= 0.308 Angle : 0.582 7.690 29530 Z= 0.307 Chirality : 0.045 0.174 3435 Planarity : 0.004 0.047 3810 Dihedral : 4.096 18.092 2980 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.83 % Allowed : 17.40 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2725 helix: 1.93 (0.20), residues: 635 sheet: 0.33 (0.20), residues: 725 loop : -1.41 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 359 HIS 0.003 0.001 HIS E 360 PHE 0.018 0.002 PHE E 414 TYR 0.013 0.001 TYR C 517 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 2.293 Fit side-chains REVERT: A 431 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8994 (mp) REVERT: B 431 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8778 (mt) REVERT: C 469 PHE cc_start: 0.8826 (p90) cc_final: 0.8398 (p90) outliers start: 61 outliers final: 33 residues processed: 210 average time/residue: 0.2852 time to fit residues: 99.2983 Evaluate side-chains 198 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 162 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 204 optimal weight: 0.1980 chunk 1 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 611 GLN B 344 GLN D 344 GLN E 344 GLN C 160 GLN C 344 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.195885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114629 restraints weight = 22305.718| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.00 r_work: 0.3026 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 21660 Z= 0.384 Angle : 0.622 8.196 29530 Z= 0.326 Chirality : 0.047 0.209 3435 Planarity : 0.004 0.036 3810 Dihedral : 4.464 18.092 2980 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.18 % Allowed : 17.68 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2725 helix: 2.02 (0.20), residues: 640 sheet: 0.24 (0.20), residues: 700 loop : -1.51 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 534 HIS 0.004 0.001 HIS E 360 PHE 0.016 0.002 PHE B 414 TYR 0.016 0.002 TYR A 517 ARG 0.004 0.001 ARG C 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 165 time to evaluate : 2.098 Fit side-chains REVERT: A 515 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8163 (mp) REVERT: D 272 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7589 (p0) REVERT: D 515 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8136 (mp) REVERT: E 272 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7517 (p0) REVERT: E 515 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8089 (mp) REVERT: E 570 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8360 (mt) REVERT: C 282 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8684 (mp) outliers start: 90 outliers final: 59 residues processed: 232 average time/residue: 0.2945 time to fit residues: 110.6621 Evaluate side-chains 224 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 158 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 180 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 205 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 597 GLN D 597 GLN E 597 GLN E 611 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.199444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120443 restraints weight = 22603.730| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.36 r_work: 0.2887 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21660 Z= 0.182 Angle : 0.517 7.105 29530 Z= 0.270 Chirality : 0.043 0.196 3435 Planarity : 0.003 0.032 3810 Dihedral : 4.155 17.408 2980 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.34 % Allowed : 19.12 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2725 helix: 2.52 (0.21), residues: 640 sheet: 0.35 (0.20), residues: 700 loop : -1.41 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.001 0.000 HIS D 360 PHE 0.013 0.001 PHE E 414 TYR 0.012 0.001 TYR B 441 ARG 0.001 0.000 ARG E 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 2.236 Fit side-chains REVERT: A 406 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8432 (ptt90) REVERT: A 515 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8086 (mp) REVERT: B 515 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8017 (mp) REVERT: D 272 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7502 (p0) REVERT: D 515 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8060 (mp) REVERT: E 272 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7421 (p0) REVERT: E 515 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8026 (mp) REVERT: E 521 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8353 (ttt90) REVERT: C 282 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8514 (mp) REVERT: C 515 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8034 (mp) outliers start: 72 outliers final: 46 residues processed: 227 average time/residue: 0.3268 time to fit residues: 117.5885 Evaluate side-chains 225 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 496 PHE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 0.0570 chunk 86 optimal weight: 8.9990 chunk 245 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 344 GLN B 597 GLN B 611 GLN D 225 ASN D 344 GLN E 344 GLN C 597 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.203402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128735 restraints weight = 22500.324| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.37 r_work: 0.3113 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21660 Z= 0.129 Angle : 0.479 7.041 29530 Z= 0.247 Chirality : 0.041 0.213 3435 Planarity : 0.003 0.027 3810 Dihedral : 3.860 16.141 2980 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.60 % Allowed : 20.60 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2725 helix: 2.90 (0.21), residues: 640 sheet: 0.63 (0.20), residues: 735 loop : -1.44 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 359 HIS 0.001 0.000 HIS D 285 PHE 0.009 0.001 PHE B 414 TYR 0.010 0.001 TYR B 441 ARG 0.001 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 2.245 Fit side-chains REVERT: A 406 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8396 (ptt90) REVERT: A 515 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7926 (mp) REVERT: B 391 ASN cc_start: 0.7971 (m-40) cc_final: 0.7682 (t0) REVERT: D 515 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7923 (mp) REVERT: E 515 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7900 (mp) REVERT: C 282 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 515 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7931 (mp) outliers start: 56 outliers final: 40 residues processed: 212 average time/residue: 0.3151 time to fit residues: 106.0698 Evaluate side-chains 208 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 515 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 45 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 114 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 57 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN B 344 GLN B 560 ASN B 611 GLN D 225 ASN D 344 GLN D 560 ASN E 560 ASN C 560 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.199434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122454 restraints weight = 22337.807| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.51 r_work: 0.2878 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21660 Z= 0.262 Angle : 0.540 8.232 29530 Z= 0.282 Chirality : 0.044 0.223 3435 Planarity : 0.003 0.031 3810 Dihedral : 4.053 16.331 2980 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.02 % Allowed : 20.42 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2725 helix: 2.69 (0.21), residues: 640 sheet: 0.46 (0.20), residues: 710 loop : -1.42 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 534 HIS 0.002 0.000 HIS B 360 PHE 0.016 0.001 PHE E 414 TYR 0.014 0.001 TYR B 441 ARG 0.002 0.000 ARG D 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 171 time to evaluate : 2.262 Fit side-chains REVERT: A 406 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8430 (ptt90) REVERT: A 515 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 391 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7741 (t0) REVERT: D 515 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8030 (mp) REVERT: D 521 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8472 (ttt-90) REVERT: E 515 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7964 (mp) REVERT: E 521 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8345 (ttt90) REVERT: C 282 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8399 (mp) REVERT: C 515 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7969 (mp) outliers start: 65 outliers final: 48 residues processed: 216 average time/residue: 0.3246 time to fit residues: 111.0732 Evaluate side-chains 227 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 9 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 182 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 206 GLN A 560 ASN B 611 GLN D 225 ASN D 560 ASN E 560 ASN E 611 GLN C 560 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.200503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120480 restraints weight = 22269.370| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.00 r_work: 0.3052 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21660 Z= 0.188 Angle : 0.507 8.286 29530 Z= 0.264 Chirality : 0.043 0.229 3435 Planarity : 0.003 0.031 3810 Dihedral : 3.987 16.502 2980 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.25 % Allowed : 20.65 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2725 helix: 2.75 (0.21), residues: 640 sheet: 0.49 (0.20), residues: 710 loop : -1.41 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 359 HIS 0.001 0.000 HIS E 360 PHE 0.013 0.001 PHE E 414 TYR 0.013 0.001 TYR B 441 ARG 0.001 0.000 ARG B 521 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 178 time to evaluate : 2.177 Fit side-chains REVERT: A 406 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8385 (ptt90) REVERT: A 515 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 391 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7795 (t0) REVERT: D 515 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8007 (mp) REVERT: D 521 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8500 (ttt-90) REVERT: E 515 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7952 (mp) REVERT: E 521 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8314 (ttt90) REVERT: C 282 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8539 (mp) REVERT: C 515 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7922 (mp) outliers start: 70 outliers final: 51 residues processed: 226 average time/residue: 0.3282 time to fit residues: 115.3847 Evaluate side-chains 232 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 560 ASN Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 217 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 21 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN B 611 GLN D 225 ASN D 560 ASN E 560 ASN C 560 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.200482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121737 restraints weight = 22368.307| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.37 r_work: 0.2932 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21660 Z= 0.189 Angle : 0.507 8.368 29530 Z= 0.265 Chirality : 0.043 0.246 3435 Planarity : 0.003 0.031 3810 Dihedral : 3.960 16.412 2980 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.16 % Allowed : 20.84 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2725 helix: 2.75 (0.21), residues: 640 sheet: 0.50 (0.20), residues: 710 loop : -1.41 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.001 0.000 HIS E 360 PHE 0.013 0.001 PHE B 414 TYR 0.013 0.001 TYR B 441 ARG 0.002 0.000 ARG D 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 2.322 Fit side-chains REVERT: A 406 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8396 (ptt90) REVERT: A 515 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7960 (mp) REVERT: B 391 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7761 (t0) REVERT: D 515 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8016 (mp) REVERT: D 521 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8469 (ttt-90) REVERT: E 515 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7915 (mp) REVERT: E 521 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8294 (ttt90) REVERT: E 570 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8131 (mt) REVERT: C 282 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8459 (mp) REVERT: C 515 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7942 (mp) outliers start: 68 outliers final: 53 residues processed: 221 average time/residue: 0.3151 time to fit residues: 110.1822 Evaluate side-chains 236 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 109 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 204 optimal weight: 0.8980 chunk 114 optimal weight: 0.0370 chunk 155 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 252 optimal weight: 0.0970 chunk 122 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 overall best weight: 1.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN D 225 ASN D 560 ASN D 597 GLN E 560 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.201215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120892 restraints weight = 22281.416| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.03 r_work: 0.2942 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21660 Z= 0.161 Angle : 0.494 8.227 29530 Z= 0.257 Chirality : 0.042 0.252 3435 Planarity : 0.003 0.030 3810 Dihedral : 3.907 16.288 2980 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.06 % Allowed : 20.93 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2725 helix: 2.86 (0.21), residues: 640 sheet: 0.55 (0.20), residues: 710 loop : -1.38 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.001 0.000 HIS D 360 PHE 0.013 0.001 PHE C 561 TYR 0.012 0.001 TYR B 441 ARG 0.002 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 174 time to evaluate : 2.262 Fit side-chains REVERT: A 406 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8377 (ptt90) REVERT: A 515 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7867 (mp) REVERT: B 391 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7718 (t0) REVERT: D 391 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7875 (t0) REVERT: D 515 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7945 (mp) REVERT: D 521 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8427 (ttt-90) REVERT: E 515 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7839 (mp) REVERT: E 521 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8222 (ttt90) REVERT: E 570 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8073 (mt) REVERT: C 282 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8436 (mp) REVERT: C 515 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7836 (mp) outliers start: 66 outliers final: 50 residues processed: 218 average time/residue: 0.3224 time to fit residues: 112.6997 Evaluate side-chains 231 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 170 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 560 ASN Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 246 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 129 optimal weight: 0.0060 chunk 241 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 218 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 1 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN D 225 ASN D 560 ASN E 560 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.201814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125210 restraints weight = 22376.955| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.38 r_work: 0.2936 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21660 Z= 0.147 Angle : 0.486 8.110 29530 Z= 0.253 Chirality : 0.042 0.257 3435 Planarity : 0.003 0.028 3810 Dihedral : 3.851 16.094 2980 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.78 % Allowed : 21.02 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2725 helix: 2.87 (0.21), residues: 640 sheet: 0.48 (0.19), residues: 735 loop : -1.38 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.001 0.000 HIS D 360 PHE 0.012 0.001 PHE A 414 TYR 0.012 0.001 TYR B 441 ARG 0.002 0.000 ARG B 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 2.210 Fit side-chains REVERT: A 406 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8398 (ptt90) REVERT: A 515 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 391 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7725 (t0) REVERT: D 391 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7834 (t0) REVERT: D 515 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7974 (mp) REVERT: E 515 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7898 (mp) REVERT: E 521 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8283 (ttt90) REVERT: E 560 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8373 (t0) REVERT: C 515 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7869 (mp) outliers start: 60 outliers final: 45 residues processed: 214 average time/residue: 0.3073 time to fit residues: 105.3044 Evaluate side-chains 226 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 560 ASN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2816 > 50: distance: 32 - 39: 32.303 distance: 39 - 40: 37.916 distance: 40 - 41: 38.149 distance: 40 - 43: 36.236 distance: 41 - 42: 68.891 distance: 41 - 47: 10.961 distance: 43 - 44: 60.366 distance: 44 - 45: 22.804 distance: 44 - 46: 39.895 distance: 47 - 48: 48.625 distance: 48 - 49: 34.479 distance: 48 - 51: 16.317 distance: 49 - 50: 54.360 distance: 49 - 52: 55.631 distance: 52 - 53: 51.213 distance: 53 - 54: 41.908 distance: 53 - 56: 40.334 distance: 54 - 55: 40.048 distance: 54 - 64: 42.255 distance: 56 - 57: 48.995 distance: 57 - 58: 52.864 distance: 57 - 59: 31.345 distance: 58 - 60: 42.560 distance: 59 - 61: 22.808 distance: 60 - 62: 44.566 distance: 61 - 62: 54.906 distance: 62 - 63: 21.333 distance: 64 - 65: 61.989 distance: 64 - 70: 50.617 distance: 65 - 66: 51.044 distance: 65 - 68: 11.343 distance: 66 - 67: 49.887 distance: 66 - 71: 39.354 distance: 68 - 69: 43.756 distance: 69 - 70: 54.139 distance: 71 - 72: 25.655 distance: 72 - 73: 45.183 distance: 72 - 75: 42.296 distance: 73 - 74: 9.485 distance: 73 - 82: 54.014 distance: 75 - 76: 40.540 distance: 76 - 77: 56.062 distance: 76 - 78: 55.418 distance: 77 - 79: 56.683 distance: 78 - 80: 42.268 distance: 79 - 81: 49.473 distance: 80 - 81: 56.543 distance: 82 - 83: 45.314 distance: 83 - 84: 47.080 distance: 83 - 86: 41.878 distance: 84 - 85: 49.787 distance: 84 - 90: 56.947 distance: 86 - 87: 3.016 distance: 87 - 88: 45.527 distance: 87 - 89: 8.629 distance: 90 - 91: 27.957 distance: 91 - 92: 54.143 distance: 91 - 94: 40.649 distance: 92 - 101: 40.799 distance: 94 - 95: 45.732 distance: 95 - 96: 60.759 distance: 96 - 97: 32.926 distance: 97 - 98: 37.993 distance: 98 - 99: 40.585 distance: 98 - 100: 41.325 distance: 101 - 102: 26.094 distance: 101 - 171: 34.546 distance: 102 - 103: 39.648 distance: 102 - 105: 22.734 distance: 103 - 104: 47.127 distance: 103 - 110: 14.003 distance: 104 - 168: 32.268 distance: 105 - 106: 26.062 distance: 106 - 107: 41.957 distance: 107 - 108: 27.342 distance: 107 - 109: 39.935 distance: 110 - 111: 50.366 distance: 111 - 112: 56.266 distance: 111 - 114: 53.129 distance: 112 - 113: 39.632 distance: 112 - 119: 49.068 distance: 114 - 115: 30.769 distance: 115 - 116: 44.575 distance: 116 - 117: 46.223 distance: 117 - 118: 27.265 distance: 119 - 120: 28.218 distance: 119 - 156: 32.177 distance: 120 - 121: 12.377 distance: 120 - 123: 42.469 distance: 121 - 122: 29.246 distance: 121 - 130: 27.588 distance: 122 - 153: 26.227 distance: 123 - 124: 17.217 distance: 124 - 125: 38.734 distance: 124 - 126: 53.184 distance: 125 - 127: 46.671 distance: 126 - 128: 60.684 distance: 127 - 129: 39.572 distance: 128 - 129: 56.673