Starting phenix.real_space_refine on Sun Sep 29 00:58:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ftg_50744/09_2024/9ftg_50744.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ftg_50744/09_2024/9ftg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ftg_50744/09_2024/9ftg_50744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ftg_50744/09_2024/9ftg_50744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ftg_50744/09_2024/9ftg_50744.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ftg_50744/09_2024/9ftg_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.82, 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: 4.87 Conformation dependent library (CDL) restraints added in 2.9 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: 2.64 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: 6.93 Time building geometry restraints manager: 5.70 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 5.400 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: 0.000 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 43.570 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.680 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.213 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: 0.2994 time to fit residues: 93.9884 Evaluate side-chains 184 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 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 fitting. rotamer outliers: 61 poor density : 172 time to evaluate : 2.200 Fit side-chains REVERT: A 622 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8373 (mp) REVERT: B 431 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8619 (mt) REVERT: E 622 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8393 (mp) REVERT: C 469 PHE cc_start: 0.8885 (p90) cc_final: 0.8523 (p90) outliers start: 61 outliers final: 33 residues processed: 210 average time/residue: 0.2744 time to fit residues: 95.5110 Evaluate side-chains 199 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 2.287 ------------------------------------------------------------------------------- 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 458 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU 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 E residue 622 LEU 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 138 optimal weight: 7.9990 chunk 77 optimal weight: 40.0000 chunk 207 optimal weight: 10.0000 chunk 170 optimal weight: 40.0000 chunk 68 optimal weight: 40.0000 chunk 250 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 222 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 344 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 21660 Z= 0.395 Angle : 0.624 8.415 29530 Z= 0.327 Chirality : 0.047 0.206 3435 Planarity : 0.004 0.036 3810 Dihedral : 4.449 18.010 2980 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.22 % Allowed : 17.45 % Favored : 78.33 % 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: -0.26 (0.16), residues: 2725 helix: 1.99 (0.21), 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 0.017 0.002 PHE B 414 TYR 0.015 0.002 TYR A 517 ARG 0.004 0.001 ARG D 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 fitting. rotamer outliers: 91 poor density : 164 time to evaluate : 2.278 Fit side-chains REVERT: A 515 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8029 (mp) REVERT: B 570 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8442 (mt) REVERT: D 272 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7668 (p0) REVERT: D 515 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8011 (mp) REVERT: E 272 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7597 (p0) REVERT: E 515 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7996 (mp) REVERT: E 570 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8404 (mt) REVERT: C 282 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8836 (mp) outliers start: 91 outliers final: 61 residues processed: 232 average time/residue: 0.2871 time to fit residues: 108.0986 Evaluate side-chains 228 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 159 time to evaluate : 2.171 ------------------------------------------------------------------------------- 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 A residue 622 LEU 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 570 LEU 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 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL 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 E residue 622 LEU 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 247 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 chunk 129 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 119 optimal weight: 40.0000 chunk 167 optimal weight: 20.0000 chunk 251 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 131 optimal weight: 20.0000 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 344 GLN A 597 GLN D 597 GLN E 611 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1648 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= 0.148 Angle : 0.500 7.014 29530 Z= 0.261 Chirality : 0.042 0.191 3435 Planarity : 0.003 0.030 3810 Dihedral : 4.074 17.301 2980 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.20 % Allowed : 19.07 % Favored : 77.73 % 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: 0.15 (0.16), residues: 2725 helix: 2.58 (0.21), residues: 640 sheet: 0.52 (0.20), residues: 725 loop : -1.44 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.002 0.000 HIS A 233 PHE 0.011 0.001 PHE E 414 TYR 0.011 0.001 TYR B 441 ARG 0.002 0.000 ARG B 406 *********************** 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 fitting. rotamer outliers: 69 poor density : 178 time to evaluate : 2.444 Fit side-chains REVERT: A 272 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7684 (p0) REVERT: A 406 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8367 (ptt90) REVERT: A 515 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 272 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7786 (p0) REVERT: B 515 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7852 (mp) REVERT: D 272 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7656 (p0) REVERT: D 515 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7904 (mp) REVERT: E 92 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5429 (mp) REVERT: E 272 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7621 (p0) REVERT: E 515 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7872 (mp) REVERT: E 521 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8285 (ttt90) REVERT: C 282 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8805 (mp) REVERT: C 515 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7831 (mp) outliers start: 69 outliers final: 46 residues processed: 224 average time/residue: 0.3044 time to fit residues: 108.3011 Evaluate side-chains 228 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 169 time to evaluate : 2.287 ------------------------------------------------------------------------------- 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 272 ASN 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 A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU 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 358 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 515 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 92 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 E residue 622 LEU 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 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 221 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 135 optimal weight: 0.6980 chunk 238 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 344 GLN A 560 ASN A 597 GLN B 560 ASN B 597 GLN B 611 GLN D 225 ASN D 560 ASN E 560 ASN E 611 GLN C 560 ASN C 597 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 21660 Z= 0.443 Angle : 0.634 7.951 29530 Z= 0.333 Chirality : 0.048 0.222 3435 Planarity : 0.004 0.041 3810 Dihedral : 4.476 17.943 2980 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.41 % Allowed : 19.12 % Favored : 76.47 % 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: -0.26 (0.16), residues: 2725 helix: 2.11 (0.21), residues: 650 sheet: 0.17 (0.20), residues: 710 loop : -1.56 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 534 HIS 0.003 0.001 HIS B 360 PHE 0.020 0.002 PHE E 414 TYR 0.017 0.002 TYR A 517 ARG 0.004 0.000 ARG D 406 *********************** 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 254 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 159 time to evaluate : 2.238 Fit side-chains REVERT: A 406 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8368 (ptt90) REVERT: A 515 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 272 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7824 (p0) REVERT: B 515 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7954 (mp) REVERT: D 272 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7614 (p0) REVERT: D 515 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8039 (mp) REVERT: E 272 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7537 (p0) REVERT: E 515 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8013 (mp) REVERT: E 521 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8371 (ttt90) REVERT: E 570 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8383 (mt) REVERT: C 282 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8822 (mp) REVERT: C 515 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7935 (mp) outliers start: 95 outliers final: 64 residues processed: 225 average time/residue: 0.3068 time to fit residues: 109.2023 Evaluate side-chains 230 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 154 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 326 GLU 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 515 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU 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 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 515 LEU 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 220 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 396 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU 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 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 220 THR 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 363 LYS 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 570 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 622 LEU 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 220 THR 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 515 LEU Chi-restraints excluded: chain C residue 560 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 220 optimal weight: 40.0000 chunk 123 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 272 ASN A 560 ASN B 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 21660 Z= 0.298 Angle : 0.566 7.688 29530 Z= 0.296 Chirality : 0.045 0.221 3435 Planarity : 0.004 0.040 3810 Dihedral : 4.365 17.278 2980 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.32 % Allowed : 19.26 % Favored : 76.43 % 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: -0.15 (0.16), residues: 2725 helix: 2.36 (0.21), residues: 640 sheet: 0.19 (0.20), residues: 710 loop : -1.52 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 359 HIS 0.002 0.001 HIS B 360 PHE 0.016 0.002 PHE E 414 TYR 0.013 0.001 TYR B 441 ARG 0.002 0.000 ARG A 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 262 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 169 time to evaluate : 2.294 Fit side-chains REVERT: A 406 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8333 (ptt90) REVERT: A 515 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7969 (mp) REVERT: B 272 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7820 (p0) REVERT: B 406 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8220 (ptt90) REVERT: B 515 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7931 (mp) REVERT: D 272 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7622 (p0) REVERT: D 515 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8035 (mp) REVERT: E 272 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7543 (p0) REVERT: E 515 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8035 (mp) REVERT: E 521 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8332 (ttt90) REVERT: C 282 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8819 (mp) REVERT: C 515 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7911 (mp) outliers start: 93 outliers final: 69 residues processed: 228 average time/residue: 0.3232 time to fit residues: 115.1458 Evaluate side-chains 246 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 165 time to evaluate : 2.239 ------------------------------------------------------------------------------- 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 272 ASN 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 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 A residue 622 LEU 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 220 THR Chi-restraints excluded: chain B residue 272 ASN 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 396 SER Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 LEU 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 220 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 363 LYS Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 503 SER 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 247 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 363 LYS Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 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 603 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 622 LEU 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 515 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 0.0170 chunk 29 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 223 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 265 optimal weight: 3.9990 chunk 165 optimal weight: 40.0000 chunk 161 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 344 GLN A 560 ASN B 611 GLN D 225 ASN D 560 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1949 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= 0.124 Angle : 0.486 7.558 29530 Z= 0.253 Chirality : 0.042 0.239 3435 Planarity : 0.003 0.031 3810 Dihedral : 4.012 16.739 2980 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.88 % Allowed : 21.21 % Favored : 75.92 % 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: 0.24 (0.17), residues: 2725 helix: 2.82 (0.21), residues: 640 sheet: 0.50 (0.20), residues: 735 loop : -1.44 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.002 0.000 HIS A 233 PHE 0.017 0.001 PHE E 561 TYR 0.012 0.001 TYR A 441 ARG 0.002 0.000 ARG E 498 *********************** 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 242 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 180 time to evaluate : 2.364 Fit side-chains REVERT: A 406 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8350 (ptt90) REVERT: B 272 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7781 (p0) REVERT: B 391 ASN cc_start: 0.7972 (m-40) cc_final: 0.7745 (t0) REVERT: B 515 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7834 (mp) REVERT: D 272 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7628 (p0) REVERT: D 515 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7927 (mp) REVERT: E 272 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7573 (p0) REVERT: E 363 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8731 (mttp) REVERT: E 515 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7922 (mp) REVERT: C 282 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8745 (mp) outliers start: 62 outliers final: 41 residues processed: 218 average time/residue: 0.3146 time to fit residues: 108.0488 Evaluate side-chains 218 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 169 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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 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 560 ASN Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU 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 367 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 272 ASN Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 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 272 ASN Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 500 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 E residue 622 LEU 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 391 ASN Chi-restraints excluded: chain C residue 500 SER 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 163 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 A 611 GLN B 611 GLN D 225 ASN D 560 ASN D 597 GLN C 560 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21660 Z= 0.233 Angle : 0.537 8.394 29530 Z= 0.281 Chirality : 0.044 0.244 3435 Planarity : 0.003 0.034 3810 Dihedral : 4.078 16.745 2980 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.20 % Allowed : 20.93 % Favored : 75.87 % 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: 0.13 (0.17), residues: 2725 helix: 2.68 (0.21), residues: 640 sheet: 0.39 (0.20), residues: 710 loop : -1.42 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 359 HIS 0.002 0.000 HIS E 360 PHE 0.015 0.001 PHE E 414 TYR 0.014 0.001 TYR B 441 ARG 0.002 0.000 ARG A 406 *********************** 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 248 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 179 time to evaluate : 2.278 Fit side-chains REVERT: A 406 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8315 (ptt90) REVERT: B 272 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7763 (p0) REVERT: B 515 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7885 (mp) REVERT: D 272 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7617 (p0) REVERT: D 515 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7970 (mp) REVERT: E 272 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7574 (p0) REVERT: E 515 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7952 (mp) REVERT: E 521 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8325 (ttt90) REVERT: C 282 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8737 (mp) outliers start: 69 outliers final: 54 residues processed: 223 average time/residue: 0.3172 time to fit residues: 110.6768 Evaluate side-chains 236 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 173 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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 483 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU 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 358 SER Chi-restraints excluded: chain B residue 367 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 272 ASN 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 439 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL 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 247 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 483 VAL Chi-restraints excluded: chain E residue 500 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 E residue 622 LEU 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 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 619 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 20.0000 chunk 253 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 246 optimal weight: 0.1980 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 233 optimal weight: 0.0010 chunk 162 optimal weight: 10.0000 overall best weight: 2.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 611 GLN D 225 ASN D 560 ASN E 597 GLN C 560 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21660 Z= 0.236 Angle : 0.534 8.305 29530 Z= 0.279 Chirality : 0.044 0.250 3435 Planarity : 0.003 0.034 3810 Dihedral : 4.108 16.922 2980 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.39 % Allowed : 20.84 % Favored : 75.78 % 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: 0.12 (0.17), residues: 2725 helix: 2.65 (0.21), residues: 640 sheet: 0.39 (0.20), residues: 710 loop : -1.43 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.002 0.000 HIS E 360 PHE 0.015 0.001 PHE B 414 TYR 0.013 0.001 TYR B 441 ARG 0.001 0.000 ARG A 406 *********************** 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 245 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 172 time to evaluate : 2.188 Fit side-chains REVERT: A 406 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8292 (ptt90) REVERT: B 272 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7752 (p0) REVERT: B 515 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7890 (mp) REVERT: D 272 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7628 (p0) REVERT: D 515 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7955 (mp) REVERT: E 272 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7570 (p0) REVERT: E 515 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7983 (mp) REVERT: E 521 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8310 (ttt90) REVERT: C 282 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8778 (mp) REVERT: C 622 LEU cc_start: 0.8852 (mt) cc_final: 0.8616 (mp) outliers start: 73 outliers final: 59 residues processed: 219 average time/residue: 0.3201 time to fit residues: 110.1353 Evaluate side-chains 239 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 171 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 483 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU 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 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 272 ASN 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 439 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL 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 247 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 483 VAL Chi-restraints excluded: chain E residue 500 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 E residue 622 LEU 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 483 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 560 ASN 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 261 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 123 optimal weight: 30.0000 chunk 181 optimal weight: 9.9990 chunk 273 optimal weight: 6.9990 chunk 252 optimal weight: 0.0770 chunk 218 optimal weight: 2.9990 chunk 22 optimal weight: 40.0000 chunk 168 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN A 560 ASN A 611 GLN B 560 ASN D 225 ASN D 560 ASN E 597 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21660 Z= 0.314 Angle : 0.569 8.341 29530 Z= 0.299 Chirality : 0.045 0.266 3435 Planarity : 0.004 0.039 3810 Dihedral : 4.220 17.035 2980 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.39 % Allowed : 20.93 % Favored : 75.68 % 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: 0.02 (0.17), residues: 2725 helix: 2.52 (0.21), residues: 640 sheet: 0.33 (0.20), residues: 710 loop : -1.45 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 359 HIS 0.002 0.001 HIS E 360 PHE 0.017 0.002 PHE E 414 TYR 0.014 0.001 TYR A 517 ARG 0.002 0.000 ARG A 406 ********************** 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 247 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 174 time to evaluate : 2.339 Fit side-chains REVERT: A 406 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8318 (ptt90) REVERT: A 498 ARG cc_start: 0.7737 (mpt-90) cc_final: 0.7457 (mtt90) REVERT: B 272 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7783 (p0) REVERT: B 515 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7919 (mp) REVERT: D 272 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7629 (p0) REVERT: D 515 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8009 (mp) REVERT: E 272 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7550 (p0) REVERT: E 515 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8008 (mp) REVERT: E 521 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8320 (ttt90) REVERT: E 570 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 282 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8798 (mp) REVERT: C 498 ARG cc_start: 0.7728 (mpt-90) cc_final: 0.7424 (mtt90) REVERT: C 622 LEU cc_start: 0.8865 (mt) cc_final: 0.8628 (mp) outliers start: 73 outliers final: 60 residues processed: 221 average time/residue: 0.3090 time to fit residues: 107.4584 Evaluate side-chains 243 residues out of total 2445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 173 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 483 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU 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 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 483 VAL 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 272 ASN 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 439 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL 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 247 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 483 VAL Chi-restraints excluded: chain E residue 500 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 E residue 622 LEU 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 483 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER 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 232 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 218 optimal weight: 6.9990 chunk 91 optimal weight: 0.2980 chunk 224 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN A 560 ASN A 611 GLN D 225 ASN D 560 ASN E 597 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 = 0.4268 r_free = 0.4268 target = 0.200381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120180 restraints weight = 22479.210| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.02 r_work: 0.2957 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21660 Z= 0.145 Angle : 0.494 8.324 29530 Z= 0.257 Chirality : 0.042 0.257 3435 Planarity : 0.003 0.032 3810 Dihedral : 3.953 16.596 2980 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.88 % Allowed : 21.62 % Favored : 75.50 % 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: 2.86 (0.21), residues: 640 sheet: 0.58 (0.20), residues: 735 loop : -1.46 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.001 0.000 HIS C 233 PHE 0.011 0.001 PHE B 414 TYR 0.010 0.001 TYR B 441 ARG 0.001 0.000 ARG A 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4189.24 seconds wall clock time: 79 minutes 42.84 seconds (4782.84 seconds total)