Starting phenix.real_space_refine on Wed May 21 04:31:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ftg_50744/05_2025/9ftg_50744.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ftg_50744/05_2025/9ftg_50744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ftg_50744/05_2025/9ftg_50744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ftg_50744/05_2025/9ftg_50744.map" model { file = "/net/cci-nas-00/data/ceres_data/9ftg_50744/05_2025/9ftg_50744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ftg_50744/05_2025/9ftg_50744.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 40 5.16 5 C 13690 2.51 5 N 3535 2.21 5 O 3935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.61, per 1000 atoms: 0.45 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=10, 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 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 280 " distance=2.04 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 280 " distance=2.03 Simple disulfide: pdb=" SG CYS C 371 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS E 371 " - pdb=" SG CYS E 373 " distance=2.03 Simple disulfide: pdb=" SG CYS D 371 " - pdb=" SG CYS D 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: 4.93 Conformation dependent library (CDL) restraints added in 2.7 seconds 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5190 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 30 sheets defined 27.2% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 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: 6.71 Time building geometry restraints manager: 5.79 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: 11026 16.67 - 33.34: 1159 33.34 - 50.01: 365 50.01 - 66.68: 65 66.68 - 83.35: 20 Dihedral angle restraints: 12635 sinusoidal: 4590 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=" CB CYS E 371 " pdb=" SG CYS E 371 " pdb=" SG CYS E 373 " pdb=" CB CYS E 373 " ideal model delta sinusoidal sigma weight residual -86.00 -118.97 32.97 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS C 371 " pdb=" SG CYS C 371 " pdb=" SG CYS C 373 " pdb=" CB CYS C 373 " ideal model delta sinusoidal sigma weight residual -86.00 -118.96 32.96 1 1.00e+01 1.00e-02 1.55e+01 ... (remaining 12632 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: 2.28 - 2.80: 5575 2.80 - 3.33: 17090 3.33 - 3.85: 31466 3.85 - 4.38: 35381 4.38 - 4.90: 66075 Nonbonded interactions: 155587 Sorted by model distance: nonbonded pdb=" OG SER D 408 " pdb=" OE2 GLU D 425 " model vdw 2.278 3.040 nonbonded pdb=" OG SER A 408 " pdb=" OE2 GLU A 425 " model vdw 2.278 3.040 nonbonded pdb=" OG SER C 408 " pdb=" OE2 GLU C 425 " model vdw 2.278 3.040 nonbonded pdb=" OG SER B 408 " pdb=" OE2 GLU B 425 " model vdw 2.279 3.040 nonbonded pdb=" OG SER E 408 " pdb=" OE2 GLU E 425 " model vdw 2.280 3.040 ... (remaining 155582 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 42.800 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.040 ------------------------------------------------------------------------------- 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 21670 Z= 0.128 Angle : 0.480 7.577 29550 Z= 0.241 Chirality : 0.043 0.258 3435 Planarity : 0.003 0.040 3810 Dihedral : 15.404 83.349 7415 Min Nonbonded Distance : 2.278 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 Details of bonding type rmsd hydrogen bonds : bond 0.29783 ( 820) hydrogen bonds : angle 7.40946 ( 2280) SS BOND : bond 0.00289 ( 10) SS BOND : angle 0.55816 ( 20) covalent geometry : bond 0.00317 (21660) covalent geometry : angle 0.47952 (29530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 2.119 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: 0.2953 time to fit residues: 92.0793 Evaluate side-chains 184 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 2.119 ------------------------------------------------------------------------------- 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: 30.0000 chunk 160 optimal weight: 3.9990 chunk 249 optimal weight: 0.5980 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 206 GLN A 272 ASN A 307 ASN A 410 ASN B 206 GLN B 272 ASN B 307 ASN B 410 ASN D 206 GLN D 272 ASN D 307 ASN D 410 ASN E 206 GLN E 272 ASN E 307 ASN E 410 ASN C 160 GLN C 206 GLN C 272 ASN C 307 ASN C 410 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.201174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120373 restraints weight = 22313.244| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.97 r_work: 0.2936 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21670 Z= 0.146 Angle : 0.548 7.721 29550 Z= 0.287 Chirality : 0.043 0.177 3435 Planarity : 0.004 0.039 3810 Dihedral : 3.950 17.606 2980 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.27 % Allowed : 17.31 % Favored : 80.42 % 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: -0.01 (0.16), residues: 2725 helix: 2.11 (0.20), residues: 635 sheet: 0.50 (0.20), residues: 730 loop : -1.40 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 359 HIS 0.002 0.001 HIS E 360 PHE 0.016 0.001 PHE E 414 TYR 0.010 0.001 TYR B 441 ARG 0.002 0.000 ARG D 426 Details of bonding type rmsd hydrogen bonds : bond 0.06100 ( 820) hydrogen bonds : angle 5.01966 ( 2280) SS BOND : bond 0.00446 ( 10) SS BOND : angle 1.48458 ( 20) covalent geometry : bond 0.00342 (21660) covalent geometry : angle 0.54726 (29530) *********************** 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 222 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 2.371 Fit side-chains REVERT: A 431 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8913 (mp) REVERT: B 431 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8731 (mt) REVERT: D 470 GLN cc_start: 0.8373 (tt0) cc_final: 0.8171 (tt0) REVERT: C 469 PHE cc_start: 0.8763 (p90) cc_final: 0.8349 (p90) outliers start: 49 outliers final: 25 residues processed: 200 average time/residue: 0.2840 time to fit residues: 93.3509 Evaluate side-chains 196 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 2.229 ------------------------------------------------------------------------------- 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 391 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 431 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 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 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 162 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 1 optimal weight: 30.0000 chunk 248 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 59 optimal weight: 0.0470 chunk 172 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 overall best weight: 3.0084 ------------------------------------------------------------------------------- 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 611 GLN D 225 ASN E 597 GLN C 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.199802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119134 restraints weight = 22156.681| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.06 r_work: 0.2996 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 21670 Z= 0.176 Angle : 0.567 8.256 29550 Z= 0.296 Chirality : 0.044 0.207 3435 Planarity : 0.004 0.035 3810 Dihedral : 4.152 17.305 2980 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.97 % Allowed : 18.00 % Favored : 79.03 % 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: 0.07 (0.16), residues: 2725 helix: 2.36 (0.21), residues: 640 sheet: 0.47 (0.20), residues: 700 loop : -1.37 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.003 0.001 HIS E 360 PHE 0.016 0.001 PHE E 414 TYR 0.013 0.001 TYR E 517 ARG 0.003 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.06072 ( 820) hydrogen bonds : angle 4.61190 ( 2280) SS BOND : bond 0.00567 ( 10) SS BOND : angle 1.44306 ( 20) covalent geometry : bond 0.00435 (21660) covalent geometry : angle 0.56627 (29530) *********************** 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 241 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 2.146 Fit side-chains REVERT: A 515 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7959 (mp) REVERT: D 272 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7436 (p0) outliers start: 64 outliers final: 44 residues processed: 219 average time/residue: 0.2823 time to fit residues: 100.4653 Evaluate side-chains 213 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 391 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 458 THR 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 391 ASN Chi-restraints excluded: chain D residue 458 THR 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 351 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 180 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 560 ASN A 597 GLN D 225 ASN D 344 GLN D 560 ASN D 597 GLN E 560 ASN E 611 GLN C 597 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.198993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117590 restraints weight = 22506.468| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.05 r_work: 0.2891 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21670 Z= 0.163 Angle : 0.550 7.414 29550 Z= 0.287 Chirality : 0.044 0.206 3435 Planarity : 0.003 0.032 3810 Dihedral : 4.183 17.247 2980 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.90 % Allowed : 18.38 % 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: 0.08 (0.16), residues: 2725 helix: 2.46 (0.21), residues: 640 sheet: 0.44 (0.20), residues: 700 loop : -1.39 (0.16), residues: 1385 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 0.015 0.001 PHE E 414 TYR 0.014 0.001 TYR C 163 ARG 0.003 0.000 ARG C 406 Details of bonding type rmsd hydrogen bonds : bond 0.05438 ( 820) hydrogen bonds : angle 4.47425 ( 2280) SS BOND : bond 0.00545 ( 10) SS BOND : angle 1.37333 ( 20) covalent geometry : bond 0.00403 (21660) covalent geometry : angle 0.54898 (29530) *********************** 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 259 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 175 time to evaluate : 2.281 Fit side-chains REVERT: A 496 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8490 (t80) REVERT: A 515 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 515 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7928 (mp) REVERT: D 515 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7975 (mp) REVERT: E 92 LEU cc_start: 0.5143 (OUTLIER) cc_final: 0.4933 (mp) REVERT: E 515 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7954 (mp) REVERT: E 570 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8179 (mt) REVERT: C 515 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7922 (mp) outliers start: 84 outliers final: 59 residues processed: 229 average time/residue: 0.2873 time to fit residues: 106.5011 Evaluate side-chains 238 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain A residue 367 SER 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 496 PHE 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 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 458 THR 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 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 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 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 247 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 391 ASN 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 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 458 THR 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 603 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 560 ASN B 597 GLN B 611 GLN D 225 ASN D 560 ASN E 560 ASN E 611 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.201100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120700 restraints weight = 22405.472| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.15 r_work: 0.2938 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21670 Z= 0.126 Angle : 0.520 6.983 29550 Z= 0.270 Chirality : 0.043 0.208 3435 Planarity : 0.003 0.032 3810 Dihedral : 4.089 17.087 2980 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.57 % Allowed : 19.07 % Favored : 77.35 % 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: 0.19 (0.16), residues: 2725 helix: 2.65 (0.21), residues: 640 sheet: 0.50 (0.20), residues: 710 loop : -1.39 (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 0.013 0.001 PHE B 414 TYR 0.012 0.001 TYR B 441 ARG 0.002 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 820) hydrogen bonds : angle 4.29028 ( 2280) SS BOND : bond 0.00452 ( 10) SS BOND : angle 1.27558 ( 20) covalent geometry : bond 0.00298 (21660) covalent geometry : angle 0.51864 (29530) *********************** 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 251 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 174 time to evaluate : 2.142 Fit side-chains REVERT: A 406 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8397 (ptt90) REVERT: A 496 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8493 (t80) REVERT: A 515 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7952 (mp) REVERT: B 515 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7972 (mp) REVERT: B 570 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8238 (mt) REVERT: D 515 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7984 (mp) REVERT: D 570 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8220 (mt) REVERT: E 92 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.5115 (mp) REVERT: E 515 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7899 (mp) REVERT: E 521 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8313 (ttt90) REVERT: C 515 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7951 (mp) outliers start: 77 outliers final: 52 residues processed: 227 average time/residue: 0.2997 time to fit residues: 108.8753 Evaluate side-chains 231 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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 496 PHE 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 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 358 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 570 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 570 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 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 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 560 ASN Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER 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 500 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 45 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 114 optimal weight: 0.0020 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 217 optimal weight: 8.9990 chunk 72 optimal weight: 0.0270 chunk 133 optimal weight: 5.9990 overall best weight: 1.6250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN B 611 GLN D 225 ASN D 560 ASN E 560 ASN E 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 = 0.4278 r_free = 0.4278 target = 0.201577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123973 restraints weight = 22285.555| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.16 r_work: 0.2961 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21670 Z= 0.116 Angle : 0.507 7.909 29550 Z= 0.263 Chirality : 0.042 0.223 3435 Planarity : 0.003 0.031 3810 Dihedral : 4.024 16.643 2980 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.48 % Allowed : 19.86 % Favored : 76.66 % 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 (0.16), residues: 2725 helix: 2.74 (0.21), residues: 640 sheet: 0.53 (0.20), residues: 710 loop : -1.39 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.001 0.000 HIS B 360 PHE 0.013 0.001 PHE B 414 TYR 0.012 0.001 TYR B 441 ARG 0.001 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 820) hydrogen bonds : angle 4.20558 ( 2280) SS BOND : bond 0.00421 ( 10) SS BOND : angle 1.21967 ( 20) covalent geometry : bond 0.00271 (21660) covalent geometry : angle 0.50666 (29530) *********************** 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 248 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 173 time to evaluate : 2.316 Fit side-chains REVERT: A 406 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8402 (ptt90) REVERT: A 496 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8443 (t80) REVERT: A 515 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7990 (mp) REVERT: B 515 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7991 (mp) REVERT: B 570 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8225 (mt) REVERT: D 406 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8461 (ptt180) REVERT: D 515 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7978 (mp) REVERT: D 570 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8203 (mt) REVERT: E 92 LEU cc_start: 0.5327 (OUTLIER) cc_final: 0.5119 (mp) REVERT: E 515 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7930 (mp) REVERT: E 521 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8333 (ttt90) REVERT: C 515 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7973 (mp) outliers start: 75 outliers final: 51 residues processed: 228 average time/residue: 0.3087 time to fit residues: 110.4431 Evaluate side-chains 234 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 406 ARG 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 570 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 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 458 THR 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 560 ASN Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 619 ILE 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 9 optimal weight: 40.0000 chunk 95 optimal weight: 4.9990 chunk 168 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 182 optimal weight: 0.1980 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN B 344 GLN B 560 ASN B 611 GLN D 225 ASN D 560 ASN E 344 GLN E 560 ASN C 225 ASN C 344 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.198269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118644 restraints weight = 22210.101| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.50 r_work: 0.2852 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21670 Z= 0.192 Angle : 0.564 8.311 29550 Z= 0.295 Chirality : 0.045 0.239 3435 Planarity : 0.004 0.035 3810 Dihedral : 4.181 16.869 2980 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.08 % Allowed : 19.30 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2725 helix: 2.51 (0.21), residues: 640 sheet: 0.40 (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 D 360 PHE 0.017 0.002 PHE E 414 TYR 0.014 0.002 TYR E 517 ARG 0.003 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.05615 ( 820) hydrogen bonds : angle 4.31861 ( 2280) SS BOND : bond 0.00574 ( 10) SS BOND : angle 1.26080 ( 20) covalent geometry : bond 0.00486 (21660) covalent geometry : angle 0.56308 (29530) *********************** 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 259 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 171 time to evaluate : 2.277 Fit side-chains REVERT: A 406 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8409 (ptt90) REVERT: A 496 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8537 (t80) REVERT: A 515 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8042 (mp) REVERT: B 515 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8021 (mp) REVERT: B 570 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8292 (mt) REVERT: D 406 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8526 (ptt180) REVERT: D 515 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8060 (mp) REVERT: D 570 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8302 (mt) REVERT: E 92 LEU cc_start: 0.5156 (OUTLIER) cc_final: 0.4948 (mp) REVERT: E 515 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8039 (mp) REVERT: E 521 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8369 (ttt90) REVERT: E 570 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8219 (mt) REVERT: C 515 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8013 (mp) outliers start: 88 outliers final: 68 residues processed: 232 average time/residue: 0.3174 time to fit residues: 117.6197 Evaluate side-chains 253 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 2.188 ------------------------------------------------------------------------------- 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 458 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 496 PHE 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 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 458 THR 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 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 220 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 406 ARG 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 570 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 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 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 458 THR 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 560 ASN Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER 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 503 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 217 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN B 560 ASN D 225 ASN D 560 ASN E 560 ASN C 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.200414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138259 restraints weight = 22248.622| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 6.34 r_work: 0.2860 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21670 Z= 0.134 Angle : 0.522 8.181 29550 Z= 0.273 Chirality : 0.043 0.240 3435 Planarity : 0.003 0.034 3810 Dihedral : 4.113 17.008 2980 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.99 % Allowed : 19.63 % Favored : 76.38 % 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: 2.66 (0.21), residues: 640 sheet: 0.48 (0.20), residues: 710 loop : -1.44 (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 0.014 0.001 PHE B 414 TYR 0.013 0.001 TYR B 441 ARG 0.002 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.04891 ( 820) hydrogen bonds : angle 4.22357 ( 2280) SS BOND : bond 0.00448 ( 10) SS BOND : angle 1.20257 ( 20) covalent geometry : bond 0.00323 (21660) covalent geometry : angle 0.52161 (29530) *********************** 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 264 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 178 time to evaluate : 2.222 Fit side-chains REVERT: A 406 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8374 (ptt90) REVERT: A 496 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8496 (t80) REVERT: A 515 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7915 (mp) REVERT: B 515 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7925 (mp) REVERT: D 406 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8461 (ptt180) REVERT: D 515 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7960 (mp) REVERT: D 570 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8190 (mt) REVERT: E 515 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7847 (mp) REVERT: E 521 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8242 (ttt90) REVERT: C 515 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7924 (mp) outliers start: 86 outliers final: 64 residues processed: 239 average time/residue: 0.3281 time to fit residues: 121.5182 Evaluate side-chains 246 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 172 time to evaluate : 2.143 ------------------------------------------------------------------------------- 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 496 PHE 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 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 458 THR 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 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 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 406 ARG 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 570 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 247 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 458 THR 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 C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 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 503 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 204 optimal weight: 0.0010 chunk 114 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 252 optimal weight: 0.4980 chunk 122 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN D 225 ASN D 560 ASN C 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.202299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124014 restraints weight = 22235.123| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.19 r_work: 0.2925 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21670 Z= 0.102 Angle : 0.495 7.930 29550 Z= 0.257 Chirality : 0.042 0.248 3435 Planarity : 0.003 0.031 3810 Dihedral : 3.944 16.465 2980 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.16 % Allowed : 20.46 % Favored : 76.38 % 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 (0.17), residues: 2725 helix: 2.90 (0.21), residues: 635 sheet: 0.48 (0.20), residues: 735 loop : -1.42 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 359 HIS 0.001 0.000 HIS D 233 PHE 0.011 0.001 PHE D 414 TYR 0.011 0.001 TYR B 441 ARG 0.003 0.000 ARG C 498 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 820) hydrogen bonds : angle 4.03962 ( 2280) SS BOND : bond 0.00348 ( 10) SS BOND : angle 1.17242 ( 20) covalent geometry : bond 0.00231 (21660) covalent geometry : angle 0.49412 (29530) *********************** 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 250 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 182 time to evaluate : 2.119 Fit side-chains REVERT: A 406 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8384 (ptt90) REVERT: A 515 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7892 (mp) REVERT: B 391 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7736 (t0) REVERT: D 515 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7881 (mp) REVERT: E 515 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7882 (mp) REVERT: C 515 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7898 (mp) outliers start: 68 outliers final: 51 residues processed: 229 average time/residue: 0.2874 time to fit residues: 105.8666 Evaluate side-chains 231 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 2.136 ------------------------------------------------------------------------------- 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 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 503 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU 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 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 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN 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 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 246 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 241 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 17 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN D 225 ASN D 560 ASN E 560 ASN C 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.200880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123258 restraints weight = 22341.476| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.31 r_work: 0.3067 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21670 Z= 0.130 Angle : 0.517 8.075 29550 Z= 0.270 Chirality : 0.043 0.259 3435 Planarity : 0.003 0.030 3810 Dihedral : 3.992 16.529 2980 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.02 % Allowed : 20.37 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2725 helix: 2.75 (0.21), residues: 640 sheet: 0.47 (0.20), residues: 735 loop : -1.42 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 359 HIS 0.002 0.000 HIS B 360 PHE 0.014 0.001 PHE D 414 TYR 0.013 0.001 TYR B 441 ARG 0.002 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 820) hydrogen bonds : angle 4.07354 ( 2280) SS BOND : bond 0.00426 ( 10) SS BOND : angle 1.17864 ( 20) covalent geometry : bond 0.00314 (21660) covalent geometry : angle 0.51652 (29530) ********************** 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 239 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 174 time to evaluate : 2.130 Fit side-chains REVERT: A 406 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8395 (ptt90) REVERT: A 515 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 391 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7770 (t0) REVERT: D 515 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7923 (mp) REVERT: D 570 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8214 (mt) REVERT: E 515 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7951 (mp) REVERT: C 515 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7949 (mp) REVERT: C 622 LEU cc_start: 0.8660 (mt) cc_final: 0.8415 (mp) outliers start: 65 outliers final: 55 residues processed: 222 average time/residue: 0.2845 time to fit residues: 102.0411 Evaluate side-chains 236 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 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 458 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 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 458 THR 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 560 ASN Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 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 458 THR 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 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 251 optimal weight: 0.7980 chunk 174 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN B 560 ASN B 597 GLN D 225 ASN D 560 ASN E 560 ASN C 225 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.199966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123212 restraints weight = 22369.024| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.14 r_work: 0.3194 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21670 Z= 0.152 Angle : 0.536 8.178 29550 Z= 0.279 Chirality : 0.044 0.263 3435 Planarity : 0.003 0.032 3810 Dihedral : 4.058 16.716 2980 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.25 % Allowed : 20.32 % 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: 0.18 (0.17), residues: 2725 helix: 2.66 (0.21), residues: 640 sheet: 0.55 (0.20), residues: 710 loop : -1.44 (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 B 360 PHE 0.015 0.001 PHE E 414 TYR 0.013 0.001 TYR B 441 ARG 0.003 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 820) hydrogen bonds : angle 4.12416 ( 2280) SS BOND : bond 0.00491 ( 10) SS BOND : angle 1.20749 ( 20) covalent geometry : bond 0.00375 (21660) covalent geometry : angle 0.53501 (29530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12787.66 seconds wall clock time: 220 minutes 18.52 seconds (13218.52 seconds total)