Starting phenix.real_space_refine on Wed Jun 18 07:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ftg_50744/06_2025/9ftg_50744.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ftg_50744/06_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_50744/06_2025/9ftg_50744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ftg_50744/06_2025/9ftg_50744.map" model { file = "/net/cci-nas-00/data/ceres_data/9ftg_50744/06_2025/9ftg_50744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ftg_50744/06_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-5710/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: 9.51, 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: 5.01 Conformation dependent library (CDL) restraints added in 2.9 seconds 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5190 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 30 sheets defined 27.2% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 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: 6.47 Time building geometry restraints manager: 5.93 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.900 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.640 ------------------------------------------------------------------------------- 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 : 2.272 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: 0.3015 time to fit residues: 94.6653 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 : 2.409 ------------------------------------------------------------------------------- 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 = 68)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120373 restraints weight = 22313.262| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.96 r_work: 0.2933 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 0.06099 ( 820) hydrogen bonds : angle 5.01966 ( 2280) SS BOND : bond 0.00446 ( 10) SS BOND : angle 1.48454 ( 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 : 2.326 Fit side-chains REVERT: A 431 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8912 (mp) REVERT: B 431 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8732 (mt) REVERT: C 469 PHE cc_start: 0.8771 (p90) cc_final: 0.8361 (p90) outliers start: 49 outliers final: 25 residues processed: 200 average time/residue: 0.2931 time to fit residues: 96.8349 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 : 2.117 ------------------------------------------------------------------------------- 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: 9.9990 chunk 20 optimal weight: 10.0000 chunk 204 optimal weight: 0.0770 chunk 1 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 59 optimal weight: 0.0060 chunk 172 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.6158 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.202951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125005 restraints weight = 22186.057| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.55 r_work: 0.2867 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1319 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= 0.117 Angle : 0.508 8.025 29550 Z= 0.263 Chirality : 0.042 0.189 3435 Planarity : 0.003 0.027 3810 Dihedral : 3.899 16.935 2980 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.74 % Allowed : 18.33 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2725 helix: 2.62 (0.20), residues: 640 sheet: 0.47 (0.19), residues: 795 loop : -1.38 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 359 HIS 0.002 0.000 HIS E 360 PHE 0.012 0.001 PHE E 414 TYR 0.010 0.001 TYR B 441 ARG 0.001 0.000 ARG D 246 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 820) hydrogen bonds : angle 4.43532 ( 2280) SS BOND : bond 0.00386 ( 10) SS BOND : angle 1.35488 ( 20) covalent geometry : bond 0.00270 (21660) covalent geometry : angle 0.50712 (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 249 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 2.177 Fit side-chains REVERT: A 515 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7950 (mp) REVERT: B 515 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 515 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7933 (mp) REVERT: E 515 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7979 (mp) REVERT: C 469 PHE cc_start: 0.8815 (p90) cc_final: 0.8395 (p90) REVERT: C 515 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7977 (mp) outliers start: 59 outliers final: 33 residues processed: 228 average time/residue: 0.2827 time to fit residues: 105.3892 Evaluate side-chains 213 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 2.135 ------------------------------------------------------------------------------- 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 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 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 391 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 180 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 271 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 205 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 597 GLN A 611 GLN B 597 GLN D 225 ASN D 597 GLN E 611 GLN C 597 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.203567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123563 restraints weight = 22528.236| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.99 r_work: 0.3018 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21670 Z= 0.106 Angle : 0.496 7.306 29550 Z= 0.257 Chirality : 0.042 0.208 3435 Planarity : 0.003 0.025 3810 Dihedral : 3.857 16.696 2980 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.23 % Allowed : 18.65 % Favored : 79.12 % 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: 0.36 (0.17), residues: 2725 helix: 2.83 (0.20), residues: 640 sheet: 0.48 (0.19), residues: 795 loop : -1.34 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 359 HIS 0.001 0.000 HIS E 360 PHE 0.012 0.001 PHE E 414 TYR 0.014 0.001 TYR E 163 ARG 0.001 0.000 ARG C 406 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 820) hydrogen bonds : angle 4.23918 ( 2280) SS BOND : bond 0.00368 ( 10) SS BOND : angle 1.24538 ( 20) covalent geometry : bond 0.00241 (21660) covalent geometry : angle 0.49466 (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 229 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 2.281 Fit side-chains REVERT: A 92 LEU cc_start: 0.5223 (OUTLIER) cc_final: 0.5022 (mp) REVERT: A 515 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7910 (mp) REVERT: B 515 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7921 (mp) REVERT: D 515 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7851 (mp) REVERT: E 515 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7921 (mp) REVERT: E 597 GLN cc_start: 0.8809 (mt0) cc_final: 0.8525 (mt0) REVERT: C 469 PHE cc_start: 0.8859 (p90) cc_final: 0.8458 (p90) REVERT: C 515 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7913 (mp) outliers start: 48 outliers final: 28 residues processed: 212 average time/residue: 0.2991 time to fit residues: 102.1317 Evaluate side-chains 207 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 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 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 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 247 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 515 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: 3.9990 chunk 86 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 B 611 GLN D 225 ASN D 597 GLN 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 = 0.4281 r_free = 0.4281 target = 0.201638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124598 restraints weight = 22427.785| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.48 r_work: 0.2913 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21670 Z= 0.137 Angle : 0.524 7.558 29550 Z= 0.272 Chirality : 0.043 0.210 3435 Planarity : 0.003 0.025 3810 Dihedral : 3.968 16.784 2980 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.92 % Allowed : 18.52 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2725 helix: 2.81 (0.20), residues: 635 sheet: 0.48 (0.20), residues: 725 loop : -1.32 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 359 HIS 0.002 0.000 HIS E 360 PHE 0.015 0.001 PHE E 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 0.04903 ( 820) hydrogen bonds : angle 4.23628 ( 2280) SS BOND : bond 0.00477 ( 10) SS BOND : angle 1.24691 ( 20) covalent geometry : bond 0.00331 (21660) covalent geometry : angle 0.52274 (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 241 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 178 time to evaluate : 2.557 Fit side-chains REVERT: A 406 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8403 (ptt90) REVERT: A 496 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8348 (t80) REVERT: A 515 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7965 (mp) REVERT: B 515 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7956 (mp) REVERT: D 515 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7910 (mp) REVERT: E 515 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7914 (mp) REVERT: C 469 PHE cc_start: 0.8829 (p90) cc_final: 0.8425 (p90) REVERT: C 515 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7966 (mp) outliers start: 63 outliers final: 48 residues processed: 216 average time/residue: 0.3100 time to fit residues: 107.0972 Evaluate side-chains 229 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 174 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 458 THR 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 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 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 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 351 VAL 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 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 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 515 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 ILE 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: 8.9990 chunk 88 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 72 optimal weight: 0.0870 chunk 133 optimal weight: 30.0000 overall best weight: 2.9964 ------------------------------------------------------------------------------- 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 611 GLN D 225 ASN D 344 GLN D 560 ASN E 344 GLN E 560 ASN E 597 GLN E 611 GLN C 344 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.199531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150290 restraints weight = 22261.115| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.84 r_work: 0.2986 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21670 Z= 0.173 Angle : 0.555 7.919 29550 Z= 0.291 Chirality : 0.044 0.231 3435 Planarity : 0.003 0.033 3810 Dihedral : 4.172 17.155 2980 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.39 % Allowed : 18.84 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2725 helix: 2.57 (0.21), residues: 640 sheet: 0.47 (0.20), residues: 710 loop : -1.40 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 534 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.002 PHE B 414 TYR 0.014 0.001 TYR A 517 ARG 0.003 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.05582 ( 820) hydrogen bonds : angle 4.32433 ( 2280) SS BOND : bond 0.00586 ( 10) SS BOND : angle 1.27733 ( 20) covalent geometry : bond 0.00429 (21660) covalent geometry : angle 0.55453 (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 249 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 176 time to evaluate : 2.165 Fit side-chains REVERT: A 406 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8392 (ptt90) REVERT: A 496 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8590 (t80) REVERT: A 515 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8058 (mp) REVERT: B 515 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8055 (mp) REVERT: D 515 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8090 (mp) REVERT: E 515 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8032 (mp) REVERT: C 515 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8038 (mp) outliers start: 73 outliers final: 52 residues processed: 222 average time/residue: 0.2981 time to fit residues: 106.9693 Evaluate side-chains 229 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 496 PHE 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 358 SER 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 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 351 VAL 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 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 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 515 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 9 optimal weight: 30.0000 chunk 95 optimal weight: 7.9990 chunk 168 optimal weight: 30.0000 chunk 261 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 182 optimal weight: 0.0670 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN B 611 GLN D 225 ASN D 560 ASN E 560 ASN E 611 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.200217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142401 restraints weight = 22198.550| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.64 r_work: 0.3249 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21670 Z= 0.146 Angle : 0.531 8.242 29550 Z= 0.277 Chirality : 0.043 0.230 3435 Planarity : 0.003 0.033 3810 Dihedral : 4.122 17.088 2980 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.43 % Allowed : 19.35 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2725 helix: 2.63 (0.21), residues: 640 sheet: 0.47 (0.20), residues: 710 loop : -1.41 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 359 HIS 0.002 0.000 HIS D 360 PHE 0.015 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 0.05078 ( 820) hydrogen bonds : angle 4.23884 ( 2280) SS BOND : bond 0.00499 ( 10) SS BOND : angle 1.22381 ( 20) covalent geometry : bond 0.00356 (21660) covalent geometry : angle 0.53035 (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 249 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 175 time to evaluate : 2.425 Fit side-chains REVERT: A 406 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8339 (ptt90) REVERT: A 515 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7961 (mp) REVERT: B 515 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7969 (mp) REVERT: D 515 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7992 (mp) REVERT: E 515 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7918 (mp) REVERT: E 521 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8256 (ttt90) REVERT: E 570 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8226 (mt) REVERT: C 515 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7936 (mp) outliers start: 74 outliers final: 62 residues processed: 221 average time/residue: 0.3018 time to fit residues: 107.3282 Evaluate side-chains 244 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 174 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 326 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 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 367 SER 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 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 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 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 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 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 515 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 217 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.203155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126088 restraints weight = 22342.183| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.20 r_work: 0.2920 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21670 Z= 0.094 Angle : 0.487 7.952 29550 Z= 0.253 Chirality : 0.042 0.245 3435 Planarity : 0.003 0.027 3810 Dihedral : 3.926 16.645 2980 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.27 % Allowed : 20.74 % Favored : 76.98 % 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: 0.34 (0.17), residues: 2725 helix: 2.86 (0.21), residues: 640 sheet: 0.61 (0.19), residues: 760 loop : -1.42 (0.17), residues: 1325 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 0.022 0.001 PHE E 561 TYR 0.011 0.001 TYR B 441 ARG 0.001 0.000 ARG E 155 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 820) hydrogen bonds : angle 4.04086 ( 2280) SS BOND : bond 0.00316 ( 10) SS BOND : angle 1.14868 ( 20) covalent geometry : bond 0.00202 (21660) covalent geometry : angle 0.48582 (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 219 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 2.404 Fit side-chains REVERT: A 406 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8363 (ptt90) REVERT: A 515 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 391 ASN cc_start: 0.8023 (m-40) cc_final: 0.7731 (t0) REVERT: D 515 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7925 (mp) REVERT: E 515 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7910 (mp) REVERT: C 515 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7923 (mp) outliers start: 49 outliers final: 41 residues processed: 201 average time/residue: 0.3248 time to fit residues: 103.8370 Evaluate side-chains 214 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 2.356 ------------------------------------------------------------------------------- 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 391 ASN Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 560 ASN 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 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 515 LEU Chi-restraints excluded: chain D residue 560 ASN 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 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain 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 500 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 109 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 204 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 252 optimal weight: 0.0030 chunk 122 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 overall best weight: 2.9596 ------------------------------------------------------------------------------- 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 D 597 GLN E 560 ASN C 560 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.199521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120306 restraints weight = 22214.978| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.36 r_work: 0.2859 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21670 Z= 0.171 Angle : 0.555 8.104 29550 Z= 0.291 Chirality : 0.045 0.255 3435 Planarity : 0.003 0.033 3810 Dihedral : 4.103 16.677 2980 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.97 % Allowed : 20.14 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2725 helix: 2.57 (0.21), residues: 640 sheet: 0.52 (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 B 534 HIS 0.002 0.000 HIS E 360 PHE 0.017 0.002 PHE B 414 TYR 0.014 0.001 TYR C 517 ARG 0.003 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 820) hydrogen bonds : angle 4.19254 ( 2280) SS BOND : bond 0.00530 ( 10) SS BOND : angle 1.22173 ( 20) covalent geometry : bond 0.00428 (21660) covalent geometry : angle 0.55412 (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 240 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 2.506 Fit side-chains REVERT: A 406 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8373 (ptt90) REVERT: A 496 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8468 (t80) REVERT: A 515 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8009 (mp) REVERT: B 391 ASN cc_start: 0.8079 (m-40) cc_final: 0.7794 (t0) REVERT: B 406 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8331 (ptt180) REVERT: B 570 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8282 (mt) REVERT: D 515 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8022 (mp) REVERT: E 515 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7949 (mp) REVERT: E 570 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8197 (mt) REVERT: C 515 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7955 (mp) outliers start: 64 outliers final: 48 residues processed: 220 average time/residue: 0.3245 time to fit residues: 113.1607 Evaluate side-chains 232 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 2.266 ------------------------------------------------------------------------------- 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 326 GLU Chi-restraints excluded: chain A residue 358 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 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 406 ARG Chi-restraints excluded: chain B residue 503 SER 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 363 LYS 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 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 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 560 ASN Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 246 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 129 optimal weight: 0.3980 chunk 241 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 1 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 560 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.201267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123425 restraints weight = 22354.954| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.28 r_work: 0.2887 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1835 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= 0.118 Angle : 0.508 7.933 29550 Z= 0.266 Chirality : 0.043 0.257 3435 Planarity : 0.003 0.031 3810 Dihedral : 4.015 16.825 2980 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.69 % Allowed : 20.56 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2725 helix: 2.75 (0.21), residues: 640 sheet: 0.58 (0.20), residues: 710 loop : -1.42 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.001 0.000 HIS D 360 PHE 0.013 0.001 PHE B 414 TYR 0.012 0.001 TYR B 441 ARG 0.002 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 820) hydrogen bonds : angle 4.09009 ( 2280) SS BOND : bond 0.00398 ( 10) SS BOND : angle 1.17557 ( 20) covalent geometry : bond 0.00276 (21660) covalent geometry : angle 0.50711 (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 228 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 2.386 Fit side-chains REVERT: A 406 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8394 (ptt90) REVERT: A 515 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 597 GLN cc_start: 0.8824 (mt0) cc_final: 0.8572 (mt0) REVERT: B 391 ASN cc_start: 0.8054 (m-40) cc_final: 0.7771 (t0) REVERT: D 515 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8025 (mp) REVERT: E 515 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7939 (mp) REVERT: E 521 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8328 (ttt90) REVERT: E 560 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8463 (t0) REVERT: C 515 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7974 (mp) outliers start: 58 outliers final: 45 residues processed: 208 average time/residue: 0.3200 time to fit residues: 105.2996 Evaluate side-chains 223 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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 326 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 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 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 363 LYS Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 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 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 36 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 251 optimal weight: 0.9980 chunk 174 optimal weight: 50.0000 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 560 ASN D 225 ASN D 560 ASN E 560 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.201673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124062 restraints weight = 22403.933| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.38 r_work: 0.2904 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21670 Z= 0.113 Angle : 0.505 7.859 29550 Z= 0.263 Chirality : 0.043 0.263 3435 Planarity : 0.003 0.030 3810 Dihedral : 3.967 16.468 2980 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.65 % Allowed : 20.46 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2725 helix: 2.81 (0.21), residues: 640 sheet: 0.50 (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 A 359 HIS 0.001 0.000 HIS D 360 PHE 0.013 0.001 PHE B 414 TYR 0.012 0.001 TYR B 441 ARG 0.001 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 820) hydrogen bonds : angle 4.03351 ( 2280) SS BOND : bond 0.00392 ( 10) SS BOND : angle 1.17991 ( 20) covalent geometry : bond 0.00263 (21660) covalent geometry : angle 0.50390 (29530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12931.04 seconds wall clock time: 220 minutes 34.01 seconds (13234.01 seconds total)