Starting phenix.real_space_refine on Sat Jul 4 12:49:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ftg_50744/07_2026/9ftg_50744.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ftg_50744/07_2026/9ftg_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ftg_50744/07_2026/9ftg_50744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ftg_50744/07_2026/9ftg_50744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ftg_50744/07_2026/9ftg_50744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ftg_50744/07_2026/9ftg_50744.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'GLU:plan': 10, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Restraints were copied for chains: B, D, E, C Time building chain proxies: 4.29, per 1000 atoms: 0.20 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 B 275 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 280 " distance=2.03 Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 280 " distance=2.04 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS D 371 " - pdb=" SG CYS D 373 " distance=2.03 Simple disulfide: pdb=" SG CYS E 371 " - pdb=" SG CYS E 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 371 " - pdb=" SG CYS C 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: 1.63 Conformation dependent library (CDL) restraints added in 947.3 milliseconds 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: 0.63 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: 3.58 Time building geometry restraints manager: 2.20 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'C' } 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: 1.240 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.460 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG E 498 TYR 0.010 0.001 TYR C 441 PHE 0.020 0.001 PHE B 414 TRP 0.005 0.001 TRP C 482 HIS 0.002 0.000 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (21660) covalent geometry : angle 0.47952 / 0.24 (29530) SS BOND : bond 0.00289 / 0.19 ( 10) SS BOND : angle 0.55816 / 0.38 ( 20) hydrogen bonds : bond 0.29783 / 20.19 ( 820) hydrogen bonds : angle 7.40946 / 5.02 ( 2280) *********************** 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 : 0.774 Fit side-chains REVERT: B 605 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7592 (ptpp) REVERT: B 608 VAL cc_start: 0.8774 (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: 0.1388 time to fit residues: 43.8067 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 : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 B 560 ASN D 206 GLN D 272 ASN D 307 ASN D 410 ASN E 206 GLN E 272 ASN E 307 ASN E 344 GLN E 410 ASN E 560 ASN C 160 GLN C 206 GLN C 272 ASN C 307 ASN C 410 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.199454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134751 restraints weight = 22418.348| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 5.69 r_work: 0.2769 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 21670 Z= 0.224 Angle : 0.615 7.927 29550 Z= 0.323 Chirality : 0.046 0.180 3435 Planarity : 0.004 0.048 3810 Dihedral : 4.235 18.516 2980 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.78 % Allowed : 17.26 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2725 helix: 1.71 (0.20), residues: 635 sheet: 0.39 (0.20), residues: 700 loop : -1.44 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 406 TYR 0.013 0.002 TYR E 517 PHE 0.020 0.002 PHE E 414 TRP 0.008 0.001 TRP B 359 HIS 0.003 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.22 (21660) covalent geometry : angle 0.61422 / 0.32 (29530) SS BOND : bond 0.00659 / 0.44 ( 10) SS BOND : angle 1.58725 / 0.99 ( 20) hydrogen bonds : bond 0.06647 / 4.56 ( 820) hydrogen bonds : angle 5.04113 / 3.43 ( 2280) *********************** 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 232 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 0.812 Fit side-chains REVERT: B 431 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8737 (mt) outliers start: 60 outliers final: 35 residues processed: 207 average time/residue: 0.1191 time to fit residues: 41.4618 Evaluate side-chains 198 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 109 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 chunk 165 optimal weight: 40.0000 chunk 124 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 GLN A 611 GLN D 344 GLN C 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.197813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116403 restraints weight = 22495.395| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.11 r_work: 0.3020 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 21670 Z= 0.204 Angle : 0.597 8.478 29550 Z= 0.311 Chirality : 0.045 0.196 3435 Planarity : 0.004 0.035 3810 Dihedral : 4.359 17.191 2980 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.85 % Allowed : 17.87 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2725 helix: 2.09 (0.21), residues: 640 sheet: 0.31 (0.20), residues: 700 loop : -1.46 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 498 TYR 0.013 0.002 TYR C 517 PHE 0.015 0.002 PHE E 414 TRP 0.008 0.001 TRP C 359 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.20 (21660) covalent geometry : angle 0.59566 / 0.31 (29530) SS BOND : bond 0.00644 / 0.43 ( 10) SS BOND : angle 1.49391 / 0.93 ( 20) hydrogen bonds : bond 0.06424 / 4.40 ( 820) hydrogen bonds : angle 4.70121 / 3.20 ( 2280) *********************** 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 257 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 174 time to evaluate : 0.566 Fit side-chains REVERT: A 496 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8641 (t80) REVERT: A 515 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8134 (mp) REVERT: B 570 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8308 (mt) REVERT: D 272 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7563 (p0) REVERT: D 515 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8132 (mp) REVERT: D 570 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8333 (mt) REVERT: E 272 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7691 (p0) REVERT: E 515 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8064 (mp) REVERT: E 570 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8299 (mt) REVERT: C 515 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8009 (mp) outliers start: 83 outliers final: 49 residues processed: 232 average time/residue: 0.1268 time to fit residues: 47.8455 Evaluate side-chains 222 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 326 GLU 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 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 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 396 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 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 224 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 229 optimal weight: 50.0000 chunk 4 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 146 optimal weight: 0.3980 chunk 261 optimal weight: 7.9990 chunk 165 optimal weight: 40.0000 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 560 ASN A 597 GLN D 225 ASN D 560 ASN D 597 GLN E 560 ASN E 597 GLN E 611 GLN C 344 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.197730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118057 restraints weight = 22452.040| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.39 r_work: 0.2843 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 21670 Z= 0.184 Angle : 0.570 7.472 29550 Z= 0.298 Chirality : 0.045 0.208 3435 Planarity : 0.004 0.038 3810 Dihedral : 4.333 17.535 2980 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.64 % Allowed : 18.42 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.16), residues: 2725 helix: 2.27 (0.21), residues: 640 sheet: 0.26 (0.20), residues: 710 loop : -1.52 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 406 TYR 0.012 0.001 TYR B 441 PHE 0.016 0.002 PHE E 414 TRP 0.008 0.001 TRP C 359 HIS 0.002 0.001 HIS E 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.18 (21660) covalent geometry : angle 0.56944 / 0.30 (29530) SS BOND : bond 0.00580 / 0.38 ( 10) SS BOND : angle 1.38209 / 0.87 ( 20) hydrogen bonds : bond 0.05725 / 3.93 ( 820) hydrogen bonds : angle 4.49777 / 3.07 ( 2280) *********************** 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 275 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 175 time to evaluate : 0.788 Fit side-chains REVERT: A 406 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8439 (ptt90) REVERT: A 496 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8574 (t80) REVERT: A 515 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 406 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8280 (ptt90) REVERT: B 515 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8019 (mp) REVERT: D 272 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7472 (p0) REVERT: D 406 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8511 (ptt180) REVERT: D 515 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8112 (mp) REVERT: E 272 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7454 (p0) REVERT: E 515 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8064 (mp) REVERT: E 521 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8374 (ttt90) REVERT: E 570 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8235 (mt) REVERT: C 515 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8009 (mp) outliers start: 100 outliers final: 66 residues processed: 246 average time/residue: 0.1334 time to fit residues: 52.0064 Evaluate side-chains 250 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 171 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 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 272 ASN Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 406 ARG Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 272 ASN 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 458 THR Chi-restraints excluded: chain E residue 483 VAL 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 Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 75 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 233 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 560 ASN B 611 GLN D 225 ASN D 560 ASN E 597 GLN E 611 GLN C 597 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.200961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120709 restraints weight = 22334.113| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.26 r_work: 0.2942 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21670 Z= 0.104 Angle : 0.504 6.906 29550 Z= 0.261 Chirality : 0.042 0.207 3435 Planarity : 0.003 0.032 3810 Dihedral : 4.107 17.017 2980 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.92 % Allowed : 20.79 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2725 helix: 2.64 (0.21), residues: 640 sheet: 0.54 (0.20), residues: 735 loop : -1.48 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 155 TYR 0.012 0.001 TYR B 441 PHE 0.013 0.001 PHE E 559 TRP 0.007 0.001 TRP D 359 HIS 0.001 0.000 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (21660) covalent geometry : angle 0.50350 / 0.26 (29530) SS BOND : bond 0.00359 / 0.24 ( 10) SS BOND : angle 1.24353 / 0.79 ( 20) hydrogen bonds : bond 0.04360 / 3.01 ( 820) hydrogen bonds : angle 4.23086 / 2.89 ( 2280) *********************** 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 247 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 0.801 Fit side-chains REVERT: A 406 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8420 (ptt90) REVERT: A 515 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8029 (mp) REVERT: B 515 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7974 (mp) REVERT: D 272 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7434 (p0) REVERT: D 515 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8079 (mp) REVERT: D 570 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8185 (mt) REVERT: E 515 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8014 (mp) REVERT: E 597 GLN cc_start: 0.8759 (mt0) cc_final: 0.8527 (mt0) REVERT: C 515 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7954 (mp) outliers start: 63 outliers final: 44 residues processed: 226 average time/residue: 0.1249 time to fit residues: 46.0136 Evaluate side-chains 229 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 391 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 67 optimal weight: 20.0000 chunk 259 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 560 ASN B 560 ASN B 611 GLN D 225 ASN D 560 ASN C 225 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 = 0.4252 r_free = 0.4252 target = 0.198867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118531 restraints weight = 22355.564| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.26 r_work: 0.2845 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21670 Z= 0.156 Angle : 0.543 7.876 29550 Z= 0.283 Chirality : 0.044 0.230 3435 Planarity : 0.003 0.034 3810 Dihedral : 4.170 16.825 2980 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.76 % Allowed : 19.91 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2725 helix: 2.61 (0.21), residues: 640 sheet: 0.39 (0.20), residues: 710 loop : -1.46 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 406 TYR 0.014 0.001 TYR B 441 PHE 0.015 0.001 PHE E 414 TRP 0.007 0.001 TRP C 359 HIS 0.002 0.000 HIS E 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (21660) covalent geometry : angle 0.54234 / 0.28 (29530) SS BOND : bond 0.00499 / 0.33 ( 10) SS BOND : angle 1.25614 / 0.80 ( 20) hydrogen bonds : bond 0.05217 / 3.58 ( 820) hydrogen bonds : angle 4.24553 / 2.90 ( 2280) *********************** 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 260 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 179 time to evaluate : 0.859 Fit side-chains REVERT: A 406 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8400 (ptt90) REVERT: A 496 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8509 (t80) REVERT: A 515 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 406 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8269 (ptt90) REVERT: B 515 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7989 (mp) REVERT: D 272 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7431 (p0) REVERT: D 515 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8096 (mp) REVERT: D 570 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8227 (mt) REVERT: E 515 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8014 (mp) REVERT: E 521 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8305 (ttt90) REVERT: C 515 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7962 (mp) outliers start: 81 outliers final: 59 residues processed: 233 average time/residue: 0.1556 time to fit residues: 56.6538 Evaluate side-chains 247 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 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 363 LYS Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG 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 483 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 135 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 chunk 55 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 61 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 165 optimal weight: 40.0000 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 344 GLN A 560 ASN B 344 GLN B 560 ASN B 611 GLN D 225 ASN D 560 ASN E 611 GLN C 225 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.196160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117757 restraints weight = 22456.420| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.36 r_work: 0.2839 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 21670 Z= 0.245 Angle : 0.613 8.226 29550 Z= 0.322 Chirality : 0.047 0.237 3435 Planarity : 0.004 0.041 3810 Dihedral : 4.421 17.230 2980 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.22 % Allowed : 19.63 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 2725 helix: 2.22 (0.21), residues: 650 sheet: 0.23 (0.19), residues: 710 loop : -1.54 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 406 TYR 0.016 0.002 TYR C 517 PHE 0.019 0.002 PHE E 414 TRP 0.009 0.002 TRP B 534 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.24 (21660) covalent geometry : angle 0.61236 / 0.32 (29530) SS BOND : bond 0.00699 / 0.46 ( 10) SS BOND : angle 1.30272 / 0.84 ( 20) hydrogen bonds : bond 0.06427 / 4.39 ( 820) hydrogen bonds : angle 4.41708 / 3.02 ( 2280) *********************** 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 263 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 172 time to evaluate : 0.637 Fit side-chains REVERT: A 406 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8437 (ptt90) REVERT: A 515 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 406 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8369 (ptt180) REVERT: B 515 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8086 (mp) REVERT: D 272 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7472 (p0) REVERT: D 515 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8191 (mp) REVERT: D 570 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8332 (mt) REVERT: E 515 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8138 (mp) REVERT: E 521 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8390 (ttt90) REVERT: E 570 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8299 (mt) REVERT: C 515 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8081 (mp) outliers start: 91 outliers final: 70 residues processed: 229 average time/residue: 0.1475 time to fit residues: 53.1476 Evaluate side-chains 251 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 170 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 483 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 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 374 THR Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 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 219 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 112 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 154 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 344 GLN A 560 ASN B 560 ASN B 611 GLN D 225 ASN D 560 ASN C 225 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.201335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121922 restraints weight = 22392.305| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.29 r_work: 0.2946 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21670 Z= 0.095 Angle : 0.490 7.729 29550 Z= 0.255 Chirality : 0.042 0.234 3435 Planarity : 0.003 0.032 3810 Dihedral : 4.034 16.894 2980 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.69 % Allowed : 21.35 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2725 helix: 2.84 (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 ARG 0.001 0.000 ARG B 498 TYR 0.011 0.001 TYR B 441 PHE 0.010 0.001 PHE A 414 TRP 0.008 0.001 TRP D 359 HIS 0.001 0.000 HIS E 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (21660) covalent geometry : angle 0.48972 / 0.25 (29530) SS BOND : bond 0.00314 / 0.21 ( 10) SS BOND : angle 1.16474 / 0.73 ( 20) hydrogen bonds : bond 0.03895 / 2.70 ( 820) hydrogen bonds : angle 4.06042 / 2.78 ( 2280) *********************** 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 242 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 0.828 Fit side-chains REVERT: A 406 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8420 (ptt90) REVERT: A 515 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 391 ASN cc_start: 0.8010 (m-40) cc_final: 0.7730 (t0) REVERT: B 515 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7959 (mp) REVERT: D 272 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7462 (p0) REVERT: D 515 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8078 (mp) REVERT: E 515 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8025 (mp) outliers start: 58 outliers final: 46 residues processed: 221 average time/residue: 0.1488 time to fit residues: 52.2803 Evaluate side-chains 232 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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 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 483 VAL 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 231 THR Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 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 E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 245 optimal weight: 7.9990 chunk 174 optimal weight: 50.0000 chunk 228 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 344 GLN A 560 ASN D 225 ASN D 560 ASN C 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.197134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119938 restraints weight = 22375.791| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.25 r_work: 0.2988 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21670 Z= 0.199 Angle : 0.581 8.763 29550 Z= 0.305 Chirality : 0.045 0.261 3435 Planarity : 0.004 0.038 3810 Dihedral : 4.259 16.950 2980 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.16 % Allowed : 20.65 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2725 helix: 2.52 (0.21), residues: 640 sheet: 0.36 (0.19), residues: 710 loop : -1.47 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 498 TYR 0.015 0.002 TYR A 517 PHE 0.018 0.002 PHE B 414 TRP 0.008 0.001 TRP B 534 HIS 0.002 0.000 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.20 (21660) covalent geometry : angle 0.58041 / 0.30 (29530) SS BOND : bond 0.00592 / 0.40 ( 10) SS BOND : angle 1.26027 / 0.81 ( 20) hydrogen bonds : bond 0.05841 / 3.99 ( 820) hydrogen bonds : angle 4.25079 / 2.91 ( 2280) *********************** 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 247 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 179 time to evaluate : 0.823 Fit side-chains REVERT: A 406 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8434 (ptt90) REVERT: A 498 ARG cc_start: 0.7500 (mpt-90) cc_final: 0.7092 (mtt90) REVERT: B 515 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8083 (mp) REVERT: D 272 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7511 (p0) REVERT: D 515 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8146 (mp) REVERT: E 515 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8142 (mp) REVERT: E 521 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8347 (ttt90) REVERT: E 570 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8199 (mt) outliers start: 68 outliers final: 58 residues processed: 219 average time/residue: 0.1452 time to fit residues: 50.7349 Evaluate side-chains 242 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 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 363 LYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 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 374 THR Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 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 231 THR 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 503 SER Chi-restraints excluded: chain C residue 603 VAL 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 145 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 174 optimal weight: 40.0000 chunk 206 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 238 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 344 GLN A 560 ASN D 225 ASN D 560 ASN D 597 GLN C 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.200360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119517 restraints weight = 22472.940| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.04 r_work: 0.2936 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21670 Z= 0.104 Angle : 0.504 8.399 29550 Z= 0.262 Chirality : 0.042 0.248 3435 Planarity : 0.003 0.033 3810 Dihedral : 4.042 16.878 2980 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.60 % Allowed : 21.58 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2725 helix: 2.81 (0.21), residues: 640 sheet: 0.50 (0.20), residues: 710 loop : -1.41 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 498 TYR 0.011 0.001 TYR A 441 PHE 0.012 0.001 PHE B 414 TRP 0.008 0.001 TRP D 359 HIS 0.001 0.000 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (21660) covalent geometry : angle 0.50341 / 0.26 (29530) SS BOND : bond 0.00381 / 0.26 ( 10) SS BOND : angle 1.18224 / 0.75 ( 20) hydrogen bonds : bond 0.04219 / 2.91 ( 820) hydrogen bonds : angle 4.04244 / 2.76 ( 2280) ********************** 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 237 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 0.815 Fit side-chains REVERT: A 406 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8385 (ptt90) REVERT: A 498 ARG cc_start: 0.7444 (mpt-90) cc_final: 0.7050 (mtt90) REVERT: B 391 ASN cc_start: 0.7994 (m-40) cc_final: 0.7716 (t0) REVERT: B 515 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7937 (mp) REVERT: D 272 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7433 (p0) REVERT: D 515 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8027 (mp) REVERT: E 515 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7992 (mp) REVERT: E 521 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8264 (ttt90) REVERT: C 622 LEU cc_start: 0.8541 (mt) cc_final: 0.8298 (mp) outliers start: 56 outliers final: 47 residues processed: 217 average time/residue: 0.1480 time to fit residues: 50.5428 Evaluate side-chains 231 residues out of total 2445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 SER 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 483 VAL 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 231 THR Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 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 363 LYS Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 521 ARG Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 114 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 265 optimal weight: 0.3980 chunk 128 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 560 ASN D 225 ASN D 560 ASN D 597 GLN C 206 GLN C 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.198359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119190 restraints weight = 22366.619| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.34 r_work: 0.2855 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21670 Z= 0.158 Angle : 0.542 8.555 29550 Z= 0.284 Chirality : 0.044 0.263 3435 Planarity : 0.003 0.035 3810 Dihedral : 4.150 16.864 2980 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.97 % Allowed : 20.93 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2725 helix: 2.64 (0.21), residues: 640 sheet: 0.44 (0.20), residues: 710 loop : -1.43 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.014 0.001 TYR B 441 PHE 0.016 0.001 PHE B 414 TRP 0.008 0.001 TRP C 359 HIS 0.002 0.000 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (21660) covalent geometry : angle 0.54175 / 0.28 (29530) SS BOND : bond 0.00502 / 0.34 ( 10) SS BOND : angle 1.22188 / 0.79 ( 20) hydrogen bonds : bond 0.05169 / 3.55 ( 820) hydrogen bonds : angle 4.13518 / 2.83 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6182.89 seconds wall clock time: 105 minutes 55.39 seconds (6355.39 seconds total)