Starting phenix.real_space_refine on Fri Feb 6 07:31:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxn_47292/02_2026/9dxn_47292.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxn_47292/02_2026/9dxn_47292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dxn_47292/02_2026/9dxn_47292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxn_47292/02_2026/9dxn_47292.map" model { file = "/net/cci-nas-00/data/ceres_data/9dxn_47292/02_2026/9dxn_47292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxn_47292/02_2026/9dxn_47292.cif" } resolution = 3.35 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= -0.001 sd= 0.075 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: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 14913 2.51 5 N 3810 2.21 5 O 4314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23169 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7732 Classifications: {'peptide': 1018} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 972} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 7783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7783 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 979} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 7654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7654 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 972} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 4.32, per 1000 atoms: 0.19 Number of scatterers: 23169 At special positions: 0 Unit cell: (117.72, 120.96, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4314 8.00 N 3810 7.00 C 14913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.97 Conformation dependent library (CDL) restraints added in 902.9 milliseconds 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5614 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 24 sheets defined 58.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 1 through 7 removed outlier: 3.582A pdb=" N PHE B 5 " --> pdb=" O MET B 1 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.830A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.558A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 removed outlier: 3.778A pdb=" N THR B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 366 " --> pdb=" O PHE B 362 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.188A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 438 through 454 removed outlier: 3.679A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.923A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 487 removed outlier: 4.091A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.810A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.672A pdb=" N SER B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 558 removed outlier: 3.535A pdb=" N VAL B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 590 through 601 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 639 through 642 removed outlier: 3.667A pdb=" N ASN B 642 " --> pdb=" O GLY B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 639 through 642' Processing helix chain 'B' and resid 643 through 655 removed outlier: 3.521A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 692 through 707 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 782 through 788 Processing helix chain 'B' and resid 801 through 804 No H-bonds generated for 'chain 'B' and resid 801 through 804' Processing helix chain 'B' and resid 836 through 848 removed outlier: 3.503A pdb=" N GLU B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 851 No H-bonds generated for 'chain 'B' and resid 849 through 851' Processing helix chain 'B' and resid 861 through 870 Processing helix chain 'B' and resid 871 through 892 removed outlier: 4.304A pdb=" N SER B 875 " --> pdb=" O ASN B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.009A pdb=" N SER B 900 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 920 removed outlier: 4.117A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 957 Processing helix chain 'B' and resid 961 through 991 removed outlier: 4.595A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 998 through 1017 removed outlier: 3.922A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B1017 " --> pdb=" O THR B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1020 No H-bonds generated for 'chain 'B' and resid 1018 through 1020' Processing helix chain 'B' and resid 1021 through 1031 Processing helix chain 'C' and resid 2 through 7 removed outlier: 4.263A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 25 removed outlier: 3.602A pdb=" N ILE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.628A pdb=" N LYS C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 removed outlier: 3.603A pdb=" N ASP C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.883A pdb=" N GLN C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 168 removed outlier: 4.441A pdb=" N LYS C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASP C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 359 removed outlier: 3.615A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 366 through 386 removed outlier: 3.785A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.299A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 423 Processing helix chain 'C' and resid 426 through 434 Processing helix chain 'C' and resid 439 through 452 removed outlier: 3.865A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 461 through 487 removed outlier: 3.857A pdb=" N ALA C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.596A pdb=" N ALA C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 537 removed outlier: 3.562A pdb=" N MET C 519 " --> pdb=" O TRP C 515 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 559 removed outlier: 3.622A pdb=" N VAL C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 639 through 642 Processing helix chain 'C' and resid 643 through 656 removed outlier: 3.511A pdb=" N ARG C 650 " --> pdb=" O ALA C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 707 removed outlier: 3.579A pdb=" N GLN C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 754 removed outlier: 4.047A pdb=" N THR C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 782 through 787 removed outlier: 3.755A pdb=" N ILE C 786 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 850 removed outlier: 3.798A pdb=" N GLU C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 893 removed outlier: 3.706A pdb=" N GLN C 865 " --> pdb=" O GLY C 861 " (cutoff:3.500A) Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 896 through 901 removed outlier: 3.539A pdb=" N VAL C 901 " --> pdb=" O ILE C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 917 removed outlier: 3.610A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA C 912 " --> pdb=" O GLY C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 954 removed outlier: 3.839A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 Processing helix chain 'C' and resid 972 through 992 Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 998 through 1017 removed outlier: 3.927A pdb=" N ALA C1002 " --> pdb=" O GLY C 998 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1034 Proline residue: C1023 - end of helix Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.546A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.803A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.671A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.587A pdb=" N LYS A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.868A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 387 Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.553A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 450 removed outlier: 5.314A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.953A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 496 removed outlier: 4.290A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 516 through 536 removed outlier: 3.597A pdb=" N ARG A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 559 removed outlier: 3.570A pdb=" N TYR A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.592A pdb=" N GLU A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 removed outlier: 3.596A pdb=" N VAL A 606 " --> pdb=" O LYS A 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 603 through 606' Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 639 through 642 removed outlier: 3.624A pdb=" N ASN A 642 " --> pdb=" O GLY A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 642' Processing helix chain 'A' and resid 643 through 657 removed outlier: 4.029A pdb=" N ARG A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 708 removed outlier: 4.271A pdb=" N LYS A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 744 through 756 removed outlier: 3.670A pdb=" N TRP A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 782 through 788 removed outlier: 3.717A pdb=" N ILE A 786 " --> pdb=" O PRO A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 860 through 867 removed outlier: 4.107A pdb=" N GLN A 865 " --> pdb=" O GLY A 861 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 867 " --> pdb=" O SER A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 893 Processing helix chain 'A' and resid 896 through 901 Processing helix chain 'A' and resid 904 through 920 removed outlier: 4.160A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 955 removed outlier: 3.839A pdb=" N ILE A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 952 " --> pdb=" O PHE A 948 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 955 " --> pdb=" O ASP A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 971 through 986 removed outlier: 4.435A pdb=" N ILE A 975 " --> pdb=" O ARG A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 Processing helix chain 'A' and resid 996 through 1017 removed outlier: 3.612A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A1013 " --> pdb=" O GLY A1009 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A1016 " --> pdb=" O VAL A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1021 through 1032 removed outlier: 4.671A pdb=" N VAL A1027 " --> pdb=" O PRO A1023 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 132 removed outlier: 3.587A pdb=" N GLU B 130 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.284A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN B 830 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B 715 " --> pdb=" O GLN B 830 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 679 through 680 removed outlier: 3.792A pdb=" N GLY B 829 " --> pdb=" O PHE B 680 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.540A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR B 327 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 141 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR B 325 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 143 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE B 323 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.540A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 284 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 278 " --> pdb=" O ASN B 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.845A pdb=" N TYR B 182 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 770 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 217 through 218 removed outlier: 4.266A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER B 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 729 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE B 235 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 731 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 250 through 252 removed outlier: 7.242A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 805 through 812 removed outlier: 5.242A pdb=" N SER A 233 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLN A 237 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N ILE B 731 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA A 236 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA A 215 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.471A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.159A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 684 " --> pdb=" O MET C 825 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 172 through 174 removed outlier: 3.528A pdb=" N ASP C 174 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 608 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 614 " --> pdb=" O THR C 624 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR C 624 " --> pdb=" O GLY C 614 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 322 through 328 removed outlier: 6.850A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 608 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 614 " --> pdb=" O THR C 624 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR C 624 " --> pdb=" O GLY C 614 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 266 through 272 removed outlier: 3.541A pdb=" N TRP C 187 " --> pdb=" O LYS C 267 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR C 182 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR C 772 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 217 through 219 removed outlier: 4.406A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 232 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER C 233 " --> pdb=" O PHE A 727 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE A 729 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE C 235 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 731 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 250 through 253 removed outlier: 3.736A pdb=" N LYS C 252 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 713 through 714 Processing sheet with id=AB8, first strand: chain 'C' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.754A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.620A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.022A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.048A pdb=" N TYR A 182 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS A 770 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.711A pdb=" N LYS A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 713 through 718 removed outlier: 5.021A pdb=" N SER A 715 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN A 830 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 790 through 792 1423 hydrogen bonds defined for protein. 4104 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: 5.20 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3856 1.30 - 1.43: 5628 1.43 - 1.56: 13859 1.56 - 1.69: 1 1.69 - 1.82: 258 Bond restraints: 23602 Sorted by residual: bond pdb=" C PRO A 31 " pdb=" O PRO A 31 " ideal model delta sigma weight residual 1.233 1.170 0.062 9.60e-03 1.09e+04 4.23e+01 bond pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 1.522 1.568 -0.046 9.40e-03 1.13e+04 2.40e+01 bond pdb=" C PRO A 368 " pdb=" O PRO A 368 " ideal model delta sigma weight residual 1.238 1.180 0.057 1.24e-02 6.50e+03 2.14e+01 bond pdb=" C THR C 93 " pdb=" O THR C 93 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.21e-02 6.83e+03 2.13e+01 bond pdb=" C PRO B 31 " pdb=" O PRO B 31 " ideal model delta sigma weight residual 1.235 1.175 0.060 1.30e-02 5.92e+03 2.10e+01 ... (remaining 23597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 31075 1.76 - 3.51: 756 3.51 - 5.27: 201 5.27 - 7.03: 38 7.03 - 8.78: 5 Bond angle restraints: 32075 Sorted by residual: angle pdb=" CA ALA C 491 " pdb=" C ALA C 491 " pdb=" O ALA C 491 " ideal model delta sigma weight residual 120.70 114.22 6.48 1.03e+00 9.43e-01 3.96e+01 angle pdb=" N THR A 934 " pdb=" CA THR A 934 " pdb=" C THR A 934 " ideal model delta sigma weight residual 112.23 104.75 7.48 1.26e+00 6.30e-01 3.52e+01 angle pdb=" CA MET A 395 " pdb=" C MET A 395 " pdb=" O MET A 395 " ideal model delta sigma weight residual 120.55 114.30 6.25 1.06e+00 8.90e-01 3.48e+01 angle pdb=" CA ILE C 685 " pdb=" C ILE C 685 " pdb=" O ILE C 685 " ideal model delta sigma weight residual 121.72 116.37 5.35 9.60e-01 1.09e+00 3.10e+01 angle pdb=" C ALA C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta sigma weight residual 120.29 127.73 -7.44 1.42e+00 4.96e-01 2.74e+01 ... (remaining 32070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13163 17.95 - 35.90: 804 35.90 - 53.85: 126 53.85 - 71.80: 14 71.80 - 89.75: 10 Dihedral angle restraints: 14117 sinusoidal: 5368 harmonic: 8749 Sorted by residual: dihedral pdb=" C THR B 489 " pdb=" N THR B 489 " pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta harmonic sigma weight residual -122.00 -135.26 13.26 0 2.50e+00 1.60e-01 2.81e+01 dihedral pdb=" CA ILE A 743 " pdb=" C ILE A 743 " pdb=" N ASN A 744 " pdb=" CA ASN A 744 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta harmonic sigma weight residual 123.40 132.94 -9.54 0 2.50e+00 1.60e-01 1.46e+01 ... (remaining 14114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3498 0.082 - 0.164: 295 0.164 - 0.247: 16 0.247 - 0.329: 1 0.329 - 0.411: 1 Chirality restraints: 3811 Sorted by residual: chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE A 743 " pdb=" CA ILE A 743 " pdb=" CG1 ILE A 743 " pdb=" CG2 ILE A 743 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE A 370 " pdb=" N ILE A 370 " pdb=" C ILE A 370 " pdb=" CB ILE A 370 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3808 not shown) Planarity restraints: 4097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 929 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C VAL A 929 " -0.093 2.00e-02 2.50e+03 pdb=" O VAL A 929 " 0.035 2.00e-02 2.50e+03 pdb=" N GLY A 930 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 361 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ASN A 361 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN A 361 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 362 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 184 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C MET B 184 " -0.055 2.00e-02 2.50e+03 pdb=" O MET B 184 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG B 185 " 0.019 2.00e-02 2.50e+03 ... (remaining 4094 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 101 2.56 - 3.14: 18813 3.14 - 3.73: 36363 3.73 - 4.31: 49746 4.31 - 4.90: 85953 Nonbonded interactions: 190976 Sorted by model distance: nonbonded pdb=" N VAL B 225 " pdb=" CE MET C 781 " model vdw 1.973 3.540 nonbonded pdb=" OH TYR C 467 " pdb=" OE1 GLN C 928 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR C 758 " pdb=" OD1 ASP C 761 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP B 408 " pdb=" OG SER B 481 " model vdw 2.235 3.040 nonbonded pdb=" O HIS B 596 " pdb=" OG1 THR B 600 " model vdw 2.241 3.040 ... (remaining 190971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 478 or (resid 479 and (name N or name CA or name C o \ r name CB )) or resid 480 through 500 or resid 516 through 1032)) selection = (chain 'B' and (resid 1 through 421 or (resid 422 through 423 and (name N or nam \ e CA or name C or name O or name CB )) or resid 424 through 449 or (resid 450 an \ d (name N or name CA or name C or name CB or name OG )) or resid 451 through 500 \ or (resid 516 and (name N or name CA or name C or name O or name CB )) or resid \ 517 through 521 or (resid 522 and (name N or name CA or name C or name O or nam \ e CB )) or resid 523 through 526 or (resid 527 and (name N or name CA or name C \ or name O or name CB )) or resid 528 through 539 or (resid 540 and (name N or na \ me CA or name C or name O or name CB )) or resid 541 through 619 or (resid 620 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me NE or name CZ )) or resid 621 through 682 or (resid 683 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1)) or resid 68 \ 4 through 849 or (resid 850 and (name N or name CA or name C or name O or name C \ B )) or resid 851 through 949 or (resid 950 and (name N or name CA or name C or \ name O or name CB )) or resid 951 through 954 or (resid 955 and (name N or name \ CA or name C or name O or name CB )) or resid 956 through 961 or (resid 962 thro \ ugh 963 and (name N or name CA or name C or name O or name CB )) or resid 964 th \ rough 968 or (resid 969 and (name N or name CA or name C or name O or name CB )) \ or resid 970 through 1020 or (resid 1021 and (name N or name CA or name C or na \ me O or name CB )) or resid 1022 through 1028 or (resid 1029 through 1032 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 1 through 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 421 or (resid 422 through 423 and (name N or name CA \ or name C or name O or name CB )) or resid 424 through 449 or (resid 450 and (n \ ame N or name CA or name C or name CB or name OG )) or resid 451 through 478 or \ (resid 479 and (name N or name CA or name C or name CB )) or resid 480 through 5 \ 00 or (resid 516 and (name N or name CA or name C or name O or name CB )) or res \ id 517 through 526 or (resid 527 and (name N or name CA or name C or name O or n \ ame CB )) or resid 528 through 539 or (resid 540 and (name N or name CA or name \ C or name O or name CB )) or resid 541 through 619 or (resid 620 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ )) or resid 621 through 682 or (resid 683 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1)) or resid 684 through 849 \ or (resid 850 and (name N or name CA or name C or name O or name CB )) or resid \ 851 through 949 or (resid 950 and (name N or name CA or name C or name O or name \ CB )) or resid 951 through 954 or (resid 955 and (name N or name CA or name C o \ r name O or name CB )) or resid 956 through 961 or (resid 962 through 963 and (n \ ame N or name CA or name C or name O or name CB )) or resid 964 through 968 or ( \ resid 969 and (name N or name CA or name C or name O or name CB )) or resid 970 \ through 1020 or (resid 1021 and (name N or name CA or name C or name O or name C \ B )) or resid 1022 through 1028 or (resid 1029 through 1032 and (name N or name \ CA or name C or name O or name CB )))) } 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: 2.880 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: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.060 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 : 0.004 0.062 23602 Z= 0.251 Angle : 0.686 8.783 32075 Z= 0.422 Chirality : 0.045 0.411 3811 Planarity : 0.004 0.054 4097 Dihedral : 11.810 89.750 8503 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.28 % Allowed : 0.93 % Favored : 98.79 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.22 % 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: 0.40 (0.16), residues: 3049 helix: 1.11 (0.14), residues: 1588 sheet: -0.85 (0.26), residues: 413 loop : -0.42 (0.21), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 586 TYR 0.020 0.001 TYR A 49 PHE 0.021 0.001 PHE A 362 TRP 0.033 0.002 TRP B 895 HIS 0.005 0.001 HIS C 525 Details of bonding type rmsd covalent geometry : bond 0.00401 (23602) covalent geometry : angle 0.68632 (32075) hydrogen bonds : bond 0.15708 ( 1399) hydrogen bonds : angle 6.92918 ( 4104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 798 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 ILE cc_start: 0.8740 (tp) cc_final: 0.8475 (tp) REVERT: B 415 ASN cc_start: 0.7879 (t0) cc_final: 0.7596 (t0) REVERT: B 417 GLU cc_start: 0.7462 (tp30) cc_final: 0.7260 (tp30) REVERT: B 554 TYR cc_start: 0.7636 (t80) cc_final: 0.7300 (t80) REVERT: B 568 ASP cc_start: 0.7920 (p0) cc_final: 0.7648 (p0) REVERT: B 770 LYS cc_start: 0.7921 (mttt) cc_final: 0.7556 (mttp) REVERT: B 887 CYS cc_start: 0.8721 (m) cc_final: 0.8070 (m) REVERT: B 946 VAL cc_start: 0.7367 (p) cc_final: 0.7135 (t) REVERT: C 87 THR cc_start: 0.8175 (p) cc_final: 0.7899 (t) REVERT: C 678 THR cc_start: 0.8835 (p) cc_final: 0.8605 (t) REVERT: C 1015 THR cc_start: 0.7600 (m) cc_final: 0.7185 (m) REVERT: A 98 THR cc_start: 0.7342 (m) cc_final: 0.6660 (p) REVERT: A 151 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 231 ASN cc_start: 0.7338 (t0) cc_final: 0.7020 (t0) REVERT: A 274 ASN cc_start: 0.7977 (p0) cc_final: 0.7542 (p0) REVERT: A 396 PHE cc_start: 0.7167 (m-10) cc_final: 0.6931 (m-80) REVERT: A 467 TYR cc_start: 0.6922 (m-10) cc_final: 0.6718 (m-10) REVERT: A 471 SER cc_start: 0.7797 (p) cc_final: 0.6841 (p) REVERT: A 519 MET cc_start: 0.5766 (mpp) cc_final: 0.4821 (ttp) REVERT: A 573 MET cc_start: 0.6972 (mtp) cc_final: 0.6771 (mtm) REVERT: A 577 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 879 ILE cc_start: 0.8334 (mm) cc_final: 0.7817 (mp) REVERT: A 887 CYS cc_start: 0.7254 (m) cc_final: 0.6821 (m) REVERT: A 899 PHE cc_start: 0.7017 (m-80) cc_final: 0.6603 (m-80) outliers start: 7 outliers final: 0 residues processed: 800 average time/residue: 0.1422 time to fit residues: 179.7893 Evaluate side-chains 464 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 592 ASN C 58 GLN C 191 ASN C 231 ASN C 415 ASN C 719 ASN C 733 GLN C1000 GLN A 469 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.160455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.137117 restraints weight = 40597.415| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.82 r_work: 0.3807 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23602 Z= 0.137 Angle : 0.614 9.616 32075 Z= 0.311 Chirality : 0.043 0.188 3811 Planarity : 0.004 0.047 4097 Dihedral : 3.899 25.375 3240 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.06 % Allowed : 12.68 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.53 (0.16), residues: 3049 helix: 1.26 (0.13), residues: 1618 sheet: -0.75 (0.25), residues: 435 loop : -0.49 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 239 TYR 0.021 0.002 TYR B 49 PHE 0.021 0.001 PHE B 516 TRP 0.011 0.001 TRP C 515 HIS 0.002 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00303 (23602) covalent geometry : angle 0.61407 (32075) hydrogen bonds : bond 0.04220 ( 1399) hydrogen bonds : angle 4.97741 ( 4104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 498 time to evaluate : 0.862 Fit side-chains TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 1 MET cc_start: 0.7361 (ttp) cc_final: 0.7093 (ttt) REVERT: B 204 ILE cc_start: 0.8287 (mt) cc_final: 0.8085 (mt) REVERT: B 289 LEU cc_start: 0.7673 (tt) cc_final: 0.7292 (tp) REVERT: B 314 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7905 (tp30) REVERT: B 414 GLU cc_start: 0.8084 (tp30) cc_final: 0.7861 (tp30) REVERT: B 415 ASN cc_start: 0.7947 (t0) cc_final: 0.7519 (t0) REVERT: B 519 MET cc_start: 0.7062 (mmt) cc_final: 0.6205 (ttt) REVERT: B 552 MET cc_start: 0.8641 (ptm) cc_final: 0.8334 (ptm) REVERT: B 554 TYR cc_start: 0.7613 (t80) cc_final: 0.7237 (t80) REVERT: B 568 ASP cc_start: 0.8072 (p0) cc_final: 0.7655 (p0) REVERT: B 763 ILE cc_start: 0.5858 (OUTLIER) cc_final: 0.5628 (mt) REVERT: B 887 CYS cc_start: 0.8904 (m) cc_final: 0.8297 (m) REVERT: B 897 ILE cc_start: 0.8605 (mm) cc_final: 0.8385 (mm) REVERT: B 1008 MET cc_start: 0.8004 (ttp) cc_final: 0.7759 (ttp) REVERT: C 184 MET cc_start: 0.8535 (tpt) cc_final: 0.8313 (tpt) REVERT: C 398 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8012 (mtm) REVERT: C 414 GLU cc_start: 0.8054 (tp30) cc_final: 0.7749 (tp30) REVERT: C 481 SER cc_start: 0.8662 (t) cc_final: 0.7818 (p) REVERT: C 662 MET cc_start: 0.7231 (mtm) cc_final: 0.6949 (ttp) REVERT: C 678 THR cc_start: 0.8941 (p) cc_final: 0.8595 (t) REVERT: C 719 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7784 (t0) REVERT: C 728 LYS cc_start: 0.8733 (tptt) cc_final: 0.8509 (tptt) REVERT: C 774 MET cc_start: 0.8065 (tpt) cc_final: 0.7409 (tpt) REVERT: C 798 MET cc_start: 0.6317 (mmm) cc_final: 0.5880 (mtm) REVERT: C 1008 MET cc_start: 0.8225 (tmm) cc_final: 0.8024 (tmm) REVERT: A 151 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7304 (tm-30) REVERT: A 274 ASN cc_start: 0.8408 (p0) cc_final: 0.8086 (p0) REVERT: A 358 PHE cc_start: 0.6343 (OUTLIER) cc_final: 0.5449 (t80) REVERT: A 396 PHE cc_start: 0.6807 (m-10) cc_final: 0.6482 (m-80) REVERT: A 478 MET cc_start: 0.8470 (tmm) cc_final: 0.8184 (tmm) REVERT: A 487 ILE cc_start: 0.8484 (mp) cc_final: 0.8266 (mp) REVERT: A 519 MET cc_start: 0.5313 (mpp) cc_final: 0.4127 (tmm) REVERT: A 552 MET cc_start: 0.7329 (ttt) cc_final: 0.6987 (ttp) REVERT: A 556 PHE cc_start: 0.8479 (t80) cc_final: 0.8098 (m-80) REVERT: A 573 MET cc_start: 0.7633 (mtp) cc_final: 0.7394 (mtm) REVERT: A 659 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7134 (pttt) REVERT: A 879 ILE cc_start: 0.8148 (mm) cc_final: 0.7870 (mp) REVERT: A 887 CYS cc_start: 0.8170 (m) cc_final: 0.7654 (m) REVERT: A 899 PHE cc_start: 0.7415 (m-80) cc_final: 0.7069 (m-80) outliers start: 51 outliers final: 33 residues processed: 532 average time/residue: 0.1243 time to fit residues: 109.9784 Evaluate side-chains 468 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 430 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 525 HIS Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 888 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 137 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 278 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 GLN B 592 ASN C 125 GLN C 191 ASN C 726 GLN A 194 ASN A 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096682 restraints weight = 39090.821| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.47 r_work: 0.3131 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 23602 Z= 0.273 Angle : 0.756 9.607 32075 Z= 0.396 Chirality : 0.049 0.275 3811 Planarity : 0.005 0.054 4097 Dihedral : 4.524 26.605 3240 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.40 % Allowed : 15.02 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.10 (0.15), residues: 3049 helix: 0.99 (0.13), residues: 1585 sheet: -0.64 (0.25), residues: 420 loop : -0.95 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 653 TYR 0.066 0.002 TYR B 541 PHE 0.032 0.002 PHE A 682 TRP 0.014 0.002 TRP C 859 HIS 0.006 0.001 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00635 (23602) covalent geometry : angle 0.75601 (32075) hydrogen bonds : bond 0.06142 ( 1399) hydrogen bonds : angle 4.98402 ( 4104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 466 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 300 LEU cc_start: 0.8891 (mt) cc_final: 0.8599 (mm) REVERT: B 310 LEU cc_start: 0.9046 (mm) cc_final: 0.8699 (mt) REVERT: B 339 GLU cc_start: 0.8193 (tp30) cc_final: 0.7599 (tp30) REVERT: B 342 LYS cc_start: 0.8214 (tptt) cc_final: 0.7891 (tttm) REVERT: B 415 ASN cc_start: 0.9006 (t0) cc_final: 0.8804 (t0) REVERT: B 552 MET cc_start: 0.8767 (ptm) cc_final: 0.8379 (ptm) REVERT: B 554 TYR cc_start: 0.7924 (t80) cc_final: 0.7668 (t80) REVERT: B 568 ASP cc_start: 0.8398 (p0) cc_final: 0.8007 (p0) REVERT: B 719 ASN cc_start: 0.8730 (t0) cc_final: 0.8441 (t0) REVERT: B 887 CYS cc_start: 0.9203 (m) cc_final: 0.8676 (m) REVERT: C 1 MET cc_start: 0.7512 (mtt) cc_final: 0.6514 (ttt) REVERT: C 844 MET cc_start: 0.8620 (mmm) cc_final: 0.8262 (tmm) REVERT: C 947 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8266 (tm-30) REVERT: C 1008 MET cc_start: 0.8408 (tmm) cc_final: 0.8080 (ttm) REVERT: A 30 LEU cc_start: 0.8886 (mt) cc_final: 0.8672 (mt) REVERT: A 151 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 274 ASN cc_start: 0.8984 (p0) cc_final: 0.8679 (p0) REVERT: A 407 ASP cc_start: 0.8665 (t70) cc_final: 0.8291 (t0) REVERT: A 487 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8685 (mp) REVERT: A 496 MET cc_start: 0.8638 (mtm) cc_final: 0.8111 (mtm) REVERT: A 556 PHE cc_start: 0.8610 (t80) cc_final: 0.8118 (m-80) REVERT: A 659 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7592 (pttt) REVERT: A 743 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8948 (mm) REVERT: A 785 ASP cc_start: 0.8557 (m-30) cc_final: 0.8118 (m-30) REVERT: A 844 MET cc_start: 0.8516 (mpp) cc_final: 0.8114 (mpp) REVERT: A 887 CYS cc_start: 0.9190 (m) cc_final: 0.8905 (m) REVERT: A 1008 MET cc_start: 0.7928 (tmm) cc_final: 0.7332 (tmm) outliers start: 109 outliers final: 67 residues processed: 536 average time/residue: 0.1319 time to fit residues: 116.2069 Evaluate side-chains 440 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 370 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 977 MET Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 525 HIS Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 CYS Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 970 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 193 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 297 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.120815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097697 restraints weight = 38321.343| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.47 r_work: 0.3130 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23602 Z= 0.127 Angle : 0.588 10.299 32075 Z= 0.298 Chirality : 0.043 0.253 3811 Planarity : 0.004 0.059 4097 Dihedral : 4.028 25.921 3240 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.27 % Allowed : 19.34 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.55 (0.16), residues: 3049 helix: 1.38 (0.13), residues: 1601 sheet: -0.47 (0.26), residues: 427 loop : -0.82 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 468 TYR 0.024 0.001 TYR C 541 PHE 0.021 0.001 PHE A 362 TRP 0.009 0.001 TRP B 754 HIS 0.002 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00281 (23602) covalent geometry : angle 0.58819 (32075) hydrogen bonds : bond 0.04305 ( 1399) hydrogen bonds : angle 4.54069 ( 4104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 430 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 300 LEU cc_start: 0.8892 (mt) cc_final: 0.8632 (mm) REVERT: B 309 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7788 (mt-10) REVERT: B 310 LEU cc_start: 0.9036 (mm) cc_final: 0.8528 (mt) REVERT: B 313 MET cc_start: 0.7771 (mtm) cc_final: 0.7514 (mtt) REVERT: B 339 GLU cc_start: 0.8073 (tp30) cc_final: 0.7721 (tp30) REVERT: B 342 LYS cc_start: 0.8047 (tptt) cc_final: 0.7823 (tttm) REVERT: B 415 ASN cc_start: 0.8869 (t0) cc_final: 0.8450 (t0) REVERT: B 540 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7183 (mtp85) REVERT: B 552 MET cc_start: 0.8705 (ptm) cc_final: 0.8243 (ptm) REVERT: B 554 TYR cc_start: 0.7937 (t80) cc_final: 0.7649 (t80) REVERT: B 568 ASP cc_start: 0.8409 (p0) cc_final: 0.7946 (p0) REVERT: B 719 ASN cc_start: 0.8650 (t0) cc_final: 0.8277 (t0) REVERT: B 887 CYS cc_start: 0.9105 (m) cc_final: 0.8596 (m) REVERT: B 937 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8409 (tt) REVERT: C 1 MET cc_start: 0.7188 (mtt) cc_final: 0.6323 (ttt) REVERT: C 78 MET cc_start: 0.9084 (ttp) cc_final: 0.8863 (ttp) REVERT: C 237 GLN cc_start: 0.8387 (tt0) cc_final: 0.8150 (tt0) REVERT: C 339 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: C 662 MET cc_start: 0.8496 (mtm) cc_final: 0.8182 (ttp) REVERT: C 678 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8784 (t) REVERT: C 728 LYS cc_start: 0.8696 (tptt) cc_final: 0.8289 (tptt) REVERT: C 744 ASN cc_start: 0.8984 (p0) cc_final: 0.8779 (t0) REVERT: C 844 MET cc_start: 0.8911 (mmm) cc_final: 0.8242 (tmm) REVERT: A 30 LEU cc_start: 0.8852 (mt) cc_final: 0.8603 (mt) REVERT: A 151 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 396 PHE cc_start: 0.8168 (m-80) cc_final: 0.7696 (m-80) REVERT: A 407 ASP cc_start: 0.8683 (t70) cc_final: 0.8287 (t0) REVERT: A 487 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8551 (mp) REVERT: A 659 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7305 (pttt) REVERT: A 662 MET cc_start: 0.7936 (ptm) cc_final: 0.7690 (ppp) REVERT: A 743 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8921 (mm) REVERT: A 785 ASP cc_start: 0.8461 (m-30) cc_final: 0.8012 (m-30) REVERT: A 844 MET cc_start: 0.8551 (mpp) cc_final: 0.8181 (mpp) REVERT: A 887 CYS cc_start: 0.9108 (m) cc_final: 0.8750 (m) outliers start: 81 outliers final: 42 residues processed: 480 average time/residue: 0.1283 time to fit residues: 103.5280 Evaluate side-chains 425 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 376 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 525 HIS Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 929 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 259 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 0.0050 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 251 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN B 872 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.093520 restraints weight = 38555.576| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.46 r_work: 0.3067 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23602 Z= 0.184 Angle : 0.616 9.685 32075 Z= 0.315 Chirality : 0.044 0.162 3811 Planarity : 0.004 0.058 4097 Dihedral : 3.982 25.232 3240 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.75 % Allowed : 19.58 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.53 (0.16), residues: 3049 helix: 1.36 (0.13), residues: 1600 sheet: -0.46 (0.26), residues: 422 loop : -0.80 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 971 TYR 0.025 0.002 TYR B 541 PHE 0.020 0.001 PHE A 682 TRP 0.007 0.001 TRP A 634 HIS 0.004 0.001 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00435 (23602) covalent geometry : angle 0.61588 (32075) hydrogen bonds : bond 0.04642 ( 1399) hydrogen bonds : angle 4.54733 ( 4104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 394 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: B 300 LEU cc_start: 0.8982 (mt) cc_final: 0.8760 (mm) REVERT: B 313 MET cc_start: 0.7994 (mtm) cc_final: 0.7790 (mtt) REVERT: B 339 GLU cc_start: 0.8063 (tp30) cc_final: 0.7716 (tp30) REVERT: B 342 LYS cc_start: 0.8021 (tptt) cc_final: 0.7766 (tttm) REVERT: B 415 ASN cc_start: 0.9137 (t0) cc_final: 0.8704 (t0) REVERT: B 552 MET cc_start: 0.8750 (ptm) cc_final: 0.8492 (ptm) REVERT: B 554 TYR cc_start: 0.8061 (t80) cc_final: 0.7837 (t80) REVERT: B 567 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7756 (mm-30) REVERT: B 568 ASP cc_start: 0.8410 (p0) cc_final: 0.7977 (p0) REVERT: B 719 ASN cc_start: 0.8638 (t0) cc_final: 0.8381 (t0) REVERT: B 858 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: B 887 CYS cc_start: 0.9135 (m) cc_final: 0.8672 (m) REVERT: B 937 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8495 (tt) REVERT: C 1 MET cc_start: 0.7125 (mtt) cc_final: 0.6357 (ttt) REVERT: C 339 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: C 662 MET cc_start: 0.8452 (mtm) cc_final: 0.8111 (ttp) REVERT: C 728 LYS cc_start: 0.8623 (tptt) cc_final: 0.8186 (tptt) REVERT: C 844 MET cc_start: 0.8830 (mmm) cc_final: 0.8505 (mmm) REVERT: A 30 LEU cc_start: 0.8824 (mt) cc_final: 0.8557 (mt) REVERT: A 151 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 358 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.8052 (t80) REVERT: A 396 PHE cc_start: 0.8521 (m-80) cc_final: 0.8181 (m-80) REVERT: A 407 ASP cc_start: 0.8683 (t70) cc_final: 0.8308 (t0) REVERT: A 487 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8522 (mp) REVERT: A 659 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7570 (pttt) REVERT: A 743 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8933 (mm) REVERT: A 785 ASP cc_start: 0.8519 (m-30) cc_final: 0.8057 (m-30) REVERT: A 844 MET cc_start: 0.8612 (mpp) cc_final: 0.8134 (mpp) REVERT: A 887 CYS cc_start: 0.9135 (m) cc_final: 0.8854 (m) REVERT: A 1008 MET cc_start: 0.8203 (tmm) cc_final: 0.7513 (tmm) outliers start: 93 outliers final: 63 residues processed: 456 average time/residue: 0.1219 time to fit residues: 92.9245 Evaluate side-chains 441 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 371 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1007 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 258 optimal weight: 0.4980 chunk 224 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 chunk 188 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 58 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096185 restraints weight = 38398.025| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.47 r_work: 0.3110 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23602 Z= 0.117 Angle : 0.557 10.767 32075 Z= 0.282 Chirality : 0.042 0.298 3811 Planarity : 0.004 0.055 4097 Dihedral : 3.832 25.674 3240 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.91 % Allowed : 21.32 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.74 (0.16), residues: 3049 helix: 1.50 (0.13), residues: 1604 sheet: -0.31 (0.26), residues: 421 loop : -0.71 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 971 TYR 0.021 0.001 TYR B 541 PHE 0.016 0.001 PHE C 948 TRP 0.009 0.001 TRP B 754 HIS 0.002 0.000 HIS C 596 Details of bonding type rmsd covalent geometry : bond 0.00260 (23602) covalent geometry : angle 0.55747 (32075) hydrogen bonds : bond 0.03890 ( 1399) hydrogen bonds : angle 4.40366 ( 4104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 408 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: B 300 LEU cc_start: 0.8946 (mt) cc_final: 0.8734 (mm) REVERT: B 342 LYS cc_start: 0.7971 (tptt) cc_final: 0.7437 (tppt) REVERT: B 415 ASN cc_start: 0.9049 (t0) cc_final: 0.8640 (t0) REVERT: B 525 HIS cc_start: 0.8668 (t-90) cc_final: 0.8429 (m170) REVERT: B 526 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7755 (t-90) REVERT: B 540 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7219 (mtp85) REVERT: B 554 TYR cc_start: 0.8054 (t80) cc_final: 0.7784 (t80) REVERT: B 567 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7777 (mm-30) REVERT: B 568 ASP cc_start: 0.8454 (p0) cc_final: 0.7943 (p0) REVERT: B 719 ASN cc_start: 0.8575 (t0) cc_final: 0.8313 (t0) REVERT: B 858 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: B 887 CYS cc_start: 0.9187 (m) cc_final: 0.8718 (m) REVERT: C 1 MET cc_start: 0.7154 (mtt) cc_final: 0.6399 (ttt) REVERT: C 339 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: C 662 MET cc_start: 0.8513 (mtm) cc_final: 0.8170 (ttp) REVERT: C 678 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8793 (t) REVERT: C 728 LYS cc_start: 0.8685 (tptt) cc_final: 0.8232 (tptt) REVERT: A 151 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 280 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8291 (mt-10) REVERT: A 355 MET cc_start: 0.8436 (tpp) cc_final: 0.8145 (tpt) REVERT: A 396 PHE cc_start: 0.8546 (m-80) cc_final: 0.8207 (m-80) REVERT: A 407 ASP cc_start: 0.8649 (t70) cc_final: 0.8373 (t0) REVERT: A 467 TYR cc_start: 0.7841 (m-10) cc_final: 0.7639 (m-10) REVERT: A 487 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8503 (mp) REVERT: A 659 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7446 (pttt) REVERT: A 743 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8905 (mm) REVERT: A 785 ASP cc_start: 0.8497 (m-30) cc_final: 0.8027 (m-30) REVERT: A 844 MET cc_start: 0.8556 (mpp) cc_final: 0.8104 (mpp) REVERT: A 887 CYS cc_start: 0.9082 (m) cc_final: 0.8796 (m) REVERT: A 1008 MET cc_start: 0.8069 (tmm) cc_final: 0.7840 (tmm) outliers start: 72 outliers final: 44 residues processed: 456 average time/residue: 0.1253 time to fit residues: 95.2009 Evaluate side-chains 427 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 375 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 743 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 260 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 242 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 67 optimal weight: 0.0070 chunk 283 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096460 restraints weight = 38327.168| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.47 r_work: 0.3113 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23602 Z= 0.116 Angle : 0.568 11.325 32075 Z= 0.285 Chirality : 0.042 0.270 3811 Planarity : 0.004 0.054 4097 Dihedral : 3.770 25.454 3240 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.70 % Allowed : 22.12 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.80 (0.16), residues: 3049 helix: 1.53 (0.13), residues: 1606 sheet: -0.26 (0.26), residues: 416 loop : -0.67 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 971 TYR 0.021 0.001 TYR B 541 PHE 0.014 0.001 PHE A 358 TRP 0.007 0.001 TRP B 754 HIS 0.001 0.000 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00256 (23602) covalent geometry : angle 0.56753 (32075) hydrogen bonds : bond 0.03759 ( 1399) hydrogen bonds : angle 4.34857 ( 4104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 402 time to evaluate : 0.808 Fit side-chains REVERT: B 300 LEU cc_start: 0.8942 (mt) cc_final: 0.8742 (mm) REVERT: B 342 LYS cc_start: 0.8029 (tptt) cc_final: 0.7502 (tppt) REVERT: B 415 ASN cc_start: 0.9042 (t0) cc_final: 0.8608 (t0) REVERT: B 525 HIS cc_start: 0.8682 (t-90) cc_final: 0.8478 (m170) REVERT: B 540 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7286 (mtp85) REVERT: B 554 TYR cc_start: 0.8047 (t80) cc_final: 0.7828 (t80) REVERT: B 567 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7782 (mm-30) REVERT: B 568 ASP cc_start: 0.8418 (p0) cc_final: 0.7910 (p0) REVERT: B 628 PHE cc_start: 0.8446 (m-80) cc_final: 0.8117 (m-80) REVERT: B 719 ASN cc_start: 0.8556 (t0) cc_final: 0.8267 (t0) REVERT: B 839 GLU cc_start: 0.7785 (tt0) cc_final: 0.7520 (pt0) REVERT: B 858 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: B 887 CYS cc_start: 0.9194 (m) cc_final: 0.8745 (m) REVERT: C 1 MET cc_start: 0.6926 (mtt) cc_final: 0.6361 (ttt) REVERT: C 339 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: C 662 MET cc_start: 0.8496 (mtm) cc_final: 0.8156 (ttp) REVERT: C 678 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8809 (t) REVERT: C 728 LYS cc_start: 0.8675 (tptt) cc_final: 0.8193 (tptt) REVERT: C 798 MET cc_start: 0.7466 (mmm) cc_final: 0.7249 (mmm) REVERT: C 844 MET cc_start: 0.8785 (mmm) cc_final: 0.8084 (tmm) REVERT: C 1008 MET cc_start: 0.8545 (ttp) cc_final: 0.8103 (ttt) REVERT: A 151 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 280 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 363 ARG cc_start: 0.6479 (mmt90) cc_final: 0.6265 (mmt90) REVERT: A 396 PHE cc_start: 0.8566 (m-80) cc_final: 0.8229 (m-80) REVERT: A 407 ASP cc_start: 0.8709 (t70) cc_final: 0.8470 (t0) REVERT: A 417 GLU cc_start: 0.8059 (tp30) cc_final: 0.7787 (tp30) REVERT: A 487 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 659 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7422 (pttt) REVERT: A 743 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8890 (mm) REVERT: A 785 ASP cc_start: 0.8489 (m-30) cc_final: 0.8082 (m-30) REVERT: A 844 MET cc_start: 0.8531 (mpp) cc_final: 0.8111 (mpp) REVERT: A 887 CYS cc_start: 0.9103 (m) cc_final: 0.8825 (m) REVERT: A 1008 MET cc_start: 0.8096 (tmm) cc_final: 0.7882 (tmm) outliers start: 67 outliers final: 49 residues processed: 442 average time/residue: 0.1324 time to fit residues: 97.8089 Evaluate side-chains 433 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 377 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 971 ARG Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 135 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 267 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN A 213 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096493 restraints weight = 38042.907| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.44 r_work: 0.3118 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23602 Z= 0.120 Angle : 0.576 12.285 32075 Z= 0.288 Chirality : 0.042 0.266 3811 Planarity : 0.004 0.052 4097 Dihedral : 3.741 25.106 3240 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.03 % Allowed : 22.04 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.82 (0.16), residues: 3049 helix: 1.54 (0.13), residues: 1606 sheet: -0.25 (0.26), residues: 416 loop : -0.63 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 971 TYR 0.020 0.001 TYR B 541 PHE 0.016 0.001 PHE C 556 TRP 0.008 0.001 TRP C 515 HIS 0.002 0.000 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00272 (23602) covalent geometry : angle 0.57574 (32075) hydrogen bonds : bond 0.03729 ( 1399) hydrogen bonds : angle 4.31850 ( 4104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 387 time to evaluate : 0.815 Fit side-chains REVERT: B 300 LEU cc_start: 0.8940 (mt) cc_final: 0.8738 (mm) REVERT: B 342 LYS cc_start: 0.8004 (tptt) cc_final: 0.7451 (tppt) REVERT: B 415 ASN cc_start: 0.9056 (t0) cc_final: 0.8594 (t0) REVERT: B 525 HIS cc_start: 0.8735 (t-90) cc_final: 0.8521 (m170) REVERT: B 526 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7782 (t-90) REVERT: B 540 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7347 (mtp85) REVERT: B 554 TYR cc_start: 0.8069 (t80) cc_final: 0.7852 (t80) REVERT: B 567 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7792 (mm-30) REVERT: B 568 ASP cc_start: 0.8423 (p0) cc_final: 0.7906 (p0) REVERT: B 573 MET cc_start: 0.8196 (mmt) cc_final: 0.7980 (mmp) REVERT: B 575 MET cc_start: 0.7940 (tpp) cc_final: 0.7605 (tpp) REVERT: B 719 ASN cc_start: 0.8589 (t0) cc_final: 0.8281 (t0) REVERT: B 839 GLU cc_start: 0.7836 (tt0) cc_final: 0.7510 (pt0) REVERT: B 858 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: B 887 CYS cc_start: 0.9224 (m) cc_final: 0.8736 (m) REVERT: C 1 MET cc_start: 0.6907 (mtt) cc_final: 0.6263 (ttt) REVERT: C 339 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: C 498 LYS cc_start: 0.8846 (tppt) cc_final: 0.8502 (ptmm) REVERT: C 662 MET cc_start: 0.8462 (mtm) cc_final: 0.8127 (ttp) REVERT: C 678 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8815 (t) REVERT: C 728 LYS cc_start: 0.8688 (tptt) cc_final: 0.8198 (tptt) REVERT: C 798 MET cc_start: 0.7440 (mmm) cc_final: 0.7200 (mmm) REVERT: C 844 MET cc_start: 0.8794 (mmm) cc_final: 0.8115 (tmm) REVERT: C 1008 MET cc_start: 0.8611 (ttp) cc_final: 0.8147 (ttt) REVERT: A 151 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 280 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8207 (mt-10) REVERT: A 363 ARG cc_start: 0.6641 (mmt90) cc_final: 0.6435 (mmt90) REVERT: A 396 PHE cc_start: 0.8604 (m-80) cc_final: 0.8291 (m-80) REVERT: A 407 ASP cc_start: 0.8772 (t70) cc_final: 0.8431 (t0) REVERT: A 487 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 659 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7461 (pttt) REVERT: A 785 ASP cc_start: 0.8503 (m-30) cc_final: 0.8102 (m-30) REVERT: A 844 MET cc_start: 0.8502 (mpp) cc_final: 0.8107 (mpp) REVERT: A 887 CYS cc_start: 0.9118 (m) cc_final: 0.8824 (m) REVERT: A 1008 MET cc_start: 0.8077 (tmm) cc_final: 0.7867 (tmm) outliers start: 75 outliers final: 55 residues processed: 437 average time/residue: 0.1302 time to fit residues: 94.4376 Evaluate side-chains 430 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 368 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 971 ARG Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 982 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 115 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 286 optimal weight: 0.6980 chunk 178 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 chunk 280 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 415 ASN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097162 restraints weight = 38419.889| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.47 r_work: 0.3126 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23602 Z= 0.115 Angle : 0.588 12.744 32075 Z= 0.292 Chirality : 0.042 0.234 3811 Planarity : 0.004 0.054 4097 Dihedral : 3.709 26.004 3240 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.46 % Allowed : 22.89 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.86 (0.16), residues: 3049 helix: 1.57 (0.13), residues: 1612 sheet: -0.15 (0.26), residues: 420 loop : -0.65 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 971 TYR 0.019 0.001 TYR B 541 PHE 0.013 0.001 PHE B 666 TRP 0.008 0.001 TRP C 515 HIS 0.002 0.000 HIS C 692 Details of bonding type rmsd covalent geometry : bond 0.00259 (23602) covalent geometry : angle 0.58811 (32075) hydrogen bonds : bond 0.03615 ( 1399) hydrogen bonds : angle 4.29541 ( 4104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 386 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 342 LYS cc_start: 0.7972 (tptt) cc_final: 0.7421 (tppt) REVERT: B 415 ASN cc_start: 0.9054 (t0) cc_final: 0.8592 (t0) REVERT: B 519 MET cc_start: 0.7935 (mmt) cc_final: 0.7573 (tmm) REVERT: B 525 HIS cc_start: 0.8744 (t-90) cc_final: 0.8522 (m170) REVERT: B 526 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7796 (t-90) REVERT: B 554 TYR cc_start: 0.8071 (t80) cc_final: 0.7854 (t80) REVERT: B 567 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7828 (mm-30) REVERT: B 568 ASP cc_start: 0.8352 (p0) cc_final: 0.7849 (p0) REVERT: B 719 ASN cc_start: 0.8581 (t0) cc_final: 0.8262 (t0) REVERT: B 858 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: B 887 CYS cc_start: 0.9232 (m) cc_final: 0.8773 (m) REVERT: C 1 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6225 (ttt) REVERT: C 339 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: C 662 MET cc_start: 0.8456 (mtm) cc_final: 0.8117 (ttp) REVERT: C 678 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8804 (t) REVERT: C 728 LYS cc_start: 0.8691 (tptt) cc_final: 0.8186 (tptt) REVERT: C 798 MET cc_start: 0.7611 (mmm) cc_final: 0.7364 (mmm) REVERT: C 844 MET cc_start: 0.8816 (mmm) cc_final: 0.8112 (tmm) REVERT: C 1008 MET cc_start: 0.8577 (ttp) cc_final: 0.8072 (ttt) REVERT: A 151 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 280 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8177 (mt-10) REVERT: A 363 ARG cc_start: 0.6713 (mmt90) cc_final: 0.6489 (mmt90) REVERT: A 396 PHE cc_start: 0.8623 (m-80) cc_final: 0.8304 (m-80) REVERT: A 407 ASP cc_start: 0.8785 (t70) cc_final: 0.8518 (t0) REVERT: A 659 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7481 (pttt) REVERT: A 785 ASP cc_start: 0.8514 (m-30) cc_final: 0.8104 (m-30) REVERT: A 844 MET cc_start: 0.8477 (mpp) cc_final: 0.8090 (mpp) REVERT: A 887 CYS cc_start: 0.9140 (m) cc_final: 0.8852 (m) outliers start: 61 outliers final: 51 residues processed: 428 average time/residue: 0.1254 time to fit residues: 89.6166 Evaluate side-chains 431 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 374 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 37 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 298 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 697 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096061 restraints weight = 38298.194| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.45 r_work: 0.3113 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.7334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23602 Z= 0.126 Angle : 0.594 11.966 32075 Z= 0.296 Chirality : 0.042 0.199 3811 Planarity : 0.004 0.054 4097 Dihedral : 3.707 26.429 3240 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.58 % Allowed : 22.89 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.91 (0.16), residues: 3049 helix: 1.59 (0.13), residues: 1606 sheet: -0.10 (0.26), residues: 422 loop : -0.62 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 971 TYR 0.020 0.001 TYR B 541 PHE 0.016 0.001 PHE C 556 TRP 0.008 0.001 TRP C 515 HIS 0.002 0.000 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00290 (23602) covalent geometry : angle 0.59449 (32075) hydrogen bonds : bond 0.03752 ( 1399) hydrogen bonds : angle 4.30135 ( 4104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 380 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 342 LYS cc_start: 0.7985 (tptt) cc_final: 0.7424 (tppt) REVERT: B 415 ASN cc_start: 0.9090 (t0) cc_final: 0.8656 (t0) REVERT: B 519 MET cc_start: 0.7918 (mmt) cc_final: 0.7574 (tmm) REVERT: B 525 HIS cc_start: 0.8714 (t-90) cc_final: 0.8503 (m170) REVERT: B 554 TYR cc_start: 0.8112 (t80) cc_final: 0.7895 (t80) REVERT: B 567 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7842 (mm-30) REVERT: B 568 ASP cc_start: 0.8373 (p0) cc_final: 0.7876 (p0) REVERT: B 719 ASN cc_start: 0.8600 (t0) cc_final: 0.8283 (t0) REVERT: B 858 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: B 887 CYS cc_start: 0.9261 (m) cc_final: 0.8788 (m) REVERT: C 1 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6281 (ttt) REVERT: C 339 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: C 662 MET cc_start: 0.8481 (mtm) cc_final: 0.8135 (ttp) REVERT: C 678 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8787 (t) REVERT: C 697 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: C 798 MET cc_start: 0.7597 (mmm) cc_final: 0.7305 (mmm) REVERT: C 844 MET cc_start: 0.8816 (mmm) cc_final: 0.8145 (tmm) REVERT: C 1008 MET cc_start: 0.8619 (ttp) cc_final: 0.8105 (ttt) REVERT: A 151 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 280 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8188 (mt-10) REVERT: A 363 ARG cc_start: 0.6947 (mmt90) cc_final: 0.6694 (mmt90) REVERT: A 396 PHE cc_start: 0.8686 (m-80) cc_final: 0.8381 (m-80) REVERT: A 407 ASP cc_start: 0.8816 (t70) cc_final: 0.7584 (t0) REVERT: A 785 ASP cc_start: 0.8493 (m-30) cc_final: 0.8105 (m-30) REVERT: A 844 MET cc_start: 0.8481 (mpp) cc_final: 0.8096 (mpp) REVERT: A 887 CYS cc_start: 0.9122 (m) cc_final: 0.8828 (m) REVERT: A 940 LYS cc_start: 0.8911 (tmtt) cc_final: 0.8696 (tmtt) REVERT: A 1008 MET cc_start: 0.7911 (tmm) cc_final: 0.7609 (tmm) outliers start: 64 outliers final: 52 residues processed: 423 average time/residue: 0.1239 time to fit residues: 88.3003 Evaluate side-chains 427 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 370 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 697 GLN Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 971 ARG Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 151 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 226 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 697 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095171 restraints weight = 38423.087| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.46 r_work: 0.3099 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.7447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23602 Z= 0.136 Angle : 0.606 12.343 32075 Z= 0.301 Chirality : 0.043 0.196 3811 Planarity : 0.004 0.055 4097 Dihedral : 3.735 25.858 3240 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.83 % Allowed : 22.53 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.92 (0.16), residues: 3049 helix: 1.61 (0.13), residues: 1604 sheet: -0.07 (0.26), residues: 421 loop : -0.63 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 971 TYR 0.020 0.001 TYR B 541 PHE 0.014 0.001 PHE A 682 TRP 0.009 0.001 TRP C 515 HIS 0.002 0.000 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00318 (23602) covalent geometry : angle 0.60593 (32075) hydrogen bonds : bond 0.03889 ( 1399) hydrogen bonds : angle 4.31797 ( 4104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5779.70 seconds wall clock time: 99 minutes 28.30 seconds (5968.30 seconds total)