Starting phenix.real_space_refine on Sat Jul 4 22:00:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kgi_22871/07_2026/7kgi_22871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kgi_22871/07_2026/7kgi_22871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kgi_22871/07_2026/7kgi_22871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kgi_22871/07_2026/7kgi_22871.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kgi_22871/07_2026/7kgi_22871.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kgi_22871/07_2026/7kgi_22871.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kgi_22871/07_2026/7kgi_22871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kgi_22871/07_2026/7kgi_22871.cif" } resolution = 3.34 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.189 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 135 5.16 5 C 15259 2.51 5 N 3804 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23533 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "B" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "C" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {' ET': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {' ET': 2, 'PTY': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Time building chain proxies: 4.53, per 1000 atoms: 0.19 Number of scatterers: 23533 At special positions: 0 Unit cell: (118.8, 114.48, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 3 15.00 O 4332 8.00 N 3804 7.00 C 15259 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: 2.17 Conformation dependent library (CDL) restraints added in 826.9 milliseconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 24 sheets defined 61.0% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.430A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.585A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.783A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 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 Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.712A pdb=" N VAL A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 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 315 removed outlier: 3.910A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.989A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 387 removed outlier: 3.942A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix removed outlier: 3.618A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 423 removed outlier: 4.515A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 Processing helix chain 'A' and resid 438 through 454 removed outlier: 3.843A pdb=" N ILE A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 460 through 496 removed outlier: 3.571A pdb=" N GLY A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.127A 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 509 through 534 removed outlier: 3.746A pdb=" N HIS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 556 removed outlier: 3.501A pdb=" N TRP A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 597 removed outlier: 3.990A pdb=" N ASP A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 648 removed outlier: 3.690A pdb=" N ALA A 648 " --> pdb=" O ASN A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 701 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 745 Processing helix chain 'A' and resid 768 through 772 removed outlier: 3.714A pdb=" N MET A 772 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 778 removed outlier: 3.534A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 795 removed outlier: 4.054A pdb=" N VAL A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 791 through 795' Processing helix chain 'A' and resid 827 through 841 Processing helix chain 'A' and resid 852 through 859 removed outlier: 4.353A pdb=" N GLN A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.968A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 removed outlier: 3.888A pdb=" N SER A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 892 " --> pdb=" O ILE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 911 removed outlier: 4.211A pdb=" N GLY A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.594A pdb=" N ALA A 930 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 976 removed outlier: 4.818A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.905A pdb=" N VAL A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1027 removed outlier: 3.825A pdb=" N GLN A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.574A pdb=" N ARG B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.576A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 71 removed outlier: 3.680A pdb=" N GLY B 71 " --> pdb=" O GLU B 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 71' Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.705A pdb=" N LYS B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.803A pdb=" N GLN B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.744A pdb=" N VAL B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 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 298 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 360 removed outlier: 4.229A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.859A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.774A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 406 through 423 Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 438 through 454 removed outlier: 3.555A pdb=" N ILE B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.642A pdb=" N ALA B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 486 removed outlier: 3.664A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 4.140A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 534 removed outlier: 3.940A pdb=" N LYS B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 removed outlier: 3.800A pdb=" N MET B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.541A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 650 removed outlier: 3.760A pdb=" N ASN B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.754A pdb=" N LYS B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 730 Processing helix chain 'B' and resid 733 through 746 removed outlier: 3.644A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 772 removed outlier: 3.565A pdb=" N ARG B 771 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET B 772 " --> pdb=" O LYS B 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 768 through 772' Processing helix chain 'B' and resid 773 through 779 removed outlier: 3.711A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 795 removed outlier: 3.994A pdb=" N VAL B 795 " --> pdb=" O SER B 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 791 through 795' Processing helix chain 'B' and resid 827 through 841 removed outlier: 3.712A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 863 Processing helix chain 'B' and resid 863 through 884 removed outlier: 3.704A pdb=" N MET B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 893 Processing helix chain 'B' and resid 895 through 911 removed outlier: 4.493A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 903 " --> pdb=" O GLY B 899 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 946 removed outlier: 3.709A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 961 Processing helix chain 'B' and resid 961 through 976 Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 986 through 1027 removed outlier: 3.654A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) Proline residue: B1013 - end of helix Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 8 through 27 removed outlier: 3.858A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.594A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 167 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 removed outlier: 3.506A pdb=" N PHE C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 316 removed outlier: 3.935A pdb=" N LEU C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 359 removed outlier: 3.725A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 4.174A pdb=" N THR C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.498A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 453 removed outlier: 5.531A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.658A pdb=" N PHE C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.733A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 removed outlier: 4.089A pdb=" N ALA C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 497 " --> pdb=" O CYS C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 534 removed outlier: 3.840A pdb=" N LYS C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 580 through 598 removed outlier: 3.634A pdb=" N THR C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 597 " --> pdb=" O ASN C 593 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN C 598 " --> pdb=" O ASN C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 647 Processing helix chain 'C' and resid 683 through 700 removed outlier: 3.862A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 730 Processing helix chain 'C' and resid 733 through 746 Processing helix chain 'C' and resid 768 through 771 Processing helix chain 'C' and resid 773 through 779 removed outlier: 3.735A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 795 No H-bonds generated for 'chain 'C' and resid 793 through 795' Processing helix chain 'C' and resid 827 through 841 removed outlier: 3.577A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 860 Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 894 removed outlier: 4.077A pdb=" N SER C 891 " --> pdb=" O ALA C 887 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL C 892 " --> pdb=" O ILE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 911 removed outlier: 3.682A pdb=" N GLY C 899 " --> pdb=" O VAL C 895 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 900 " --> pdb=" O VAL C 896 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 903 " --> pdb=" O GLY C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 946 Processing helix chain 'C' and resid 949 through 976 removed outlier: 4.599A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 986 through 1027 removed outlier: 3.623A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE C1009 " --> pdb=" O THR C1005 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 7.866A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 820 " --> pdb=" O PHE A 672 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 672 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131 removed outlier: 7.866A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER A 817 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 819 " --> pdb=" O TRP A 708 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 708 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.865A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.892A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 603 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 570 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.729A pdb=" N LYS A 182 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE A 763 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N MET A 184 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN A 765 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE A 186 " --> pdb=" O GLN A 765 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA8, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA9, first strand: chain 'A' and resid 796 through 803 removed outlier: 3.737A pdb=" N SER B 235 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.164A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP B 83 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 11.838A pdb=" N GLN B 806 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N SER B 817 " --> pdb=" O GLN B 806 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER B 817 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN B 709 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 819 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 707 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 821 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.164A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP B 83 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 11.838A pdb=" N GLN B 806 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N SER B 817 " --> pdb=" O GLN B 806 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER B 673 " --> pdb=" O THR B 851 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 7.178A pdb=" N LEU B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.171A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 603 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL B 619 " --> pdb=" O GLY B 609 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.373A pdb=" N LYS B 182 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN B 761 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 252 removed outlier: 3.581A pdb=" N LEU B 251 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 797 Processing sheet with id=AB8, first strand: chain 'B' and resid 796 through 797 removed outlier: 7.577A pdb=" N ASP B 716 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N SER C 235 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 718 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.720A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 12.070A pdb=" N GLN C 806 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N SER C 817 " --> pdb=" O GLN C 806 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 817 " --> pdb=" O GLU C 710 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.720A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 12.070A pdb=" N GLN C 806 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N SER C 817 " --> pdb=" O GLN C 806 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 5.717A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN C 292 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR C 327 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY C 141 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE C 325 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN C 143 " --> pdb=" O PHE C 323 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N PHE C 323 " --> pdb=" O ASN C 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 5.717A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN C 292 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL C 619 " --> pdb=" O GLY C 609 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.079A pdb=" N LYS C 182 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN C 761 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 782 1567 hydrogen bonds defined for protein. 4581 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: 4.70 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3842 1.26 - 1.40: 5228 1.40 - 1.54: 13984 1.54 - 1.68: 647 1.68 - 1.81: 264 Bond restraints: 23965 Sorted by residual: bond pdb=" C SER A 969 " pdb=" O SER A 969 " ideal model delta sigma weight residual 1.236 1.116 0.120 1.15e-02 7.56e+03 1.09e+02 bond pdb=" C GLN B 691 " pdb=" O GLN B 691 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.19e-02 7.06e+03 7.06e+01 bond pdb=" C ASP C 407 " pdb=" O ASP C 407 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.25e-02 6.40e+03 4.56e+01 bond pdb=" C PHE C 939 " pdb=" O PHE C 939 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.26e-02 6.30e+03 4.18e+01 bond pdb=" C GLN B 863 " pdb=" O GLN B 863 " ideal model delta sigma weight residual 1.235 1.150 0.085 1.33e-02 5.65e+03 4.11e+01 ... (remaining 23960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 32192 3.58 - 7.15: 272 7.15 - 10.73: 17 10.73 - 14.31: 0 14.31 - 17.88: 4 Bond angle restraints: 32485 Sorted by residual: angle pdb=" CA PHE A 11 " pdb=" C PHE A 11 " pdb=" O PHE A 11 " ideal model delta sigma weight residual 120.55 110.34 10.21 1.06e+00 8.90e-01 9.27e+01 angle pdb=" CA PHE B 824 " pdb=" C PHE B 824 " pdb=" O PHE B 824 " ideal model delta sigma weight residual 121.19 111.76 9.43 1.10e+00 8.26e-01 7.36e+01 angle pdb=" CA SER A 969 " pdb=" C SER A 969 " pdb=" O SER A 969 " ideal model delta sigma weight residual 121.00 112.00 9.00 1.05e+00 9.07e-01 7.35e+01 angle pdb=" CA PHE C 11 " pdb=" C PHE C 11 " pdb=" O PHE C 11 " ideal model delta sigma weight residual 119.97 111.11 8.86 1.15e+00 7.56e-01 5.93e+01 angle pdb=" CA PHE C 939 " pdb=" C PHE C 939 " pdb=" O PHE C 939 " ideal model delta sigma weight residual 119.97 111.75 8.22 1.15e+00 7.56e-01 5.11e+01 ... (remaining 32480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.60: 13991 29.60 - 59.19: 451 59.19 - 88.79: 45 88.79 - 118.39: 3 118.39 - 147.99: 1 Dihedral angle restraints: 14491 sinusoidal: 5674 harmonic: 8817 Sorted by residual: dihedral pdb=" C ASP B 106 " pdb=" N ASP B 106 " pdb=" CA ASP B 106 " pdb=" CB ASP B 106 " ideal model delta harmonic sigma weight residual -122.60 -136.40 13.80 0 2.50e+00 1.60e-01 3.05e+01 dihedral pdb=" C GLU C 592 " pdb=" N GLU C 592 " pdb=" CA GLU C 592 " pdb=" CB GLU C 592 " ideal model delta harmonic sigma weight residual -122.60 -111.12 -11.48 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" C3 PTY C1102 " pdb=" O11 PTY C1102 " pdb=" P1 PTY C1102 " pdb=" O12 PTY C1102 " ideal model delta sinusoidal sigma weight residual -59.77 88.22 -147.99 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 14488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3613 0.083 - 0.167: 230 0.167 - 0.250: 25 0.250 - 0.333: 2 0.333 - 0.417: 3 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CA GLU C 592 " pdb=" N GLU C 592 " pdb=" C GLU C 592 " pdb=" CB GLU C 592 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ASP B 106 " pdb=" N ASP B 106 " pdb=" C ASP B 106 " pdb=" CB ASP B 106 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA ILE C 186 " pdb=" N ILE C 186 " pdb=" C ILE C 186 " pdb=" CB ILE C 186 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 3870 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 174 " -0.025 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C LYS A 174 " 0.090 2.00e-02 2.50e+03 pdb=" O LYS A 174 " -0.033 2.00e-02 2.50e+03 pdb=" N VAL A 175 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 573 " 0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C PHE C 573 " -0.081 2.00e-02 2.50e+03 pdb=" O PHE C 573 " 0.029 2.00e-02 2.50e+03 pdb=" N GLN C 574 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 969 " -0.022 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C SER A 969 " 0.079 2.00e-02 2.50e+03 pdb=" O SER A 969 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU A 970 " -0.028 2.00e-02 2.50e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 174 2.60 - 3.17: 20879 3.17 - 3.75: 36246 3.75 - 4.32: 50366 4.32 - 4.90: 84871 Nonbonded interactions: 192536 Sorted by model distance: nonbonded pdb=" O MET B 647 " pdb=" OG1 THR B 651 " model vdw 2.021 3.040 nonbonded pdb=" OE2 GLU C 281 " pdb=" OG1 THR C 605 " model vdw 2.121 3.040 nonbonded pdb=" O MET A 435 " pdb=" OG1 THR A 439 " model vdw 2.127 3.040 nonbonded pdb=" OD1 ASP A 739 " pdb=" N ILE A 740 " model vdw 2.149 3.120 nonbonded pdb=" NH2 ARG A 363 " pdb=" O ILE A 496 " model vdw 2.157 3.120 ... (remaining 192531 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 1027) selection = (chain 'B' and resid 1 through 1027) selection = (chain 'C' and resid 1 through 1027) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.570 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 0.120 23965 Z= 0.299 Angle : 0.792 17.882 32485 Z= 0.499 Chirality : 0.045 0.417 3873 Planarity : 0.005 0.088 4068 Dihedral : 14.358 147.987 8785 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.82 % Allowed : 1.17 % Favored : 98.01 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.16), residues: 3048 helix: 1.86 (0.13), residues: 1670 sheet: -0.11 (0.24), residues: 453 loop : -0.24 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.015 0.001 TYR B 77 PHE 0.032 0.001 PHE A 972 TRP 0.004 0.001 TRP C 512 HIS 0.002 0.000 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.30 (23965) covalent geometry : angle 0.79181 / 0.50 (32485) hydrogen bonds : bond 0.14542 / 9.59 ( 1490) hydrogen bonds : angle 6.26214 / 4.56 ( 4581) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 566 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: A 245 GLN cc_start: 0.8074 (mt0) cc_final: 0.7829 (mt0) REVERT: A 328 ASP cc_start: 0.8552 (t0) cc_final: 0.8206 (t0) REVERT: A 468 LYS cc_start: 0.7333 (tptt) cc_final: 0.7092 (tptt) REVERT: A 553 MET cc_start: 0.6402 (tmm) cc_final: 0.6078 (tmm) REVERT: A 570 MET cc_start: 0.7720 (ptt) cc_final: 0.7517 (ptt) REVERT: A 747 SER cc_start: 0.7681 (m) cc_final: 0.7450 (t) REVERT: A 769 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7409 (mtmm) REVERT: A 772 MET cc_start: 0.8069 (tpp) cc_final: 0.7712 (tpt) REVERT: A 810 TYR cc_start: 0.8624 (t80) cc_final: 0.8213 (t80) REVERT: A 885 SER cc_start: 0.7647 (m) cc_final: 0.7257 (p) REVERT: A 908 MET cc_start: 0.8298 (mmp) cc_final: 0.8055 (mmm) REVERT: A 931 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6681 (tptp) REVERT: A 965 ILE cc_start: 0.6967 (mm) cc_final: 0.6746 (mm) REVERT: B 101 GLU cc_start: 0.7610 (mp0) cc_final: 0.7217 (mt-10) REVERT: B 310 ILE cc_start: 0.7988 (mt) cc_final: 0.7715 (mt) REVERT: B 836 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7366 (mt-10) REVERT: C 1 MET cc_start: 0.4966 (mmt) cc_final: 0.4355 (tpt) REVERT: C 66 GLU cc_start: 0.7396 (tt0) cc_final: 0.7086 (tt0) REVERT: C 205 ASN cc_start: 0.7296 (m-40) cc_final: 0.6994 (m-40) REVERT: C 214 ILE cc_start: 0.9005 (mt) cc_final: 0.8727 (mt) REVERT: C 837 GLN cc_start: 0.7479 (mt0) cc_final: 0.7161 (mt0) REVERT: C 967 MET cc_start: 0.8802 (mtp) cc_final: 0.8573 (mtm) REVERT: C 1015 PHE cc_start: 0.7861 (m-80) cc_final: 0.7579 (m-80) outliers start: 21 outliers final: 6 residues processed: 575 average time/residue: 0.1390 time to fit residues: 128.5886 Evaluate side-chains 504 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 496 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 TYR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 440 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 574 GLN A 779 ASN A 805 GLN B 44 ASN B 104 GLN B 282 ASN B 859 GLN C 120 GLN C 128 GLN C 161 ASN C 604 ASN C 677 GLN C 701 ASN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.158124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.124880 restraints weight = 26855.114| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.77 r_work: 0.3067 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23965 Z= 0.202 Angle : 0.637 10.869 32485 Z= 0.332 Chirality : 0.045 0.254 3873 Planarity : 0.005 0.065 4068 Dihedral : 7.271 171.993 3298 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.91 % Allowed : 9.04 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.15), residues: 3048 helix: 1.86 (0.12), residues: 1705 sheet: -0.27 (0.23), residues: 477 loop : -0.13 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 813 TYR 0.019 0.002 TYR A 555 PHE 0.027 0.002 PHE A1015 TRP 0.010 0.001 TRP B 800 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (23965) covalent geometry : angle 0.63720 / 0.33 (32485) hydrogen bonds : bond 0.04968 / 3.31 ( 1490) hydrogen bonds : angle 4.83379 / 3.52 ( 4581) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 499 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8087 (mtmm) REVERT: A 165 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7736 (mm-30) REVERT: A 304 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6969 (pt0) REVERT: A 321 MET cc_start: 0.8446 (mtt) cc_final: 0.8225 (mtt) REVERT: A 468 LYS cc_start: 0.7784 (tptt) cc_final: 0.7576 (tptt) REVERT: A 474 MET cc_start: 0.8010 (tpt) cc_final: 0.6470 (tpt) REVERT: A 539 MET cc_start: 0.8335 (mpp) cc_final: 0.7962 (mpp) REVERT: A 565 ASP cc_start: 0.6808 (t0) cc_final: 0.5501 (p0) REVERT: A 769 LYS cc_start: 0.8180 (ptpt) cc_final: 0.7970 (pttt) REVERT: A 772 MET cc_start: 0.8244 (tpp) cc_final: 0.7800 (tpt) REVERT: A 832 MET cc_start: 0.7040 (mtm) cc_final: 0.6801 (mtm) REVERT: A 908 MET cc_start: 0.8854 (mmp) cc_final: 0.8445 (mmm) REVERT: A 965 ILE cc_start: 0.6495 (mm) cc_final: 0.6191 (mm) REVERT: B 192 LYS cc_start: 0.7784 (mttp) cc_final: 0.7537 (mttm) REVERT: B 310 ILE cc_start: 0.8120 (mt) cc_final: 0.7760 (mt) REVERT: B 346 GLU cc_start: 0.7910 (tt0) cc_final: 0.7593 (tt0) REVERT: B 681 ASN cc_start: 0.8535 (m110) cc_final: 0.8253 (m-40) REVERT: B 836 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7712 (mt-10) REVERT: B 849 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: B 868 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8599 (mp) REVERT: B 948 MET cc_start: 0.7591 (mtp) cc_final: 0.7323 (ttm) REVERT: C 1 MET cc_start: 0.6154 (mmt) cc_final: 0.5076 (tpt) REVERT: C 29 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8112 (mttt) REVERT: C 205 ASN cc_start: 0.8146 (m-40) cc_final: 0.7574 (m-40) REVERT: C 596 LYS cc_start: 0.7375 (ttmm) cc_final: 0.6893 (mmtt) REVERT: C 638 LYS cc_start: 0.7589 (tptp) cc_final: 0.7211 (tptp) REVERT: C 639 MET cc_start: 0.7985 (mtp) cc_final: 0.7714 (mtp) REVERT: C 799 GLN cc_start: 0.8107 (pt0) cc_final: 0.7874 (pt0) REVERT: C 837 GLN cc_start: 0.8085 (mt0) cc_final: 0.7809 (mt0) REVERT: C 967 MET cc_start: 0.9130 (mtp) cc_final: 0.8776 (mtm) outliers start: 49 outliers final: 33 residues processed: 521 average time/residue: 0.1392 time to fit residues: 115.7818 Evaluate side-chains 510 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 474 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 750 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 291 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 83 optimal weight: 0.0040 chunk 76 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 300 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN A 779 ASN B 44 ASN B 239 GLN B 298 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 161 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.159202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.126081 restraints weight = 26759.942| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.77 r_work: 0.3088 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23965 Z= 0.136 Angle : 0.558 9.985 32485 Z= 0.290 Chirality : 0.042 0.236 3873 Planarity : 0.004 0.060 4068 Dihedral : 6.750 173.739 3296 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.22 % Allowed : 11.50 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.15), residues: 3048 helix: 2.04 (0.13), residues: 1699 sheet: -0.11 (0.24), residues: 455 loop : -0.12 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 218 TYR 0.013 0.001 TYR A 555 PHE 0.024 0.001 PHE A1015 TRP 0.008 0.001 TRP B 800 HIS 0.001 0.000 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (23965) covalent geometry : angle 0.55790 / 0.29 (32485) hydrogen bonds : bond 0.04332 / 2.88 ( 1490) hydrogen bonds : angle 4.53209 / 3.30 ( 4581) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 510 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8117 (mtpt) REVERT: A 125 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8207 (mm110) REVERT: A 165 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: A 321 MET cc_start: 0.8442 (mtt) cc_final: 0.8224 (mtt) REVERT: A 358 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7459 (t80) REVERT: A 468 LYS cc_start: 0.7736 (tptt) cc_final: 0.7465 (tptt) REVERT: A 539 MET cc_start: 0.8385 (mpp) cc_final: 0.8027 (mpp) REVERT: A 553 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6346 (tmm) REVERT: A 565 ASP cc_start: 0.6581 (t0) cc_final: 0.5386 (p0) REVERT: A 654 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 706 MET cc_start: 0.3659 (mtp) cc_final: 0.2796 (mpp) REVERT: A 714 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: A 772 MET cc_start: 0.8213 (tpp) cc_final: 0.7799 (tpt) REVERT: A 942 MET cc_start: 0.6646 (tmm) cc_final: 0.6061 (tmm) REVERT: A 965 ILE cc_start: 0.6408 (mm) cc_final: 0.6168 (mm) REVERT: B 112 LYS cc_start: 0.8084 (mttt) cc_final: 0.7804 (mtpt) REVERT: B 192 LYS cc_start: 0.7814 (mttp) cc_final: 0.7575 (mttm) REVERT: B 267 ASN cc_start: 0.8151 (t0) cc_final: 0.7906 (t0) REVERT: B 269 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7208 (mt-10) REVERT: B 310 ILE cc_start: 0.8015 (mt) cc_final: 0.7744 (mm) REVERT: B 346 GLU cc_start: 0.7896 (tt0) cc_final: 0.7576 (tt0) REVERT: B 681 ASN cc_start: 0.8549 (m110) cc_final: 0.8296 (m-40) REVERT: B 836 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 863 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8879 (pm20) REVERT: B 868 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8560 (mp) REVERT: B 943 LEU cc_start: 0.8314 (mp) cc_final: 0.8079 (mp) REVERT: B 948 MET cc_start: 0.7627 (mtp) cc_final: 0.7377 (ttm) REVERT: C 1 MET cc_start: 0.6180 (mmt) cc_final: 0.5120 (tpt) REVERT: C 29 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8135 (mttt) REVERT: C 112 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8044 (mttt) REVERT: C 205 ASN cc_start: 0.8019 (m-40) cc_final: 0.7454 (m-40) REVERT: C 526 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8323 (tp) REVERT: C 550 PHE cc_start: 0.7380 (t80) cc_final: 0.7004 (t80) REVERT: C 596 LYS cc_start: 0.7367 (ttmm) cc_final: 0.6956 (mmtt) REVERT: C 638 LYS cc_start: 0.7523 (tptp) cc_final: 0.7125 (tptp) REVERT: C 837 GLN cc_start: 0.8057 (mt0) cc_final: 0.7722 (mt0) REVERT: C 942 MET cc_start: 0.8372 (ttp) cc_final: 0.8145 (ttp) outliers start: 57 outliers final: 33 residues processed: 540 average time/residue: 0.1552 time to fit residues: 133.5879 Evaluate side-chains 517 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 477 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 750 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 295 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 273 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN B 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN C 120 GLN C 128 GLN C 146 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.155300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.121765 restraints weight = 26880.368| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.77 r_work: 0.3030 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23965 Z= 0.206 Angle : 0.617 11.302 32485 Z= 0.320 Chirality : 0.044 0.235 3873 Planarity : 0.005 0.063 4068 Dihedral : 6.577 162.242 3294 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.04 % Allowed : 13.02 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.15), residues: 3048 helix: 1.80 (0.12), residues: 1699 sheet: -0.24 (0.23), residues: 477 loop : -0.19 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 185 TYR 0.016 0.002 TYR B 883 PHE 0.021 0.002 PHE A1015 TRP 0.012 0.001 TRP A 556 HIS 0.002 0.001 HIS C 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (23965) covalent geometry : angle 0.61744 / 0.32 (32485) hydrogen bonds : bond 0.04861 / 3.23 ( 1490) hydrogen bonds : angle 4.64505 / 3.37 ( 4581) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 488 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8473 (t80) cc_final: 0.8199 (t80) REVERT: A 8 ARG cc_start: 0.7026 (mtm-85) cc_final: 0.6822 (mtm180) REVERT: A 34 ARG cc_start: 0.8507 (ttt-90) cc_final: 0.8269 (ttt-90) REVERT: A 35 PHE cc_start: 0.8233 (m-80) cc_final: 0.8007 (m-80) REVERT: A 73 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8141 (mtpt) REVERT: A 125 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8299 (mm110) REVERT: A 165 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: A 225 GLU cc_start: 0.8131 (tt0) cc_final: 0.7841 (tp30) REVERT: A 264 ASP cc_start: 0.7977 (t70) cc_final: 0.7737 (t0) REVERT: A 358 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.6752 (t80) REVERT: A 474 MET cc_start: 0.7736 (tpt) cc_final: 0.6445 (tpt) REVERT: A 486 LEU cc_start: 0.7858 (mm) cc_final: 0.7610 (mm) REVERT: A 539 MET cc_start: 0.8407 (tpp) cc_final: 0.8021 (mpp) REVERT: A 553 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6260 (tmm) REVERT: A 654 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7176 (tp30) REVERT: A 714 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 965 ILE cc_start: 0.6425 (mm) cc_final: 0.6171 (mm) REVERT: A 967 MET cc_start: 0.7669 (tpp) cc_final: 0.7458 (tpp) REVERT: B 73 LYS cc_start: 0.8166 (ptpt) cc_final: 0.7689 (ptmm) REVERT: B 192 LYS cc_start: 0.7800 (mttp) cc_final: 0.7562 (mttm) REVERT: B 267 ASN cc_start: 0.8161 (t0) cc_final: 0.7915 (t0) REVERT: B 269 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 310 ILE cc_start: 0.8087 (mt) cc_final: 0.7744 (mt) REVERT: B 346 GLU cc_start: 0.7955 (tt0) cc_final: 0.7649 (tt0) REVERT: B 656 MET cc_start: 0.7696 (mmt) cc_final: 0.7333 (mmt) REVERT: B 681 ASN cc_start: 0.8542 (m110) cc_final: 0.8271 (m-40) REVERT: B 836 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7556 (mt-10) REVERT: B 849 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: B 883 TYR cc_start: 0.8828 (m-80) cc_final: 0.8603 (m-80) REVERT: B 948 MET cc_start: 0.7839 (mtp) cc_final: 0.7587 (ttm) REVERT: C 1 MET cc_start: 0.6223 (mmt) cc_final: 0.5332 (tpt) REVERT: C 29 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8274 (mttt) REVERT: C 112 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8163 (mttt) REVERT: C 189 ASP cc_start: 0.8005 (t70) cc_final: 0.7769 (t70) REVERT: C 205 ASN cc_start: 0.8254 (m-40) cc_final: 0.7571 (m-40) REVERT: C 526 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8363 (tp) REVERT: C 550 PHE cc_start: 0.7399 (t80) cc_final: 0.7041 (t80) REVERT: C 596 LYS cc_start: 0.7436 (ttmm) cc_final: 0.6938 (mmtt) REVERT: C 638 LYS cc_start: 0.7608 (tptp) cc_final: 0.7048 (tptp) REVERT: C 769 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8450 (ptmm) REVERT: C 837 GLN cc_start: 0.8107 (mt0) cc_final: 0.7768 (mt0) REVERT: C 1019 ILE cc_start: 0.8186 (mm) cc_final: 0.7955 (mm) outliers start: 78 outliers final: 50 residues processed: 532 average time/residue: 0.1457 time to fit residues: 123.5374 Evaluate side-chains 530 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 474 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 73 optimal weight: 0.9980 chunk 243 optimal weight: 9.9990 chunk 295 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 chunk 235 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN B 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 ASN C 590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.158296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.125083 restraints weight = 26636.824| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.78 r_work: 0.3075 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23965 Z= 0.122 Angle : 0.546 10.857 32485 Z= 0.283 Chirality : 0.041 0.228 3873 Planarity : 0.004 0.062 4068 Dihedral : 6.209 152.699 3294 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.57 % Allowed : 15.13 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.15), residues: 3048 helix: 2.01 (0.13), residues: 1695 sheet: -0.18 (0.24), residues: 473 loop : -0.09 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.011 0.001 TYR C 883 PHE 0.019 0.001 PHE A1015 TRP 0.006 0.001 TRP B 800 HIS 0.001 0.000 HIS C 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (23965) covalent geometry : angle 0.54599 / 0.28 (32485) hydrogen bonds : bond 0.04049 / 2.69 ( 1490) hydrogen bonds : angle 4.41801 / 3.21 ( 4581) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 509 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8163 (mttm) REVERT: A 125 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8248 (mm110) REVERT: A 165 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7938 (mm-30) REVERT: A 225 GLU cc_start: 0.8115 (tt0) cc_final: 0.7854 (mm-30) REVERT: A 264 ASP cc_start: 0.7990 (t70) cc_final: 0.7727 (t0) REVERT: A 358 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.6584 (t80) REVERT: A 486 LEU cc_start: 0.7595 (mm) cc_final: 0.7268 (mm) REVERT: A 539 MET cc_start: 0.8378 (tpp) cc_final: 0.7940 (mpp) REVERT: A 553 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6254 (tmm) REVERT: A 596 LYS cc_start: 0.7455 (tmtt) cc_final: 0.7211 (tppt) REVERT: A 654 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7196 (tp30) REVERT: A 714 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: A 813 ARG cc_start: 0.7871 (mpt-90) cc_final: 0.7127 (mpt-90) REVERT: A 913 MET cc_start: 0.7962 (mpp) cc_final: 0.7457 (tmm) REVERT: A 942 MET cc_start: 0.6667 (tmm) cc_final: 0.6069 (tmm) REVERT: A 965 ILE cc_start: 0.6449 (mm) cc_final: 0.6187 (mm) REVERT: A 967 MET cc_start: 0.7683 (tpp) cc_final: 0.7427 (tpp) REVERT: B 73 LYS cc_start: 0.8151 (ptpt) cc_final: 0.7653 (ptmm) REVERT: B 101 GLU cc_start: 0.8412 (mp0) cc_final: 0.7852 (mt-10) REVERT: B 102 MET cc_start: 0.8703 (mmm) cc_final: 0.8389 (mmm) REVERT: B 192 LYS cc_start: 0.7710 (mttp) cc_final: 0.7468 (mttm) REVERT: B 267 ASN cc_start: 0.8133 (t0) cc_final: 0.7887 (t0) REVERT: B 269 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 310 ILE cc_start: 0.8008 (mt) cc_final: 0.7713 (mm) REVERT: B 358 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 593 ASN cc_start: 0.7691 (m-40) cc_final: 0.7376 (m110) REVERT: B 656 MET cc_start: 0.7570 (mmt) cc_final: 0.7326 (mmt) REVERT: B 681 ASN cc_start: 0.8529 (m110) cc_final: 0.8267 (m-40) REVERT: B 836 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 849 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: B 863 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8935 (pm20) REVERT: B 868 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8517 (mp) REVERT: B 883 TYR cc_start: 0.8796 (m-80) cc_final: 0.8594 (m-80) REVERT: C 1 MET cc_start: 0.6181 (mmt) cc_final: 0.5349 (tpt) REVERT: C 112 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8090 (mttt) REVERT: C 189 ASP cc_start: 0.7935 (t70) cc_final: 0.7704 (t70) REVERT: C 205 ASN cc_start: 0.8057 (m-40) cc_final: 0.7411 (m-40) REVERT: C 550 PHE cc_start: 0.7374 (t80) cc_final: 0.7023 (t80) REVERT: C 596 LYS cc_start: 0.7412 (ttmm) cc_final: 0.6926 (mmtt) REVERT: C 638 LYS cc_start: 0.7353 (tptp) cc_final: 0.6832 (tptp) REVERT: C 769 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8408 (ptmm) REVERT: C 837 GLN cc_start: 0.8056 (mt0) cc_final: 0.7720 (mt0) REVERT: C 942 MET cc_start: 0.8404 (ttp) cc_final: 0.8199 (ttp) outliers start: 66 outliers final: 39 residues processed: 553 average time/residue: 0.1478 time to fit residues: 130.1595 Evaluate side-chains 535 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 488 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 116 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 293 optimal weight: 0.8980 chunk 210 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 217 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 264 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN B 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.158367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.125288 restraints weight = 26920.343| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.77 r_work: 0.3075 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23965 Z= 0.125 Angle : 0.545 10.830 32485 Z= 0.280 Chirality : 0.041 0.255 3873 Planarity : 0.004 0.061 4068 Dihedral : 6.057 146.103 3294 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.85 % Allowed : 15.28 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.15), residues: 3048 helix: 2.08 (0.13), residues: 1691 sheet: -0.15 (0.23), residues: 487 loop : -0.13 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.009 0.001 TYR C 883 PHE 0.019 0.001 PHE A1015 TRP 0.006 0.001 TRP B 800 HIS 0.001 0.000 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (23965) covalent geometry : angle 0.54459 / 0.28 (32485) hydrogen bonds : bond 0.03966 / 2.64 ( 1490) hydrogen bonds : angle 4.35472 / 3.16 ( 4581) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 503 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8413 (ttt-90) cc_final: 0.8118 (ttt-90) REVERT: A 73 LYS cc_start: 0.8461 (mmmm) cc_final: 0.8182 (mttm) REVERT: A 125 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8209 (mm110) REVERT: A 165 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: A 225 GLU cc_start: 0.8120 (tt0) cc_final: 0.7829 (mm-30) REVERT: A 358 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.6470 (t80) REVERT: A 474 MET cc_start: 0.7725 (tpt) cc_final: 0.6219 (tpt) REVERT: A 539 MET cc_start: 0.8315 (tpp) cc_final: 0.7904 (mpp) REVERT: A 553 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6263 (tmm) REVERT: A 596 LYS cc_start: 0.7479 (tmtt) cc_final: 0.7268 (tppt) REVERT: A 654 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7200 (tp30) REVERT: A 714 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: A 813 ARG cc_start: 0.7872 (mpt-90) cc_final: 0.7156 (mpt-90) REVERT: A 913 MET cc_start: 0.7942 (mpp) cc_final: 0.7517 (tmm) REVERT: A 942 MET cc_start: 0.6727 (tmm) cc_final: 0.6157 (tmm) REVERT: A 965 ILE cc_start: 0.6476 (mm) cc_final: 0.6205 (mm) REVERT: A 967 MET cc_start: 0.7721 (tpp) cc_final: 0.7412 (tpp) REVERT: B 73 LYS cc_start: 0.8142 (ptpt) cc_final: 0.7669 (ptmm) REVERT: B 101 GLU cc_start: 0.8488 (mp0) cc_final: 0.8023 (mt-10) REVERT: B 192 LYS cc_start: 0.7737 (mttp) cc_final: 0.7499 (mttm) REVERT: B 211 ASN cc_start: 0.8170 (t0) cc_final: 0.7876 (t0) REVERT: B 267 ASN cc_start: 0.8064 (t0) cc_final: 0.7813 (t0) REVERT: B 269 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7198 (mt-10) REVERT: B 310 ILE cc_start: 0.7989 (mt) cc_final: 0.7665 (mt) REVERT: B 358 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7013 (t80) REVERT: B 593 ASN cc_start: 0.7712 (m-40) cc_final: 0.7381 (m110) REVERT: B 656 MET cc_start: 0.7533 (mmt) cc_final: 0.7313 (mmt) REVERT: B 681 ASN cc_start: 0.8520 (m110) cc_final: 0.8251 (m-40) REVERT: B 695 MET cc_start: 0.8902 (mmt) cc_final: 0.8690 (mmt) REVERT: B 836 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 849 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: B 883 TYR cc_start: 0.8775 (m-80) cc_final: 0.8560 (m-80) REVERT: C 1 MET cc_start: 0.6197 (mmt) cc_final: 0.5378 (tpt) REVERT: C 112 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8097 (mttt) REVERT: C 205 ASN cc_start: 0.8061 (m-40) cc_final: 0.7438 (m-40) REVERT: C 436 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7540 (mtpp) REVERT: C 550 PHE cc_start: 0.7385 (t80) cc_final: 0.7022 (t80) REVERT: C 596 LYS cc_start: 0.7381 (ttmm) cc_final: 0.6894 (mmtt) REVERT: C 638 LYS cc_start: 0.7377 (tptp) cc_final: 0.6878 (tptp) REVERT: C 769 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8359 (ptmm) REVERT: C 834 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: C 837 GLN cc_start: 0.8070 (mt0) cc_final: 0.7717 (mt0) REVERT: C 942 MET cc_start: 0.8407 (ttp) cc_final: 0.8205 (ttp) REVERT: C 1019 ILE cc_start: 0.8171 (mm) cc_final: 0.7934 (mm) outliers start: 73 outliers final: 48 residues processed: 553 average time/residue: 0.1497 time to fit residues: 132.4049 Evaluate side-chains 544 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 489 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 236 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 273 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.156729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.123360 restraints weight = 26744.950| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.78 r_work: 0.3051 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23965 Z= 0.158 Angle : 0.571 11.123 32485 Z= 0.294 Chirality : 0.042 0.259 3873 Planarity : 0.004 0.061 4068 Dihedral : 5.932 139.192 3292 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.16 % Allowed : 15.56 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 3048 helix: 1.99 (0.12), residues: 1694 sheet: -0.13 (0.24), residues: 476 loop : -0.18 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.011 0.001 TYR B 883 PHE 0.021 0.001 PHE A 918 TRP 0.009 0.001 TRP B 800 HIS 0.002 0.000 HIS C 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (23965) covalent geometry : angle 0.57113 / 0.29 (32485) hydrogen bonds : bond 0.04270 / 2.83 ( 1490) hydrogen bonds : angle 4.41616 / 3.20 ( 4581) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 500 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8196 (mttm) REVERT: A 125 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8251 (mm110) REVERT: A 165 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7923 (mm-30) REVERT: A 225 GLU cc_start: 0.8152 (tt0) cc_final: 0.7849 (mm-30) REVERT: A 358 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.6443 (t80) REVERT: A 474 MET cc_start: 0.7721 (tpt) cc_final: 0.6405 (tpt) REVERT: A 539 MET cc_start: 0.8407 (tpp) cc_final: 0.7966 (mpp) REVERT: A 553 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6339 (tmm) REVERT: A 595 LEU cc_start: 0.7593 (tp) cc_final: 0.7367 (tp) REVERT: A 596 LYS cc_start: 0.7551 (tmtt) cc_final: 0.7325 (tppt) REVERT: A 654 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7205 (tp30) REVERT: A 714 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: A 782 VAL cc_start: 0.5577 (OUTLIER) cc_final: 0.5213 (m) REVERT: A 913 MET cc_start: 0.7940 (mpp) cc_final: 0.7485 (tmm) REVERT: A 931 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6436 (pptt) REVERT: A 965 ILE cc_start: 0.6446 (mm) cc_final: 0.6109 (mm) REVERT: A 967 MET cc_start: 0.7794 (tpp) cc_final: 0.7438 (tpp) REVERT: B 73 LYS cc_start: 0.8170 (ptpt) cc_final: 0.7702 (ptmm) REVERT: B 101 GLU cc_start: 0.8522 (mp0) cc_final: 0.8058 (mt-10) REVERT: B 192 LYS cc_start: 0.7726 (mttp) cc_final: 0.7493 (mttm) REVERT: B 211 ASN cc_start: 0.8177 (t0) cc_final: 0.7871 (t0) REVERT: B 267 ASN cc_start: 0.8099 (t0) cc_final: 0.7839 (t0) REVERT: B 269 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 310 ILE cc_start: 0.8049 (mt) cc_final: 0.7725 (mt) REVERT: B 358 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7136 (t80) REVERT: B 656 MET cc_start: 0.7630 (mmt) cc_final: 0.7368 (mmt) REVERT: B 681 ASN cc_start: 0.8492 (m110) cc_final: 0.8244 (m-40) REVERT: B 695 MET cc_start: 0.8869 (mmt) cc_final: 0.8599 (mmt) REVERT: B 824 PHE cc_start: 0.7795 (p90) cc_final: 0.7524 (p90) REVERT: B 836 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7557 (mt-10) REVERT: B 883 TYR cc_start: 0.8785 (m-80) cc_final: 0.8547 (m-80) REVERT: C 1 MET cc_start: 0.6102 (mmt) cc_final: 0.5438 (tpt) REVERT: C 3 GLN cc_start: 0.6168 (OUTLIER) cc_final: 0.5936 (tt0) REVERT: C 66 GLU cc_start: 0.8003 (tt0) cc_final: 0.7648 (tt0) REVERT: C 112 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8100 (mttt) REVERT: C 164 GLU cc_start: 0.7529 (tt0) cc_final: 0.7041 (pt0) REVERT: C 189 ASP cc_start: 0.7998 (t70) cc_final: 0.7745 (t70) REVERT: C 205 ASN cc_start: 0.8246 (m-40) cc_final: 0.7566 (m-40) REVERT: C 230 ILE cc_start: 0.8366 (pt) cc_final: 0.8150 (pt) REVERT: C 307 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7749 (mtp85) REVERT: C 526 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8341 (tp) REVERT: C 546 THR cc_start: 0.8429 (t) cc_final: 0.8115 (m) REVERT: C 550 PHE cc_start: 0.7376 (t80) cc_final: 0.7054 (t80) REVERT: C 585 ARG cc_start: 0.8110 (tmt-80) cc_final: 0.7727 (tmt170) REVERT: C 596 LYS cc_start: 0.7419 (ttmm) cc_final: 0.6923 (mmtt) REVERT: C 638 LYS cc_start: 0.7378 (tptp) cc_final: 0.6873 (tptp) REVERT: C 703 LYS cc_start: 0.7870 (mttt) cc_final: 0.7373 (mttt) REVERT: C 769 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8414 (ptmm) REVERT: C 834 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: C 837 GLN cc_start: 0.8084 (mt0) cc_final: 0.7743 (mt0) REVERT: C 942 MET cc_start: 0.8520 (ttp) cc_final: 0.8303 (ttp) outliers start: 81 outliers final: 60 residues processed: 552 average time/residue: 0.1489 time to fit residues: 131.5778 Evaluate side-chains 555 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 485 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 799 GLN Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 165 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 237 optimal weight: 7.9990 chunk 52 optimal weight: 50.0000 chunk 157 optimal weight: 0.0980 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN B 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.155932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.122521 restraints weight = 26740.002| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.78 r_work: 0.3043 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23965 Z= 0.172 Angle : 0.587 11.122 32485 Z= 0.302 Chirality : 0.043 0.274 3873 Planarity : 0.005 0.062 4068 Dihedral : 5.913 133.659 3292 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.16 % Allowed : 16.06 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3048 helix: 1.91 (0.12), residues: 1697 sheet: -0.23 (0.24), residues: 472 loop : -0.23 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 8 TYR 0.013 0.001 TYR B 883 PHE 0.020 0.002 PHE C 352 TRP 0.011 0.001 TRP B 800 HIS 0.001 0.000 HIS C 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (23965) covalent geometry : angle 0.58730 / 0.30 (32485) hydrogen bonds : bond 0.04426 / 2.93 ( 1490) hydrogen bonds : angle 4.46266 / 3.23 ( 4581) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 498 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8219 (mttm) REVERT: A 125 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8170 (mm110) REVERT: A 165 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: A 225 GLU cc_start: 0.8156 (tt0) cc_final: 0.7846 (mm-30) REVERT: A 358 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.6377 (t80) REVERT: A 539 MET cc_start: 0.8420 (tpp) cc_final: 0.7976 (mpp) REVERT: A 553 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6404 (tmm) REVERT: A 596 LYS cc_start: 0.7572 (tmtt) cc_final: 0.7337 (tppt) REVERT: A 654 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7189 (tp30) REVERT: A 714 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: A 779 ASN cc_start: 0.7639 (m-40) cc_final: 0.7288 (m110) REVERT: A 782 VAL cc_start: 0.5611 (OUTLIER) cc_final: 0.5249 (m) REVERT: A 965 ILE cc_start: 0.6443 (mm) cc_final: 0.6125 (mm) REVERT: A 967 MET cc_start: 0.7810 (tpp) cc_final: 0.7333 (tpp) REVERT: B 101 GLU cc_start: 0.8536 (mp0) cc_final: 0.8066 (mt-10) REVERT: B 192 LYS cc_start: 0.7716 (mttp) cc_final: 0.7473 (mttm) REVERT: B 211 ASN cc_start: 0.8166 (t0) cc_final: 0.7861 (t0) REVERT: B 267 ASN cc_start: 0.8118 (t0) cc_final: 0.7861 (t0) REVERT: B 269 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7285 (mt-10) REVERT: B 310 ILE cc_start: 0.7993 (mt) cc_final: 0.7665 (mt) REVERT: B 358 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7079 (t80) REVERT: B 366 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 593 ASN cc_start: 0.7671 (m-40) cc_final: 0.7398 (m110) REVERT: B 656 MET cc_start: 0.7672 (mmt) cc_final: 0.7408 (mmt) REVERT: B 681 ASN cc_start: 0.8489 (m110) cc_final: 0.8255 (m-40) REVERT: B 695 MET cc_start: 0.8821 (mmt) cc_final: 0.8504 (mmt) REVERT: B 824 PHE cc_start: 0.7836 (p90) cc_final: 0.7564 (p90) REVERT: B 836 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 863 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8883 (pm20) REVERT: B 883 TYR cc_start: 0.8730 (m-80) cc_final: 0.8451 (m-80) REVERT: C 1 MET cc_start: 0.6093 (mmt) cc_final: 0.5451 (tpt) REVERT: C 66 GLU cc_start: 0.7980 (tt0) cc_final: 0.7564 (tt0) REVERT: C 112 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8095 (mttt) REVERT: C 164 GLU cc_start: 0.7508 (tt0) cc_final: 0.6979 (pt0) REVERT: C 189 ASP cc_start: 0.8043 (t70) cc_final: 0.7839 (t70) REVERT: C 205 ASN cc_start: 0.8269 (m-40) cc_final: 0.7594 (m-40) REVERT: C 230 ILE cc_start: 0.8383 (pt) cc_final: 0.8164 (pt) REVERT: C 307 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7722 (mtp85) REVERT: C 526 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8366 (tp) REVERT: C 546 THR cc_start: 0.8431 (t) cc_final: 0.8093 (m) REVERT: C 585 ARG cc_start: 0.8136 (tmt-80) cc_final: 0.7760 (tmt170) REVERT: C 638 LYS cc_start: 0.7383 (tptp) cc_final: 0.6877 (tptp) REVERT: C 703 LYS cc_start: 0.7938 (mttt) cc_final: 0.7439 (mttt) REVERT: C 769 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8421 (ptmm) REVERT: C 834 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: C 837 GLN cc_start: 0.8065 (mt0) cc_final: 0.7723 (mt0) REVERT: C 1019 ILE cc_start: 0.8172 (mm) cc_final: 0.7921 (mm) outliers start: 81 outliers final: 63 residues processed: 547 average time/residue: 0.1507 time to fit residues: 131.2653 Evaluate side-chains 557 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 484 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 799 GLN Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 41 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 127 optimal weight: 50.0000 chunk 1 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 294 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 83 optimal weight: 0.0070 overall best weight: 6.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 714 GLN ** 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 = 0.3556 r_free = 0.3556 target = 0.154607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.121086 restraints weight = 26911.555| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.78 r_work: 0.3023 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23965 Z= 0.212 Angle : 0.623 11.298 32485 Z= 0.320 Chirality : 0.045 0.282 3873 Planarity : 0.005 0.063 4068 Dihedral : 5.974 131.084 3292 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.12 % Allowed : 16.26 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3048 helix: 1.76 (0.12), residues: 1699 sheet: -0.30 (0.23), residues: 475 loop : -0.28 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 34 TYR 0.014 0.001 TYR A 275 PHE 0.021 0.002 PHE A 388 TRP 0.013 0.001 TRP B 800 HIS 0.002 0.001 HIS C 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 (23965) covalent geometry : angle 0.62330 / 0.32 (32485) hydrogen bonds : bond 0.04727 / 3.13 ( 1490) hydrogen bonds : angle 4.56022 / 3.30 ( 4581) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 490 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8578 (mmmm) cc_final: 0.8274 (mttm) REVERT: A 125 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8197 (mm110) REVERT: A 165 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: A 225 GLU cc_start: 0.8159 (tt0) cc_final: 0.7861 (tp30) REVERT: A 358 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.6452 (t80) REVERT: A 474 MET cc_start: 0.7779 (tpt) cc_final: 0.6456 (tpt) REVERT: A 539 MET cc_start: 0.8377 (tpp) cc_final: 0.7958 (mpp) REVERT: A 596 LYS cc_start: 0.7598 (tmtt) cc_final: 0.7377 (tppt) REVERT: A 654 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7186 (tp30) REVERT: A 714 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: A 779 ASN cc_start: 0.7541 (m-40) cc_final: 0.7235 (m110) REVERT: A 931 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6443 (pptt) REVERT: A 965 ILE cc_start: 0.6429 (mm) cc_final: 0.6113 (mm) REVERT: A 967 MET cc_start: 0.7816 (tpp) cc_final: 0.7343 (tpp) REVERT: B 267 ASN cc_start: 0.8197 (t0) cc_final: 0.7941 (t0) REVERT: B 269 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7248 (mt-10) REVERT: B 284 LYS cc_start: 0.7209 (tppt) cc_final: 0.6592 (mmmt) REVERT: B 310 ILE cc_start: 0.7996 (mt) cc_final: 0.7658 (mt) REVERT: B 366 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8041 (mp) REVERT: B 656 MET cc_start: 0.7684 (mmt) cc_final: 0.7376 (mmt) REVERT: B 681 ASN cc_start: 0.8495 (m110) cc_final: 0.8266 (m-40) REVERT: B 695 MET cc_start: 0.8799 (mmt) cc_final: 0.8456 (mmt) REVERT: B 710 GLU cc_start: 0.8351 (pt0) cc_final: 0.7299 (mm-30) REVERT: B 836 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7469 (mt-10) REVERT: B 883 TYR cc_start: 0.8714 (m-80) cc_final: 0.8453 (m-80) REVERT: C 1 MET cc_start: 0.6111 (mmt) cc_final: 0.5483 (tpt) REVERT: C 66 GLU cc_start: 0.7974 (tt0) cc_final: 0.7543 (tt0) REVERT: C 112 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8122 (mttt) REVERT: C 164 GLU cc_start: 0.7535 (tt0) cc_final: 0.7077 (pt0) REVERT: C 189 ASP cc_start: 0.8076 (t70) cc_final: 0.7874 (t70) REVERT: C 205 ASN cc_start: 0.8281 (m-40) cc_final: 0.7616 (m-40) REVERT: C 230 ILE cc_start: 0.8373 (pt) cc_final: 0.8145 (pt) REVERT: C 321 MET cc_start: 0.9018 (mtt) cc_final: 0.8801 (mtt) REVERT: C 498 LYS cc_start: 0.8180 (mttt) cc_final: 0.7708 (ptpt) REVERT: C 526 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8413 (tp) REVERT: C 546 THR cc_start: 0.8438 (t) cc_final: 0.8090 (m) REVERT: C 638 LYS cc_start: 0.7380 (tptp) cc_final: 0.6863 (tptp) REVERT: C 769 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8486 (ptmm) REVERT: C 834 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: C 837 GLN cc_start: 0.8093 (mt0) cc_final: 0.7750 (mt0) REVERT: C 1019 ILE cc_start: 0.8221 (mm) cc_final: 0.7987 (mm) outliers start: 80 outliers final: 64 residues processed: 540 average time/residue: 0.1429 time to fit residues: 122.9926 Evaluate side-chains 558 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 487 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 799 GLN Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 274 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 54 optimal weight: 40.0000 chunk 63 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 714 GLN ** 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 = 0.3551 r_free = 0.3551 target = 0.154189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.120588 restraints weight = 26788.066| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.78 r_work: 0.3016 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23965 Z= 0.213 Angle : 0.632 11.432 32485 Z= 0.325 Chirality : 0.045 0.228 3873 Planarity : 0.005 0.063 4068 Dihedral : 6.000 126.681 3292 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.88 % Allowed : 16.73 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3048 helix: 1.68 (0.12), residues: 1691 sheet: -0.35 (0.23), residues: 475 loop : -0.33 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 34 TYR 0.015 0.002 TYR B 883 PHE 0.024 0.002 PHE A 388 TRP 0.014 0.001 TRP B 800 HIS 0.002 0.001 HIS C 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (23965) covalent geometry : angle 0.63243 / 0.33 (32485) hydrogen bonds : bond 0.04808 / 3.18 ( 1490) hydrogen bonds : angle 4.60940 / 3.34 ( 4581) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 490 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8268 (m-80) cc_final: 0.8058 (m-80) REVERT: A 73 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8276 (mttm) REVERT: A 125 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8185 (mm110) REVERT: A 165 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: A 225 GLU cc_start: 0.8158 (tt0) cc_final: 0.7867 (tp30) REVERT: A 358 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.6369 (t80) REVERT: A 539 MET cc_start: 0.8372 (tpp) cc_final: 0.7990 (mpp) REVERT: A 596 LYS cc_start: 0.7604 (tmtt) cc_final: 0.7371 (tppt) REVERT: A 654 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7058 (tp30) REVERT: A 714 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: A 779 ASN cc_start: 0.7519 (m-40) cc_final: 0.7232 (m110) REVERT: A 782 VAL cc_start: 0.5895 (OUTLIER) cc_final: 0.5579 (m) REVERT: A 908 MET cc_start: 0.8183 (mmm) cc_final: 0.7736 (mmm) REVERT: A 931 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6554 (pptt) REVERT: A 965 ILE cc_start: 0.6433 (mm) cc_final: 0.6119 (mm) REVERT: A 967 MET cc_start: 0.7866 (tpp) cc_final: 0.7352 (tpp) REVERT: B 267 ASN cc_start: 0.8225 (t0) cc_final: 0.7981 (t0) REVERT: B 269 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7252 (mt-10) REVERT: B 284 LYS cc_start: 0.7365 (tppt) cc_final: 0.6733 (mmmt) REVERT: B 310 ILE cc_start: 0.8020 (mt) cc_final: 0.7681 (mt) REVERT: B 366 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8078 (mp) REVERT: B 656 MET cc_start: 0.7681 (mmt) cc_final: 0.7376 (mmt) REVERT: B 681 ASN cc_start: 0.8493 (m110) cc_final: 0.8266 (m-40) REVERT: B 695 MET cc_start: 0.8812 (mmt) cc_final: 0.8444 (mmt) REVERT: B 710 GLU cc_start: 0.8371 (pt0) cc_final: 0.7304 (mm-30) REVERT: B 836 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7444 (mt-10) REVERT: B 883 TYR cc_start: 0.8645 (m-80) cc_final: 0.8378 (m-80) REVERT: C 1 MET cc_start: 0.6115 (mmt) cc_final: 0.5491 (tpt) REVERT: C 66 GLU cc_start: 0.7961 (tt0) cc_final: 0.7530 (tt0) REVERT: C 112 LYS cc_start: 0.8504 (mtpp) cc_final: 0.8109 (mttt) REVERT: C 164 GLU cc_start: 0.7522 (tt0) cc_final: 0.7051 (pt0) REVERT: C 189 ASP cc_start: 0.8067 (t70) cc_final: 0.7858 (t70) REVERT: C 205 ASN cc_start: 0.8299 (m-40) cc_final: 0.7951 (m-40) REVERT: C 230 ILE cc_start: 0.8392 (pt) cc_final: 0.8171 (pt) REVERT: C 321 MET cc_start: 0.8999 (mtt) cc_final: 0.8773 (mtt) REVERT: C 436 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7671 (mtpp) REVERT: C 498 LYS cc_start: 0.8151 (mttt) cc_final: 0.7653 (ptpt) REVERT: C 526 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8339 (tp) REVERT: C 546 THR cc_start: 0.8440 (t) cc_final: 0.8092 (m) REVERT: C 638 LYS cc_start: 0.7398 (tptp) cc_final: 0.6878 (tptp) REVERT: C 769 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8493 (ptmm) REVERT: C 834 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: C 837 GLN cc_start: 0.8098 (mt0) cc_final: 0.7768 (mt0) REVERT: C 1019 ILE cc_start: 0.8250 (mm) cc_final: 0.7978 (mm) outliers start: 74 outliers final: 64 residues processed: 538 average time/residue: 0.1577 time to fit residues: 134.8664 Evaluate side-chains 557 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 485 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 799 GLN Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 53 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN C 143 ASN ** C 714 GLN ** 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 = 0.3566 r_free = 0.3566 target = 0.155608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.122175 restraints weight = 26817.826| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.78 r_work: 0.3037 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23965 Z= 0.156 Angle : 0.597 11.066 32485 Z= 0.306 Chirality : 0.043 0.193 3873 Planarity : 0.005 0.062 4068 Dihedral : 5.877 123.162 3292 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.08 % Allowed : 16.49 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.15), residues: 3048 helix: 1.82 (0.13), residues: 1690 sheet: -0.27 (0.23), residues: 473 loop : -0.31 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 34 TYR 0.011 0.001 TYR B 883 PHE 0.020 0.001 PHE C 352 TRP 0.012 0.001 TRP B 800 HIS 0.001 0.000 HIS C 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (23965) covalent geometry : angle 0.59667 / 0.31 (32485) hydrogen bonds : bond 0.04402 / 2.91 ( 1490) hydrogen bonds : angle 4.49722 / 3.25 ( 4581) =============================================================================== Job complete usr+sys time: 5574.88 seconds wall clock time: 96 minutes 18.14 seconds (5778.14 seconds total)