Starting phenix.real_space_refine on Sun Aug 9 03:50:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vvk_65383/08_2026/9vvk_65383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vvk_65383/08_2026/9vvk_65383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vvk_65383/08_2026/9vvk_65383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vvk_65383/08_2026/9vvk_65383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vvk_65383/08_2026/9vvk_65383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vvk_65383/08_2026/9vvk_65383.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 19669 2.51 5 N 5593 2.21 5 O 5948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31314 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7830 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 971} Chain breaks: 1 Chain: "B" Number of atoms: 7830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7830 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 971} Chain breaks: 1 Chain: "C" Number of atoms: 7830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7830 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 971} Chain breaks: 1 Chain: "D" Number of atoms: 7824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7824 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 971} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.89, per 1000 atoms: 0.22 Number of scatterers: 31314 At special positions: 0 Unit cell: (183.18, 133.3, 172.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 5948 8.00 N 5593 7.00 C 19669 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: 2.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7568 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 32 sheets defined 42.8% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 removed outlier: 3.831A pdb=" N ARG A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.197A pdb=" N LEU A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 44' Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.608A pdb=" N ILE A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 4.126A pdb=" N ALA A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 3.803A pdb=" N ASN A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.702A pdb=" N ALA A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.680A pdb=" N LEU A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 192 Processing helix chain 'A' and resid 248 through 266 removed outlier: 3.500A pdb=" N TYR A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 260 " --> pdb=" O CYS A 256 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.905A pdb=" N GLU A 301 " --> pdb=" O HIS A 297 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.580A pdb=" N GLN A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 316 " --> pdb=" O GLN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.642A pdb=" N LEU A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.891A pdb=" N SER A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.791A pdb=" N ASP A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.627A pdb=" N ALA A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 474 removed outlier: 3.680A pdb=" N LYS A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 470 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.885A pdb=" N LYS A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.756A pdb=" N ALA A 515 " --> pdb=" O PRO A 511 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.904A pdb=" N ARG A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 557 removed outlier: 4.075A pdb=" N ARG A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 595 removed outlier: 3.759A pdb=" N ARG A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 616 through 631 removed outlier: 3.635A pdb=" N THR A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 629 " --> pdb=" O GLN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.995A pdb=" N ALA A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 653 " --> pdb=" O PRO A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 697 removed outlier: 4.408A pdb=" N TYR A 685 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.867A pdb=" N ARG A 716 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 723 " --> pdb=" O SER A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 749 removed outlier: 4.136A pdb=" N TYR A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP A 748 " --> pdb=" O TYR A 744 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 Processing helix chain 'A' and resid 795 through 804 removed outlier: 3.615A pdb=" N LEU A 802 " --> pdb=" O TYR A 798 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 822 removed outlier: 4.023A pdb=" N TYR A 821 " --> pdb=" O GLY A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 841 removed outlier: 3.774A pdb=" N SER A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 832 " --> pdb=" O GLY A 828 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 834 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 839 " --> pdb=" O GLN A 835 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 859 removed outlier: 3.665A pdb=" N GLU A 850 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 857 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 858 " --> pdb=" O ALA A 854 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 859 " --> pdb=" O GLY A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.929A pdb=" N VAL A 872 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 876 " --> pdb=" O VAL A 872 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 878 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.051A pdb=" N PHE A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 893 through 897 removed outlier: 4.024A pdb=" N PHE A 897 " --> pdb=" O PRO A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 908 removed outlier: 3.634A pdb=" N ARG A 908 " --> pdb=" O LEU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 927 Processing helix chain 'A' and resid 943 through 947 Processing helix chain 'A' and resid 951 through 963 removed outlier: 4.000A pdb=" N GLN A 955 " --> pdb=" O GLY A 951 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 959 " --> pdb=" O GLN A 955 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 978 removed outlier: 3.694A pdb=" N THR A 967 " --> pdb=" O PHE A 963 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 969 " --> pdb=" O SER A 965 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.841A pdb=" N PHE A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.587A pdb=" N ARG B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.109A pdb=" N LEU B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 44' Processing helix chain 'B' and resid 63 through 75 removed outlier: 3.519A pdb=" N ILE B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 4.348A pdb=" N ALA B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 removed outlier: 3.694A pdb=" N GLY B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 removed outlier: 3.732A pdb=" N ALA B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.695A pdb=" N LEU B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 176 through 192 removed outlier: 3.538A pdb=" N ARG B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 267 removed outlier: 3.549A pdb=" N TYR B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N CYS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.932A pdb=" N GLU B 301 " --> pdb=" O HIS B 297 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.542A pdb=" N GLN B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 316 " --> pdb=" O GLN B 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 316' Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.625A pdb=" N LEU B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.885A pdb=" N SER B 404 " --> pdb=" O PRO B 400 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 430 removed outlier: 3.589A pdb=" N ASP B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 458 through 473 removed outlier: 3.639A pdb=" N LYS B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.622A pdb=" N ARG B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 521 removed outlier: 3.673A pdb=" N GLY B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 515 " --> pdb=" O PRO B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 removed outlier: 3.725A pdb=" N LEU B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 removed outlier: 4.090A pdb=" N ARG B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 594 removed outlier: 3.684A pdb=" N ARG B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 588 " --> pdb=" O PRO B 584 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 removed outlier: 3.599A pdb=" N ASN B 608 " --> pdb=" O ARG B 605 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 609 " --> pdb=" O GLY B 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 605 through 609' Processing helix chain 'B' and resid 616 through 631 removed outlier: 3.774A pdb=" N THR B 620 " --> pdb=" O PRO B 616 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 622 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 628 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 629 " --> pdb=" O GLN B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 removed outlier: 3.905A pdb=" N ALA B 653 " --> pdb=" O PRO B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 694 removed outlier: 4.199A pdb=" N TYR B 685 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 686 " --> pdb=" O LEU B 682 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 691 " --> pdb=" O LYS B 687 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 694 " --> pdb=" O GLU B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 723 removed outlier: 3.954A pdb=" N ARG B 716 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 749 removed outlier: 4.043A pdb=" N TYR B 744 " --> pdb=" O GLN B 740 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP B 748 " --> pdb=" O TYR B 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS B 749 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 795 through 806 removed outlier: 3.522A pdb=" N LYS B 804 " --> pdb=" O GLU B 800 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 822 removed outlier: 4.067A pdb=" N VAL B 820 " --> pdb=" O THR B 817 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR B 821 " --> pdb=" O GLY B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 841 removed outlier: 3.514A pdb=" N SER B 831 " --> pdb=" O GLY B 827 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 835 " --> pdb=" O SER B 831 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 839 " --> pdb=" O GLN B 835 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 859 removed outlier: 3.860A pdb=" N ILE B 849 " --> pdb=" O ARG B 845 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 850 " --> pdb=" O PHE B 846 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 857 " --> pdb=" O TYR B 853 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 858 " --> pdb=" O ALA B 854 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 859 " --> pdb=" O GLY B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 884 removed outlier: 4.456A pdb=" N VAL B 872 " --> pdb=" O PRO B 868 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 873 " --> pdb=" O THR B 869 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 881 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 884 " --> pdb=" O LEU B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.272A pdb=" N PHE B 890 " --> pdb=" O SER B 886 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 893 through 897 removed outlier: 3.880A pdb=" N ARG B 896 " --> pdb=" O ASP B 893 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 897 " --> pdb=" O PRO B 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 893 through 897' Processing helix chain 'B' and resid 900 through 908 removed outlier: 3.640A pdb=" N ARG B 908 " --> pdb=" O LEU B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 927 Processing helix chain 'B' and resid 943 through 949 removed outlier: 3.545A pdb=" N LEU B 947 " --> pdb=" O ASP B 943 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 949 " --> pdb=" O ILE B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 963 removed outlier: 4.355A pdb=" N GLN B 955 " --> pdb=" O GLY B 951 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 956 " --> pdb=" O ALA B 952 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR B 957 " --> pdb=" O LYS B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 978 removed outlier: 3.686A pdb=" N THR B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 973 " --> pdb=" O GLU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 990 removed outlier: 3.627A pdb=" N PHE B 989 " --> pdb=" O ALA B 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 25 removed outlier: 3.589A pdb=" N PHE C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 4.261A pdb=" N LEU C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 44' Processing helix chain 'C' and resid 64 through 74 removed outlier: 3.713A pdb=" N ALA C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C 74 " --> pdb=" O THR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 removed outlier: 4.361A pdb=" N ALA C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 116 removed outlier: 3.815A pdb=" N LEU C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 126 removed outlier: 3.505A pdb=" N ILE C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 126' Processing helix chain 'C' and resid 140 through 148 removed outlier: 3.866A pdb=" N LEU C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 176 through 192 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.673A pdb=" N MET C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 258 " --> pdb=" O LYS C 254 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 260 " --> pdb=" O CYS C 256 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 267 " --> pdb=" O ALA C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 299 removed outlier: 4.378A pdb=" N THR C 298 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 308 through 316 removed outlier: 4.031A pdb=" N ARG C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 316 " --> pdb=" O GLN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.854A pdb=" N LEU C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 412 removed outlier: 3.712A pdb=" N VAL C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 430 removed outlier: 3.838A pdb=" N ASP C 430 " --> pdb=" O GLN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 437 removed outlier: 3.644A pdb=" N ALA C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 444 removed outlier: 4.381A pdb=" N ILE C 444 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.736A pdb=" N LEU C 450 " --> pdb=" O ARG C 447 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU C 451 " --> pdb=" O PRO C 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 447 through 451' Processing helix chain 'C' and resid 458 through 474 removed outlier: 4.108A pdb=" N LYS C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 466 " --> pdb=" O LYS C 462 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 470 " --> pdb=" O PHE C 466 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 489 removed outlier: 3.624A pdb=" N LEU C 489 " --> pdb=" O ASP C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.505A pdb=" N ARG C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 508 " --> pdb=" O GLN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 removed outlier: 3.576A pdb=" N ALA C 515 " --> pdb=" O PRO C 511 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 518 " --> pdb=" O PHE C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.693A pdb=" N LEU C 548 " --> pdb=" O ARG C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 557 removed outlier: 4.147A pdb=" N TYR C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG C 557 " --> pdb=" O PRO C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 577 removed outlier: 3.646A pdb=" N VAL C 575 " --> pdb=" O ALA C 571 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 576 " --> pdb=" O THR C 572 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 577 " --> pdb=" O TYR C 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 571 through 577' Processing helix chain 'C' and resid 583 through 595 removed outlier: 3.743A pdb=" N ARG C 587 " --> pdb=" O ASP C 583 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 588 " --> pdb=" O PRO C 584 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 594 " --> pdb=" O THR C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 616 through 631 removed outlier: 3.526A pdb=" N THR C 620 " --> pdb=" O PRO C 616 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 628 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 629 " --> pdb=" O GLN C 625 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 631 " --> pdb=" O ALA C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 653 removed outlier: 4.016A pdb=" N ALA C 653 " --> pdb=" O PRO C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 694 removed outlier: 4.177A pdb=" N TYR C 685 " --> pdb=" O THR C 681 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP C 694 " --> pdb=" O GLU C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 723 removed outlier: 3.597A pdb=" N SER C 719 " --> pdb=" O GLN C 715 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 720 " --> pdb=" O ARG C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 749 removed outlier: 3.719A pdb=" N TYR C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP C 748 " --> pdb=" O TYR C 744 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS C 749 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 776 Processing helix chain 'C' and resid 788 through 793 removed outlier: 4.043A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS C 793 " --> pdb=" O LEU C 789 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 788 through 793' Processing helix chain 'C' and resid 795 through 805 removed outlier: 3.585A pdb=" N ARG C 803 " --> pdb=" O TRP C 799 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 804 " --> pdb=" O GLU C 800 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 805 " --> pdb=" O ALA C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 822 removed outlier: 3.991A pdb=" N TYR C 821 " --> pdb=" O GLY C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 841 removed outlier: 3.750A pdb=" N SER C 831 " --> pdb=" O GLY C 827 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 832 " --> pdb=" O GLY C 828 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 835 " --> pdb=" O SER C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 860 removed outlier: 3.733A pdb=" N ILE C 849 " --> pdb=" O ARG C 845 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 850 " --> pdb=" O PHE C 846 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU C 851 " --> pdb=" O GLU C 847 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 854 " --> pdb=" O GLU C 850 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 859 " --> pdb=" O GLY C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.994A pdb=" N VAL C 872 " --> pdb=" O PRO C 868 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 878 " --> pdb=" O GLY C 874 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA C 879 " --> pdb=" O ASP C 875 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 881 " --> pdb=" O ALA C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 909 removed outlier: 3.519A pdb=" N LEU C 904 " --> pdb=" O PRO C 900 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY C 905 " --> pdb=" O GLU C 901 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C 906 " --> pdb=" O SER C 902 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 908 " --> pdb=" O LEU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 927 Processing helix chain 'C' and resid 943 through 947 Processing helix chain 'C' and resid 951 through 963 removed outlier: 4.111A pdb=" N GLN C 955 " --> pdb=" O GLY C 951 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 956 " --> pdb=" O ALA C 952 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 978 removed outlier: 3.640A pdb=" N THR C 967 " --> pdb=" O PHE C 963 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU C 969 " --> pdb=" O SER C 965 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE C 970 " --> pdb=" O PRO C 966 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 971 " --> pdb=" O THR C 967 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 25 removed outlier: 3.862A pdb=" N PHE D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 75 removed outlier: 3.573A pdb=" N ILE D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 4.358A pdb=" N ALA D 93 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 116 removed outlier: 3.559A pdb=" N LEU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN D 116 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 removed outlier: 3.696A pdb=" N ALA D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D 125 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 148 removed outlier: 3.854A pdb=" N LEU D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.591A pdb=" N GLU D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D 190 " --> pdb=" O ARG D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 267 removed outlier: 3.558A pdb=" N TYR D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 260 " --> pdb=" O CYS D 256 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 266 " --> pdb=" O PHE D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.554A pdb=" N HIS D 297 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR D 298 " --> pdb=" O VAL D 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 294 through 298' Processing helix chain 'D' and resid 299 through 304 removed outlier: 3.628A pdb=" N ILE D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.557A pdb=" N LEU D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 316 " --> pdb=" O GLN D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 325 removed outlier: 3.754A pdb=" N LEU D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.513A pdb=" N SER D 404 " --> pdb=" O PRO D 400 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 428 removed outlier: 3.541A pdb=" N VAL D 428 " --> pdb=" O PHE D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 437 removed outlier: 3.632A pdb=" N ALA D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 473 removed outlier: 4.448A pdb=" N LYS D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU D 464 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL D 470 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR D 471 " --> pdb=" O LEU D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 489 removed outlier: 3.585A pdb=" N LYS D 488 " --> pdb=" O PRO D 485 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 489 " --> pdb=" O ASP D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 520 removed outlier: 3.719A pdb=" N GLY D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 520 " --> pdb=" O ARG D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 540 Processing helix chain 'D' and resid 545 through 550 removed outlier: 4.019A pdb=" N ARG D 550 " --> pdb=" O SER D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 557 removed outlier: 3.946A pdb=" N ARG D 557 " --> pdb=" O PRO D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 577 removed outlier: 3.553A pdb=" N VAL D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 577 " --> pdb=" O TYR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 594 removed outlier: 3.732A pdb=" N ARG D 587 " --> pdb=" O ASP D 583 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 588 " --> pdb=" O PRO D 584 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 594 " --> pdb=" O THR D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 609 Processing helix chain 'D' and resid 616 through 631 removed outlier: 3.527A pdb=" N THR D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 628 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 629 " --> pdb=" O GLN D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 653 removed outlier: 3.854A pdb=" N MET D 647 " --> pdb=" O ASN D 643 " (cutoff:3.500A) Proline residue: D 649 - end of helix removed outlier: 3.900A pdb=" N ALA D 653 " --> pdb=" O PRO D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 694 removed outlier: 4.327A pdb=" N TYR D 685 " --> pdb=" O THR D 681 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 686 " --> pdb=" O LEU D 682 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 691 " --> pdb=" O LYS D 687 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP D 694 " --> pdb=" O GLU D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 723 removed outlier: 3.837A pdb=" N ARG D 716 " --> pdb=" O PRO D 712 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 720 " --> pdb=" O ARG D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 749 removed outlier: 3.993A pdb=" N TYR D 744 " --> pdb=" O GLN D 740 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP D 748 " --> pdb=" O TYR D 744 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS D 749 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 778 Processing helix chain 'D' and resid 795 through 806 removed outlier: 3.532A pdb=" N LYS D 804 " --> pdb=" O GLU D 800 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 805 " --> pdb=" O ALA D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 822 removed outlier: 4.245A pdb=" N VAL D 820 " --> pdb=" O THR D 817 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR D 821 " --> pdb=" O GLY D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 841 removed outlier: 3.664A pdb=" N SER D 831 " --> pdb=" O GLY D 827 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 832 " --> pdb=" O GLY D 828 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 835 " --> pdb=" O SER D 831 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 839 " --> pdb=" O GLN D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 860 removed outlier: 3.671A pdb=" N ILE D 849 " --> pdb=" O ARG D 845 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 851 " --> pdb=" O GLU D 847 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA D 854 " --> pdb=" O GLU D 850 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 884 removed outlier: 4.288A pdb=" N VAL D 872 " --> pdb=" O PRO D 868 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 873 " --> pdb=" O THR D 869 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 878 " --> pdb=" O GLY D 874 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA D 879 " --> pdb=" O ASP D 875 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 880 " --> pdb=" O LEU D 876 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 884 " --> pdb=" O LEU D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.130A pdb=" N PHE D 890 " --> pdb=" O SER D 886 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 891 " --> pdb=" O ALA D 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 886 through 891' Processing helix chain 'D' and resid 893 through 897 removed outlier: 3.983A pdb=" N ARG D 896 " --> pdb=" O ASP D 893 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE D 897 " --> pdb=" O PRO D 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 893 through 897' Processing helix chain 'D' and resid 900 through 909 removed outlier: 3.683A pdb=" N ARG D 908 " --> pdb=" O LEU D 904 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 909 " --> pdb=" O GLY D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 927 Processing helix chain 'D' and resid 943 through 947 Processing helix chain 'D' and resid 951 through 963 removed outlier: 4.262A pdb=" N GLN D 955 " --> pdb=" O GLY D 951 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 956 " --> pdb=" O ALA D 952 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR D 957 " --> pdb=" O LYS D 953 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE D 963 " --> pdb=" O ASN D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 978 removed outlier: 3.827A pdb=" N THR D 967 " --> pdb=" O PHE D 963 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU D 969 " --> pdb=" O SER D 965 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D 970 " --> pdb=" O PRO D 966 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 976 " --> pdb=" O GLU D 972 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.674A pdb=" N GLU A 47 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 49 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 32 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 29 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 7 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL A 31 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 78 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 79 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 159 Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 223 removed outlier: 3.573A pdb=" N ILE A 209 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 276 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 288 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 277 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE A 286 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 223 removed outlier: 4.944A pdb=" N SER A 230 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 239 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN A 232 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LYS A 237 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL A 238 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG A 341 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS A 394 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS A 340 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 392 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 342 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 390 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 528 removed outlier: 6.943A pdb=" N ASP A 528 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 601 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 602 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 636 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 635 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA A 665 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 637 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N CYS A 667 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 662 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS A 703 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N MET A 666 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 700 " --> pdb=" O HIS A 730 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N HIS A 732 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A 702 " --> pdb=" O HIS A 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 998 through 1001 removed outlier: 3.559A pdb=" N ILE A1010 " --> pdb=" O HIS A 998 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A1000 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1008 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A1013 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N MET A1027 " --> pdb=" O GLU A1013 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A1015 " --> pdb=" O THR A1025 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR A1025 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 998 through 1001 removed outlier: 3.559A pdb=" N ILE A1010 " --> pdb=" O HIS A 998 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A1000 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1008 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A1013 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N MET A1027 " --> pdb=" O GLU A1013 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A1015 " --> pdb=" O THR A1025 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR A1025 " --> pdb=" O ILE A1015 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A1026 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A1037 " --> pdb=" O VAL A1026 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.636A pdb=" N VAL B 29 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 7 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 78 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 79 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AB1, first strand: chain 'B' and resid 221 through 223 removed outlier: 3.793A pdb=" N ILE B 209 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 273 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 221 through 223 removed outlier: 4.471A pdb=" N HIS B 208 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER B 230 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE B 239 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN B 232 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LYS B 237 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL B 238 " --> pdb=" O ARG B 341 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B 341 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 342 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 390 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 391 " --> pdb=" O ASP B 372 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 372 " --> pdb=" O LYS B 391 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 345 through 346 removed outlier: 3.867A pdb=" N ARG B 352 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 527 through 528 removed outlier: 3.750A pdb=" N GLN B 601 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B 600 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ARG B 636 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N MET B 602 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE B 638 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B 604 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE B 635 " --> pdb=" O GLU B 663 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 665 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 637 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS B 667 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA B 701 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 664 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LYS B 703 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N MET B 666 " --> pdb=" O LYS B 703 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 732 " --> pdb=" O ILE B 702 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1000 through 1001 Processing sheet with id=AB6, first strand: chain 'B' and resid 1010 through 1015 removed outlier: 3.779A pdb=" N GLY B1011 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B1013 " --> pdb=" O MET B1027 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET B1027 " --> pdb=" O GLU B1013 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE B1015 " --> pdb=" O THR B1025 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR B1025 " --> pdb=" O ILE B1015 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG B1024 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B1039 " --> pdb=" O ARG B1024 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B1037 " --> pdb=" O VAL B1026 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N CYS B1028 " --> pdb=" O ARG B1035 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG B1035 " --> pdb=" O CYS B1028 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.716A pdb=" N GLU C 47 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 49 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR C 32 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 29 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 7 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL C 31 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LYS C 4 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR C 80 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU C 6 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 79 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 4.131A pdb=" N ARG C 169 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL C 157 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 158 " --> pdb=" O TYR C 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 221 through 223 removed outlier: 3.563A pdb=" N GLU C 210 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 227 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AC2, first strand: chain 'C' and resid 239 through 242 removed outlier: 3.505A pdb=" N CYS C 394 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 342 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL C 390 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 345 through 346 removed outlier: 3.532A pdb=" N ARG C 352 " --> pdb=" O ASP C 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 527 through 528 removed outlier: 6.856A pdb=" N ASP C 528 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 600 " --> pdb=" O ILE C 634 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ARG C 636 " --> pdb=" O LEU C 600 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET C 602 " --> pdb=" O ARG C 636 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE C 638 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU C 604 " --> pdb=" O PHE C 638 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP C 633 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLU C 663 " --> pdb=" O ASP C 633 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N PHE C 635 " --> pdb=" O GLU C 663 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA C 665 " --> pdb=" O PHE C 635 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE C 637 " --> pdb=" O ALA C 665 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N CYS C 667 " --> pdb=" O ILE C 637 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C 700 " --> pdb=" O HIS C 730 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N HIS C 732 " --> pdb=" O LEU C 700 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE C 702 " --> pdb=" O HIS C 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1010 through 1015 removed outlier: 7.675A pdb=" N MET C1027 " --> pdb=" O GLU C1013 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE C1015 " --> pdb=" O THR C1025 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR C1025 " --> pdb=" O ILE C1015 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C1024 " --> pdb=" O VAL C1039 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C1037 " --> pdb=" O VAL C1026 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N CYS C1028 " --> pdb=" O ARG C1035 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C1035 " --> pdb=" O CYS C1028 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.852A pdb=" N GLU D 47 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 30 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 31 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS D 4 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N TYR D 80 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU D 6 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 79 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 155 through 159 removed outlier: 4.087A pdb=" N LYS D 158 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR D 198 " --> pdb=" O LYS D 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 221 through 228 removed outlier: 5.033A pdb=" N GLN D 212 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU D 226 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU D 210 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP D 228 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N HIS D 208 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 209 " --> pdb=" O PHE D 276 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 239 through 242 removed outlier: 3.890A pdb=" N GLU D 240 " --> pdb=" O GLN D 339 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D 339 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS D 394 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 342 through 343 removed outlier: 3.938A pdb=" N VAL D 390 " --> pdb=" O ILE D 342 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 345 through 346 removed outlier: 3.638A pdb=" N ASP D 346 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 352 " --> pdb=" O ASP D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 527 through 528 removed outlier: 6.899A pdb=" N ASP D 528 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU D 600 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ARG D 636 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N MET D 602 " --> pdb=" O ARG D 636 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE D 638 " --> pdb=" O MET D 602 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU D 604 " --> pdb=" O PHE D 638 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 701 " --> pdb=" O VAL D 664 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS D 732 " --> pdb=" O ILE D 702 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1000 through 1003 removed outlier: 3.780A pdb=" N VAL D1000 " --> pdb=" O LEU D1008 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D1008 " --> pdb=" O VAL D1000 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D1006 " --> pdb=" O LEU D1002 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 1010 through 1015 removed outlier: 3.962A pdb=" N GLU D1013 " --> pdb=" O MET D1027 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N MET D1027 " --> pdb=" O GLU D1013 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE D1015 " --> pdb=" O THR D1025 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N THR D1025 " --> pdb=" O ILE D1015 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D1037 " --> pdb=" O VAL D1026 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS D1028 " --> pdb=" O ARG D1035 " (cutoff:3.500A) 806 hydrogen bonds defined for protein. 2307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.91 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9298 1.33 - 1.46: 7581 1.46 - 1.59: 14891 1.59 - 1.71: 0 1.71 - 1.84: 164 Bond restraints: 31934 Sorted by residual: bond pdb=" N VAL A 866 " pdb=" CA VAL A 866 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.08e-02 8.57e+03 1.02e+01 bond pdb=" CB ARG A 845 " pdb=" CG ARG A 845 " ideal model delta sigma weight residual 1.520 1.429 0.091 3.00e-02 1.11e+03 9.19e+00 bond pdb=" N ARG D 170 " pdb=" CA ARG D 170 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.17e-02 7.31e+03 8.13e+00 bond pdb=" N PRO C 480 " pdb=" CD PRO C 480 " ideal model delta sigma weight residual 1.473 1.510 -0.037 1.40e-02 5.10e+03 7.10e+00 bond pdb=" C PRO C 57 " pdb=" O PRO C 57 " ideal model delta sigma weight residual 1.238 1.207 0.031 1.22e-02 6.72e+03 6.48e+00 ... (remaining 31929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 42592 2.62 - 5.24: 700 5.24 - 7.86: 116 7.86 - 10.48: 19 10.48 - 13.10: 6 Bond angle restraints: 43433 Sorted by residual: angle pdb=" CA LYS D 508 " pdb=" CB LYS D 508 " pdb=" CG LYS D 508 " ideal model delta sigma weight residual 114.10 123.82 -9.72 2.00e+00 2.50e-01 2.36e+01 angle pdb=" C ASP A 893 " pdb=" CA ASP A 893 " pdb=" CB ASP A 893 " ideal model delta sigma weight residual 111.14 118.63 -7.49 1.56e+00 4.11e-01 2.30e+01 angle pdb=" CB GLN A 678 " pdb=" CG GLN A 678 " pdb=" CD GLN A 678 " ideal model delta sigma weight residual 112.60 119.75 -7.15 1.70e+00 3.46e-01 1.77e+01 angle pdb=" CB GLN B 678 " pdb=" CG GLN B 678 " pdb=" CD GLN B 678 " ideal model delta sigma weight residual 112.60 119.64 -7.04 1.70e+00 3.46e-01 1.71e+01 angle pdb=" C ALA B 752 " pdb=" N ASP B 753 " pdb=" CA ASP B 753 " ideal model delta sigma weight residual 122.17 115.84 6.33 1.54e+00 4.22e-01 1.69e+01 ... (remaining 43428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16830 17.99 - 35.97: 1848 35.97 - 53.96: 523 53.96 - 71.95: 68 71.95 - 89.93: 34 Dihedral angle restraints: 19303 sinusoidal: 7491 harmonic: 11812 Sorted by residual: dihedral pdb=" C ASP A 893 " pdb=" N ASP A 893 " pdb=" CA ASP A 893 " pdb=" CB ASP A 893 " ideal model delta harmonic sigma weight residual -122.60 -131.86 9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CA ASP D 372 " pdb=" CB ASP D 372 " pdb=" CG ASP D 372 " pdb=" OD1 ASP D 372 " ideal model delta sinusoidal sigma weight residual -30.00 -89.48 59.48 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP D 431 " pdb=" CB ASP D 431 " pdb=" CG ASP D 431 " pdb=" OD1 ASP D 431 " ideal model delta sinusoidal sigma weight residual -30.00 -87.74 57.74 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 19300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4096 0.065 - 0.129: 780 0.129 - 0.194: 37 0.194 - 0.258: 9 0.258 - 0.323: 2 Chirality restraints: 4924 Sorted by residual: chirality pdb=" CG LEU C 860 " pdb=" CB LEU C 860 " pdb=" CD1 LEU C 860 " pdb=" CD2 LEU C 860 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CG LEU A 842 " pdb=" CB LEU A 842 " pdb=" CD1 LEU A 842 " pdb=" CD2 LEU A 842 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CG LEU D 494 " pdb=" CB LEU D 494 " pdb=" CD1 LEU D 494 " pdb=" CD2 LEU D 494 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 4921 not shown) Planarity restraints: 5783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 240 " -0.022 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" CD GLU A 240 " 0.079 2.00e-02 2.50e+03 pdb=" OE1 GLU A 240 " -0.028 2.00e-02 2.50e+03 pdb=" OE2 GLU A 240 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 579 " -0.025 2.00e-02 2.50e+03 3.31e-02 1.92e+01 pdb=" CG PHE A 579 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 PHE A 579 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 579 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE A 579 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 579 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 579 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 156 " 0.033 2.00e-02 2.50e+03 2.87e-02 1.44e+01 pdb=" CG PHE A 156 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE A 156 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 156 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 156 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 156 " 0.007 2.00e-02 2.50e+03 ... (remaining 5780 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 786 2.71 - 3.26: 30036 3.26 - 3.80: 49760 3.80 - 4.35: 61096 4.35 - 4.90: 99397 Nonbonded interactions: 241075 Sorted by model distance: nonbonded pdb=" O ASN D 421 " pdb=" OD1 ASN D 421 " model vdw 2.160 3.040 nonbonded pdb=" O ASP A 893 " pdb=" OD1 ASP A 893 " model vdw 2.189 3.040 nonbonded pdb=" O ARG D 516 " pdb=" OE1 GLU D 520 " model vdw 2.301 3.040 nonbonded pdb=" O ASN C 421 " pdb=" OD1 ASN C 421 " model vdw 2.303 3.040 nonbonded pdb=" O GLU A 88 " pdb=" OE1 GLU A 88 " model vdw 2.356 3.040 ... (remaining 241070 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 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 1045)) selection = (chain 'B' and (resid 1 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 1045)) selection = (chain 'C' and (resid 1 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 1045)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.840 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 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 : 0.005 0.091 31934 Z= 0.225 Angle : 0.843 13.104 43433 Z= 0.445 Chirality : 0.049 0.323 4924 Planarity : 0.008 0.128 5783 Dihedral : 16.277 89.934 11735 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.51 % Favored : 92.41 % Rotamer: Outliers : 0.87 % Allowed : 25.41 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -4.12 (0.11), residues: 4112 helix: -3.07 (0.10), residues: 1496 sheet: -2.32 (0.22), residues: 480 loop : -2.55 (0.11), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG C 447 TYR 0.060 0.003 TYR C 268 PHE 0.074 0.003 PHE A 579 TRP 0.011 0.001 TRP D 517 HIS 0.021 0.002 HIS D 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.23 (31934) covalent geometry : angle 0.84271 / 0.44 (43433) hydrogen bonds : bond 0.24403 / 16.64 ( 797) hydrogen bonds : angle 8.71195 / 6.09 ( 2307) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 301 time to evaluate : 1.200 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8761 (tmtt) REVERT: A 236 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: B 133 MET cc_start: 0.3720 (mpp) cc_final: 0.3093 (mpp) REVERT: B 610 VAL cc_start: 0.8019 (m) cc_final: 0.7800 (m) REVERT: B 947 LEU cc_start: 0.8099 (mp) cc_final: 0.7764 (pp) REVERT: C 61 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.5678 (m-80) REVERT: C 133 MET cc_start: 0.2220 (mpp) cc_final: 0.1819 (mpp) REVERT: C 151 MET cc_start: 0.3253 (ttt) cc_final: 0.2783 (ttt) REVERT: C 226 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: C 298 THR cc_start: 0.8428 (p) cc_final: 0.8130 (t) REVERT: C 421 ASN cc_start: 0.8285 (t0) cc_final: 0.8076 (m110) REVERT: C 610 VAL cc_start: 0.8072 (m) cc_final: 0.7872 (m) REVERT: D 26 VAL cc_start: 0.2930 (OUTLIER) cc_final: 0.2710 (t) REVERT: D 151 MET cc_start: 0.0400 (ptp) cc_final: -0.0262 (ptm) REVERT: D 299 VAL cc_start: 0.7661 (p) cc_final: 0.7237 (p) REVERT: D 338 LEU cc_start: 0.9142 (pt) cc_final: 0.8797 (pp) REVERT: D 602 MET cc_start: 0.7781 (ppp) cc_final: 0.7470 (ppp) REVERT: D 604 LEU cc_start: 0.8090 (tt) cc_final: 0.7671 (tp) outliers start: 28 outliers final: 11 residues processed: 328 average time/residue: 0.2225 time to fit residues: 114.9664 Evaluate side-chains 199 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 1033 GLN Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 508 LYS Chi-restraints excluded: chain D residue 1042 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.0570 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 297 HIS ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN B 116 ASN B 730 HIS C 205 ASN C 265 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN D 730 HIS D 973 HIS ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.076667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.060341 restraints weight = 251363.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.061612 restraints weight = 152428.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.062360 restraints weight = 109346.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.062632 restraints weight = 89172.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.063004 restraints weight = 80124.358| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 31934 Z= 0.154 Angle : 0.626 8.946 43433 Z= 0.304 Chirality : 0.043 0.222 4924 Planarity : 0.004 0.055 5783 Dihedral : 3.754 55.286 4612 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 3.17 % Allowed : 21.47 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.87 (0.12), residues: 4112 helix: -1.80 (0.12), residues: 1532 sheet: -1.82 (0.23), residues: 484 loop : -1.96 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 166 TYR 0.020 0.001 TYR A 83 PHE 0.012 0.001 PHE A 531 TRP 0.015 0.001 TRP B 517 HIS 0.008 0.001 HIS D 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (31934) covalent geometry : angle 0.62620 / 0.30 (43433) hydrogen bonds : bond 0.04261 / 2.82 ( 797) hydrogen bonds : angle 5.91992 / 4.14 ( 2307) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 185 time to evaluate : 1.327 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: symmetry clash REVERT: A 595 MET cc_start: 0.7124 (mmt) cc_final: 0.6866 (tpp) REVERT: B 595 MET cc_start: 0.6976 (tpp) cc_final: 0.6584 (tpp) REVERT: B 947 LEU cc_start: 0.8547 (mp) cc_final: 0.8117 (pp) REVERT: C 226 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: C 255 MET cc_start: 0.9018 (ppp) cc_final: 0.8258 (ppp) REVERT: C 421 ASN cc_start: 0.9031 (t0) cc_final: 0.8743 (m-40) REVERT: C 595 MET cc_start: 0.6743 (mmp) cc_final: 0.6515 (tpp) REVERT: C 647 MET cc_start: 0.8153 (mmm) cc_final: 0.7820 (mmm) REVERT: C 684 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6308 (t80) REVERT: C 1033 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8365 (mp10) REVERT: D 255 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7999 (ptt) REVERT: D 388 MET cc_start: 0.8200 (mmm) cc_final: 0.7739 (mmp) REVERT: D 595 MET cc_start: 0.6952 (tpp) cc_final: 0.6722 (tpp) REVERT: D 602 MET cc_start: 0.8208 (ppp) cc_final: 0.7647 (ppp) REVERT: D 604 LEU cc_start: 0.8669 (tt) cc_final: 0.8240 (tp) REVERT: D 993 ARG cc_start: 0.9116 (mmm160) cc_final: 0.8761 (mmm-85) outliers start: 102 outliers final: 60 residues processed: 267 average time/residue: 0.1917 time to fit residues: 86.1194 Evaluate side-chains 215 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 782 GLU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 858 ARG Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 340 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 384 TYR Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 1026 VAL Chi-restraints excluded: chain C residue 1033 GLN Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 684 TYR Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 753 ASP Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 820 VAL Chi-restraints excluded: chain D residue 888 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 365 optimal weight: 4.9990 chunk 291 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 218 optimal weight: 40.0000 chunk 328 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 366 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 ASN ** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN B 597 ASN B 643 ASN ** B 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN C 328 GLN C 597 ASN C 691 GLN ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 ASN ** D 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.072885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.057453 restraints weight = 259427.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.058891 restraints weight = 175162.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.058786 restraints weight = 122937.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.059061 restraints weight = 102045.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.059215 restraints weight = 93068.186| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 31934 Z= 0.232 Angle : 0.724 8.538 43433 Z= 0.358 Chirality : 0.044 0.223 4924 Planarity : 0.005 0.042 5783 Dihedral : 3.996 57.584 4581 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 3.95 % Allowed : 21.50 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.19 (0.12), residues: 4112 helix: -1.01 (0.13), residues: 1568 sheet: -1.62 (0.21), residues: 584 loop : -1.69 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 495 TYR 0.015 0.002 TYR A 49 PHE 0.022 0.002 PHE D 989 TRP 0.022 0.002 TRP A 748 HIS 0.008 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (31934) covalent geometry : angle 0.72352 / 0.36 (43433) hydrogen bonds : bond 0.04426 / 2.91 ( 797) hydrogen bonds : angle 5.77168 / 4.07 ( 2307) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 142 time to evaluate : 1.235 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8646 (mm) REVERT: A 586 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8369 (pp20) REVERT: A 595 MET cc_start: 0.7387 (mmt) cc_final: 0.7024 (tpp) REVERT: A 610 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8487 (m) REVERT: A 661 ILE cc_start: 0.5962 (OUTLIER) cc_final: 0.5655 (mt) REVERT: A 889 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8892 (tp30) REVERT: B 236 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: B 340 CYS cc_start: 0.9317 (p) cc_final: 0.9030 (p) REVERT: B 573 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7813 (p90) REVERT: B 586 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8389 (pp20) REVERT: B 595 MET cc_start: 0.7090 (tpp) cc_final: 0.6478 (tpp) REVERT: B 782 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8818 (pm20) REVERT: B 947 LEU cc_start: 0.8569 (mp) cc_final: 0.8128 (pp) REVERT: C 151 MET cc_start: 0.5818 (ttt) cc_final: 0.5614 (ttt) REVERT: C 255 MET cc_start: 0.8994 (ppp) cc_final: 0.8362 (ppp) REVERT: C 256 CYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7301 (p) REVERT: C 421 ASN cc_start: 0.8938 (t0) cc_final: 0.8440 (m-40) REVERT: C 586 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8377 (pp20) REVERT: C 595 MET cc_start: 0.6922 (mmp) cc_final: 0.6545 (tpp) REVERT: C 684 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6670 (t80) REVERT: C 702 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.7037 (mt) REVERT: C 782 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8927 (pm20) REVERT: D 229 CYS cc_start: 0.6622 (m) cc_final: 0.5998 (m) REVERT: D 255 MET cc_start: 0.8498 (ptt) cc_final: 0.8175 (ptt) REVERT: D 595 MET cc_start: 0.7027 (tpp) cc_final: 0.6430 (tpp) REVERT: D 702 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7267 (mt) outliers start: 127 outliers final: 70 residues processed: 257 average time/residue: 0.1812 time to fit residues: 78.1518 Evaluate side-chains 215 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 130 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 889 GLU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 484 TYR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 573 TYR Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 782 GLU Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 1026 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 684 TYR Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 753 ASP Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 800 GLU Chi-restraints excluded: chain D residue 845 ARG Chi-restraints excluded: chain D residue 888 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 224 optimal weight: 50.0000 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 50.0000 chunk 390 optimal weight: 0.3980 chunk 128 optimal weight: 7.9990 chunk 357 optimal weight: 10.0000 chunk 201 optimal weight: 0.0770 chunk 254 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 chunk 21 optimal weight: 40.0000 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 973 HIS B 768 GLN C 465 ASN D 597 ASN ** D 768 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 = 0.3949 r_free = 0.3949 target = 0.074602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.058357 restraints weight = 252053.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.059489 restraints weight = 154399.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.060169 restraints weight = 114104.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.060446 restraints weight = 94892.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.060714 restraints weight = 86121.101| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31934 Z= 0.093 Angle : 0.539 8.727 43433 Z= 0.252 Chirality : 0.042 0.183 4924 Planarity : 0.003 0.041 5783 Dihedral : 3.142 34.339 4575 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 2.61 % Allowed : 22.86 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.67 (0.13), residues: 4112 helix: -0.52 (0.13), residues: 1584 sheet: -1.31 (0.22), residues: 584 loop : -1.46 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 408 TYR 0.020 0.001 TYR A 49 PHE 0.013 0.001 PHE C 413 TRP 0.017 0.001 TRP C 748 HIS 0.007 0.001 HIS B 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (31934) covalent geometry : angle 0.53937 / 0.25 (43433) hydrogen bonds : bond 0.02848 / 1.87 ( 797) hydrogen bonds : angle 5.04684 / 3.52 ( 2307) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 143 time to evaluate : 1.421 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: symmetry clash revert: symmetry clash REVERT: A 586 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8306 (pp20) REVERT: A 595 MET cc_start: 0.7349 (mmt) cc_final: 0.6808 (tpp) REVERT: A 875 ASP cc_start: 0.8699 (m-30) cc_final: 0.8345 (p0) REVERT: A 1023 MET cc_start: 0.9167 (tpp) cc_final: 0.8962 (tpp) REVERT: A 1041 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7391 (p0) REVERT: B 340 CYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9049 (p) REVERT: B 595 MET cc_start: 0.7052 (tpp) cc_final: 0.6277 (tpp) REVERT: B 947 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8023 (pp) REVERT: C 255 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8186 (ppp) REVERT: C 256 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7136 (p) REVERT: C 421 ASN cc_start: 0.8937 (t0) cc_final: 0.8337 (m110) REVERT: C 595 MET cc_start: 0.6847 (mmt) cc_final: 0.6402 (tpp) REVERT: C 684 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6646 (t80) REVERT: D 229 CYS cc_start: 0.6733 (m) cc_final: 0.6156 (m) REVERT: D 255 MET cc_start: 0.8490 (ptt) cc_final: 0.8182 (ptt) REVERT: D 595 MET cc_start: 0.7041 (tpp) cc_final: 0.6294 (tpp) outliers start: 84 outliers final: 45 residues processed: 211 average time/residue: 0.1769 time to fit residues: 63.3453 Evaluate side-chains 188 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 384 TYR Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 1026 VAL Chi-restraints excluded: chain C residue 1029 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 845 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 142 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 314 optimal weight: 0.0570 chunk 385 optimal weight: 7.9990 chunk 410 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 597 ASN C 601 GLN C 730 HIS D 597 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.072651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.056114 restraints weight = 258487.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.057137 restraints weight = 164229.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.057512 restraints weight = 123866.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.058081 restraints weight = 106788.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.058208 restraints weight = 95580.758| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 31934 Z= 0.170 Angle : 0.603 10.113 43433 Z= 0.289 Chirality : 0.042 0.218 4924 Planarity : 0.004 0.046 5783 Dihedral : 3.470 33.452 4575 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.23 % Favored : 94.75 % Rotamer: Outliers : 3.39 % Allowed : 22.52 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.35 (0.13), residues: 4112 helix: -0.22 (0.13), residues: 1592 sheet: -1.22 (0.21), residues: 604 loop : -1.28 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 227 TYR 0.019 0.001 TYR A 49 PHE 0.013 0.001 PHE D 989 TRP 0.021 0.002 TRP A 748 HIS 0.007 0.001 HIS D 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (31934) covalent geometry : angle 0.60333 / 0.29 (43433) hydrogen bonds : bond 0.03197 / 2.12 ( 797) hydrogen bonds : angle 5.22125 / 3.66 ( 2307) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 146 time to evaluate : 1.203 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8419 (mm) REVERT: A 169 ARG cc_start: 0.2293 (OUTLIER) cc_final: 0.2022 (ptp90) REVERT: A 586 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8257 (pp20) REVERT: A 595 MET cc_start: 0.7554 (mmt) cc_final: 0.7201 (tpp) REVERT: A 875 ASP cc_start: 0.8824 (m-30) cc_final: 0.8497 (p0) REVERT: A 1041 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7599 (p0) REVERT: B 236 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: B 340 CYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9094 (p) REVERT: B 586 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8275 (pp20) REVERT: B 782 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8883 (pm20) REVERT: B 947 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7984 (pp) REVERT: C 255 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8163 (ppp) REVERT: C 256 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7112 (p) REVERT: C 421 ASN cc_start: 0.8988 (t0) cc_final: 0.8753 (m-40) REVERT: C 586 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8252 (pp20) REVERT: C 595 MET cc_start: 0.6969 (mmt) cc_final: 0.6383 (tpp) REVERT: C 684 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6852 (t80) REVERT: C 702 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.7118 (mt) REVERT: C 740 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7911 (mm-40) REVERT: C 782 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8830 (pm20) REVERT: C 875 ASP cc_start: 0.8649 (m-30) cc_final: 0.8330 (p0) REVERT: D 16 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8865 (tpt170) REVERT: D 229 CYS cc_start: 0.7273 (m) cc_final: 0.6842 (m) REVERT: D 255 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8330 (ptt) REVERT: D 702 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7229 (mt) outliers start: 109 outliers final: 64 residues processed: 235 average time/residue: 0.1694 time to fit residues: 68.2043 Evaluate side-chains 225 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 142 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 782 GLU Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 740 GLN Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1029 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 800 GLU Chi-restraints excluded: chain D residue 845 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 55 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 333 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 354 optimal weight: 30.0000 chunk 56 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** D 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.072473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.056449 restraints weight = 260790.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.057501 restraints weight = 162982.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.057878 restraints weight = 120910.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.058380 restraints weight = 104624.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.058526 restraints weight = 93746.259| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 31934 Z= 0.146 Angle : 0.576 9.757 43433 Z= 0.276 Chirality : 0.042 0.191 4924 Planarity : 0.004 0.086 5783 Dihedral : 3.484 33.789 4575 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 3.36 % Allowed : 22.86 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.13), residues: 4112 helix: -0.24 (0.13), residues: 1644 sheet: -1.09 (0.22), residues: 604 loop : -1.19 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.016 0.001 TYR A 49 PHE 0.013 0.001 PHE D 989 TRP 0.023 0.002 TRP C 748 HIS 0.006 0.001 HIS B 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (31934) covalent geometry : angle 0.57621 / 0.28 (43433) hydrogen bonds : bond 0.02967 / 1.96 ( 797) hydrogen bonds : angle 5.06352 / 3.55 ( 2307) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 146 time to evaluate : 1.178 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 253 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8966 (t80) REVERT: A 586 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8232 (pp20) REVERT: A 595 MET cc_start: 0.7685 (mmt) cc_final: 0.7284 (tpp) REVERT: A 661 ILE cc_start: 0.6056 (OUTLIER) cc_final: 0.5773 (mt) REVERT: A 875 ASP cc_start: 0.8858 (m-30) cc_final: 0.8597 (p0) REVERT: A 1041 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7912 (p0) REVERT: B 236 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: B 340 CYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9088 (p) REVERT: B 388 MET cc_start: 0.8046 (mmt) cc_final: 0.7629 (mmt) REVERT: B 947 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7986 (pp) REVERT: C 255 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8139 (ppp) REVERT: C 256 CYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6991 (p) REVERT: C 421 ASN cc_start: 0.9031 (t0) cc_final: 0.8740 (m-40) REVERT: C 586 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8171 (pp20) REVERT: C 595 MET cc_start: 0.7042 (mmt) cc_final: 0.6458 (tpp) REVERT: C 702 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.7072 (mt) REVERT: C 740 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7958 (mm-40) REVERT: C 824 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: C 875 ASP cc_start: 0.8728 (m-30) cc_final: 0.8386 (p0) REVERT: D 16 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8800 (tpt170) REVERT: D 229 CYS cc_start: 0.7285 (m) cc_final: 0.6813 (m) REVERT: D 255 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8355 (ptt) REVERT: D 702 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7283 (mt) outliers start: 108 outliers final: 70 residues processed: 236 average time/residue: 0.1799 time to fit residues: 72.0170 Evaluate side-chains 229 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 142 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 740 GLN Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 824 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1029 ILE Chi-restraints excluded: chain C residue 1040 ARG Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 684 TYR Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 845 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 95 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 chunk 116 optimal weight: 50.0000 chunk 249 optimal weight: 0.9990 chunk 371 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 201 optimal weight: 0.0980 chunk 274 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 GLN A 691 GLN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** D 768 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 = 0.3882 r_free = 0.3882 target = 0.072223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.056232 restraints weight = 259636.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.057290 restraints weight = 162157.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.057801 restraints weight = 120813.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.058208 restraints weight = 103167.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.058316 restraints weight = 92611.856| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 31934 Z= 0.140 Angle : 0.580 11.958 43433 Z= 0.276 Chirality : 0.042 0.192 4924 Planarity : 0.004 0.048 5783 Dihedral : 3.515 34.245 4575 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 3.45 % Allowed : 23.05 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.14 (0.13), residues: 4112 helix: -0.16 (0.13), residues: 1684 sheet: -1.04 (0.22), residues: 584 loop : -1.11 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1035 TYR 0.013 0.001 TYR A 49 PHE 0.011 0.001 PHE D 989 TRP 0.024 0.002 TRP C 748 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (31934) covalent geometry : angle 0.58045 / 0.28 (43433) hydrogen bonds : bond 0.02900 / 1.92 ( 797) hydrogen bonds : angle 4.98963 / 3.50 ( 2307) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 144 time to evaluate : 1.222 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: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 253 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8955 (t80) REVERT: A 586 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8194 (pp20) REVERT: A 595 MET cc_start: 0.7687 (mmt) cc_final: 0.7051 (tpp) REVERT: A 875 ASP cc_start: 0.8784 (m-30) cc_final: 0.8549 (p0) REVERT: A 1041 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8015 (p0) REVERT: B 236 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: B 340 CYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9061 (p) REVERT: B 388 MET cc_start: 0.8061 (mmt) cc_final: 0.7714 (mmt) REVERT: B 586 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8151 (pp20) REVERT: B 782 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8947 (pm20) REVERT: B 947 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7991 (pp) REVERT: C 129 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7409 (tp) REVERT: C 255 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8136 (ppp) REVERT: C 256 CYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6901 (p) REVERT: C 586 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8171 (pp20) REVERT: C 595 MET cc_start: 0.7106 (mmt) cc_final: 0.6457 (tpp) REVERT: C 740 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7933 (mm-40) REVERT: C 771 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7813 (mt) REVERT: C 782 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8908 (pm20) REVERT: C 824 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: C 875 ASP cc_start: 0.8742 (m-30) cc_final: 0.8444 (p0) REVERT: D 16 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8773 (tpt170) REVERT: D 229 CYS cc_start: 0.7379 (m) cc_final: 0.6823 (m) REVERT: D 255 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8348 (ptt) REVERT: D 412 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8767 (mt-10) REVERT: D 702 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7216 (mt) outliers start: 111 outliers final: 78 residues processed: 237 average time/residue: 0.1765 time to fit residues: 72.1388 Evaluate side-chains 241 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 143 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 517 TRP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 782 GLU Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 740 GLN Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 824 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1026 VAL Chi-restraints excluded: chain C residue 1029 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 684 TYR Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 845 ARG Chi-restraints excluded: chain D residue 1008 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 328 optimal weight: 0.1980 chunk 43 optimal weight: 0.0070 chunk 333 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 chunk 175 optimal weight: 0.6980 chunk 111 optimal weight: 0.2980 chunk 326 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 38 optimal weight: 0.0870 chunk 190 optimal weight: 10.0000 chunk 343 optimal weight: 0.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 ASN C 994 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.074031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.058234 restraints weight = 255222.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.059353 restraints weight = 155902.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.059784 restraints weight = 112932.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.060344 restraints weight = 95185.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.060647 restraints weight = 85015.636| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31934 Z= 0.089 Angle : 0.562 10.414 43433 Z= 0.258 Chirality : 0.042 0.222 4924 Planarity : 0.003 0.048 5783 Dihedral : 3.086 34.466 4575 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.25 % Rotamer: Outliers : 1.77 % Allowed : 25.07 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 4112 helix: 0.05 (0.13), residues: 1644 sheet: -0.91 (0.23), residues: 524 loop : -1.02 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 252 TYR 0.014 0.001 TYR A 49 PHE 0.008 0.001 PHE D 970 TRP 0.015 0.001 TRP C 748 HIS 0.004 0.001 HIS B 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (31934) covalent geometry : angle 0.56214 / 0.26 (43433) hydrogen bonds : bond 0.02433 / 1.61 ( 797) hydrogen bonds : angle 4.54595 / 3.14 ( 2307) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 1.165 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: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8935 (t80) REVERT: A 595 MET cc_start: 0.7549 (mmt) cc_final: 0.6985 (tpp) REVERT: A 875 ASP cc_start: 0.8791 (m-30) cc_final: 0.8457 (p0) REVERT: B 236 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: B 340 CYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9057 (p) REVERT: B 388 MET cc_start: 0.7834 (mmt) cc_final: 0.7273 (mmt) REVERT: B 947 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7986 (pp) REVERT: C 156 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8724 (t80) REVERT: C 255 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7977 (ppp) REVERT: C 256 CYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6903 (p) REVERT: C 340 CYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 595 MET cc_start: 0.6966 (mmt) cc_final: 0.6470 (tpp) REVERT: C 875 ASP cc_start: 0.8638 (m-30) cc_final: 0.8329 (p0) REVERT: D 16 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8601 (tpt170) REVERT: D 229 CYS cc_start: 0.7078 (m) cc_final: 0.6583 (m) REVERT: D 255 MET cc_start: 0.8542 (ptt) cc_final: 0.8289 (ptt) outliers start: 57 outliers final: 37 residues processed: 195 average time/residue: 0.1725 time to fit residues: 58.6569 Evaluate side-chains 186 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 340 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 1026 VAL Chi-restraints excluded: chain C residue 1029 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 114 optimal weight: 9.9990 chunk 275 optimal weight: 7.9990 chunk 397 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 287 optimal weight: 0.0370 chunk 305 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 121 optimal weight: 50.0000 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS A 212 GLN C 994 GLN ** D 768 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 = 0.3889 r_free = 0.3889 target = 0.072487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.056696 restraints weight = 260215.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.057613 restraints weight = 162787.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.058159 restraints weight = 120792.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.058526 restraints weight = 102065.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.058875 restraints weight = 91717.148| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31934 Z= 0.130 Angle : 0.582 10.610 43433 Z= 0.273 Chirality : 0.042 0.228 4924 Planarity : 0.004 0.086 5783 Dihedral : 3.296 33.962 4575 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.50 % Favored : 95.48 % Rotamer: Outliers : 2.17 % Allowed : 24.98 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 4112 helix: -0.02 (0.13), residues: 1696 sheet: -0.85 (0.22), residues: 604 loop : -1.00 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 281 TYR 0.026 0.001 TYR A 83 PHE 0.011 0.001 PHE C 988 TRP 0.016 0.001 TRP C 748 HIS 0.003 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (31934) covalent geometry : angle 0.58153 / 0.27 (43433) hydrogen bonds : bond 0.02764 / 1.82 ( 797) hydrogen bonds : angle 4.77339 / 3.32 ( 2307) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 139 time to evaluate : 1.261 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: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8483 (mm) REVERT: A 253 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8881 (t80) REVERT: A 586 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8283 (pp20) REVERT: A 595 MET cc_start: 0.7627 (mmt) cc_final: 0.7201 (tpp) REVERT: A 661 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5765 (mt) REVERT: A 875 ASP cc_start: 0.8837 (m-30) cc_final: 0.8583 (p0) REVERT: A 890 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: A 1041 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7718 (p0) REVERT: B 236 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: B 388 MET cc_start: 0.7801 (mmt) cc_final: 0.7488 (mmt) REVERT: B 412 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8455 (mt-10) REVERT: B 586 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8230 (pp20) REVERT: B 647 MET cc_start: 0.8018 (mmt) cc_final: 0.7699 (mpp) REVERT: B 947 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7983 (pp) REVERT: C 156 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8685 (t80) REVERT: C 255 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8066 (ppp) REVERT: C 256 CYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6973 (p) REVERT: C 586 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8261 (pp20) REVERT: C 595 MET cc_start: 0.7021 (mmt) cc_final: 0.6382 (tpp) REVERT: C 875 ASP cc_start: 0.8734 (m-30) cc_final: 0.8481 (p0) REVERT: D 16 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8775 (tpt170) REVERT: D 229 CYS cc_start: 0.7274 (m) cc_final: 0.6557 (m) REVERT: D 255 MET cc_start: 0.8675 (ptt) cc_final: 0.8403 (ptt) outliers start: 70 outliers final: 45 residues processed: 195 average time/residue: 0.1674 time to fit residues: 57.1704 Evaluate side-chains 198 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 138 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 890 PHE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1026 VAL Chi-restraints excluded: chain C residue 1029 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 845 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 40 optimal weight: 9.9990 chunk 289 optimal weight: 7.9990 chunk 390 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 297 optimal weight: 0.1980 chunk 243 optimal weight: 8.9990 chunk 393 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** D 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.072170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.056244 restraints weight = 260439.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.057226 restraints weight = 162159.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.057961 restraints weight = 121514.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.058330 restraints weight = 100401.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.058448 restraints weight = 90446.271| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31934 Z= 0.132 Angle : 0.590 12.585 43433 Z= 0.277 Chirality : 0.042 0.234 4924 Planarity : 0.004 0.048 5783 Dihedral : 3.460 34.566 4575 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 1.86 % Allowed : 25.32 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 4112 helix: -0.09 (0.13), residues: 1724 sheet: -0.80 (0.22), residues: 596 loop : -0.98 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 37 TYR 0.016 0.001 TYR A 83 PHE 0.012 0.001 PHE D 989 TRP 0.023 0.002 TRP C 748 HIS 0.005 0.001 HIS D 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (31934) covalent geometry : angle 0.59012 / 0.28 (43433) hydrogen bonds : bond 0.02815 / 1.86 ( 797) hydrogen bonds : angle 4.80882 / 3.34 ( 2307) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 1.309 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: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8514 (mm) REVERT: A 253 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8849 (t80) REVERT: A 595 MET cc_start: 0.7703 (mmt) cc_final: 0.7053 (tpp) REVERT: A 661 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5738 (mt) REVERT: A 875 ASP cc_start: 0.8839 (m-30) cc_final: 0.8621 (p0) REVERT: A 890 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: A 1041 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7611 (p0) REVERT: B 236 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: B 586 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8145 (pp20) REVERT: B 647 MET cc_start: 0.8054 (mmt) cc_final: 0.7850 (mpp) REVERT: B 947 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8034 (pp) REVERT: C 156 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8666 (t80) REVERT: C 255 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8095 (ppp) REVERT: C 256 CYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6984 (p) REVERT: C 388 MET cc_start: 0.7599 (mmt) cc_final: 0.7319 (mmt) REVERT: C 586 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8217 (pp20) REVERT: C 595 MET cc_start: 0.7088 (mmt) cc_final: 0.6409 (tpp) REVERT: C 875 ASP cc_start: 0.8762 (m-30) cc_final: 0.8527 (p0) REVERT: D 16 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8728 (tpt170) REVERT: D 229 CYS cc_start: 0.7297 (m) cc_final: 0.6564 (m) REVERT: D 255 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8441 (ptt) outliers start: 60 outliers final: 44 residues processed: 188 average time/residue: 0.1706 time to fit residues: 56.2836 Evaluate side-chains 194 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 136 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 890 PHE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 971 ASN Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1029 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 845 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 311 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 212 optimal weight: 0.0270 chunk 14 optimal weight: 40.0000 chunk 253 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 chunk 347 optimal weight: 8.9990 chunk 374 optimal weight: 10.0000 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** D 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.072313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.056422 restraints weight = 260479.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.057413 restraints weight = 162112.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.058094 restraints weight = 121564.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.058329 restraints weight = 101251.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.058651 restraints weight = 92144.919| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31934 Z= 0.114 Angle : 0.578 11.042 43433 Z= 0.270 Chirality : 0.042 0.223 4924 Planarity : 0.004 0.066 5783 Dihedral : 3.379 34.190 4575 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 2.08 % Allowed : 25.10 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 4112 helix: -0.06 (0.13), residues: 1728 sheet: -0.79 (0.22), residues: 600 loop : -0.92 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 341 TYR 0.017 0.001 TYR A 83 PHE 0.009 0.001 PHE C 989 TRP 0.020 0.001 TRP C 748 HIS 0.004 0.001 HIS D 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (31934) covalent geometry : angle 0.57842 / 0.27 (43433) hydrogen bonds : bond 0.02680 / 1.77 ( 797) hydrogen bonds : angle 4.72831 / 3.28 ( 2307) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6151.45 seconds wall clock time: 106 minutes 43.30 seconds (6403.30 seconds total)