Starting phenix.real_space_refine on Mon Mar 25 00:47:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h64_6668/03_2024/5h64_6668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h64_6668/03_2024/5h64_6668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h64_6668/03_2024/5h64_6668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h64_6668/03_2024/5h64_6668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h64_6668/03_2024/5h64_6668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h64_6668/03_2024/5h64_6668.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 244 5.16 5 C 28458 2.51 5 N 8112 2.21 5 O 8438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 1698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 2225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 2421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45252 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2101, 15617 Classifications: {'peptide': 2101} Incomplete info: {'truncation_to_alanine': 371} Link IDs: {'CIS': 46, 'PTRANS': 89, 'TRANS': 1965} Chain breaks: 5 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1326 Unresolved non-hydrogen angles: 1681 Unresolved non-hydrogen dihedrals: 1105 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 26, 'ASP:plan': 23, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 7, 'HIS:plan': 11, 'PHE:plan': 13, 'GLU:plan': 30, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 702 Chain: "B" Number of atoms: 4553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 4553 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 733} Chain breaks: 14 Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 1832 Unresolved non-hydrogen angles: 2437 Unresolved non-hydrogen dihedrals: 1497 Unresolved non-hydrogen chiralities: 199 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 16, 'TYR:plan': 18, 'ASN:plan1': 27, 'TRP:plan': 13, 'ASP:plan': 37, 'PHE:plan': 26, 'GLU:plan': 33, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1034 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "a" Number of atoms: 15617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2101, 15617 Classifications: {'peptide': 2101} Incomplete info: {'truncation_to_alanine': 371} Link IDs: {'CIS': 46, 'PTRANS': 89, 'TRANS': 1965} Chain breaks: 5 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1326 Unresolved non-hydrogen angles: 1681 Unresolved non-hydrogen dihedrals: 1105 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 26, 'ASP:plan': 23, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 7, 'HIS:plan': 11, 'PHE:plan': 13, 'GLU:plan': 30, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 702 Chain: "b" Number of atoms: 4553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 4553 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 733} Chain breaks: 14 Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 1832 Unresolved non-hydrogen angles: 2437 Unresolved non-hydrogen dihedrals: 1505 Unresolved non-hydrogen chiralities: 199 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 16, 'TYR:plan': 18, 'ASN:plan1': 27, 'TRP:plan': 13, 'ASP:plan': 37, 'PHE:plan': 26, 'GLU:plan': 33, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1034 Chain: "c" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Time building chain proxies: 22.57, per 1000 atoms: 0.50 Number of scatterers: 45252 At special positions: 0 Unit cell: (304.424, 228.645, 150.252, 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 244 16.00 O 8438 8.00 N 8112 7.00 C 28458 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 - 3.50 Amino acid : False - 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: 21.24 Conformation dependent library (CDL) restraints added in 8.9 seconds 12684 Ramachandran restraints generated. 6342 Oldfield, 0 Emsley, 6342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12244 Finding SS restraints... Secondary structure from input PDB file: 322 helices and 38 sheets defined 61.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.69 Creating SS restraints... Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.011A pdb=" N CYS A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.653A pdb=" N GLN A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 removed outlier: 4.053A pdb=" N TRP A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 237 " --> pdb=" O TRP A 233 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.894A pdb=" N GLU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 4.240A pdb=" N ILE A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.531A pdb=" N MET A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.569A pdb=" N THR A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 341 through 346 removed outlier: 4.443A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 4.786A pdb=" N CYS A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 365 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 382 through 389 removed outlier: 4.091A pdb=" N SER A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 389 " --> pdb=" O ASN A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 389' Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.539A pdb=" N ARG A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 521 through 532 removed outlier: 5.306A pdb=" N ARG A 526 " --> pdb=" O TYR A 522 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Proline residue: A 529 - end of helix removed outlier: 4.158A pdb=" N LYS A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 removed outlier: 3.665A pdb=" N LEU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.388A pdb=" N THR A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 604 Processing helix chain 'A' and resid 609 through 619 removed outlier: 3.509A pdb=" N LYS A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 626 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 646 through 656 removed outlier: 4.164A pdb=" N GLN A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 676 removed outlier: 4.601A pdb=" N TYR A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 701 through 711 removed outlier: 3.650A pdb=" N ARG A 708 " --> pdb=" O VAL A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.749A pdb=" N ALA A 724 " --> pdb=" O SER A 720 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 735 through 748 removed outlier: 3.808A pdb=" N THR A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 752 Processing helix chain 'A' and resid 756 through 769 Proline residue: A 765 - end of helix Processing helix chain 'A' and resid 770 through 773 Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'A' and resid 794 through 801 Processing helix chain 'A' and resid 802 through 813 removed outlier: 3.659A pdb=" N GLU A 812 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 836 removed outlier: 3.784A pdb=" N MET A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 826 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 829 " --> pdb=" O MET A 825 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 842 Processing helix chain 'A' and resid 843 through 855 Processing helix chain 'A' and resid 861 through 874 removed outlier: 3.632A pdb=" N LEU A 865 " --> pdb=" O TYR A 861 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 866 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 871 " --> pdb=" O VAL A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 886 through 898 Proline residue: A 896 - end of helix Processing helix chain 'A' and resid 901 through 915 removed outlier: 4.178A pdb=" N GLN A 908 " --> pdb=" O GLY A 904 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 909 " --> pdb=" O MET A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 925 Processing helix chain 'A' and resid 935 through 941 Processing helix chain 'A' and resid 941 through 946 removed outlier: 4.053A pdb=" N GLU A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 966 removed outlier: 3.703A pdb=" N ARG A 957 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 960 " --> pdb=" O MET A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 987 Processing helix chain 'A' and resid 990 through 992 No H-bonds generated for 'chain 'A' and resid 990 through 992' Processing helix chain 'A' and resid 993 through 1007 removed outlier: 3.822A pdb=" N PHE A 997 " --> pdb=" O VAL A 993 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 999 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1026 removed outlier: 3.759A pdb=" N LEU A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1046 removed outlier: 5.382A pdb=" N THR A1036 " --> pdb=" O ASP A1032 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET A1038 " --> pdb=" O ILE A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1065 Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1076 through 1085 removed outlier: 4.090A pdb=" N ARG A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A1082 " --> pdb=" O MET A1078 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1091 No H-bonds generated for 'chain 'A' and resid 1089 through 1091' Processing helix chain 'A' and resid 1092 through 1105 removed outlier: 3.636A pdb=" N PHE A1103 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1121 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1127 through 1144 removed outlier: 3.909A pdb=" N SER A1131 " --> pdb=" O ALA A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1165 Proline residue: A1158 - end of helix removed outlier: 3.712A pdb=" N ARG A1161 " --> pdb=" O HIS A1157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1184 removed outlier: 4.343A pdb=" N SER A1171 " --> pdb=" O PRO A1167 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1189 removed outlier: 3.952A pdb=" N TYR A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1202 removed outlier: 3.809A pdb=" N VAL A1195 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A1200 " --> pdb=" O ASN A1196 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1222 Processing helix chain 'A' and resid 1256 through 1268 Processing helix chain 'A' and resid 1274 through 1291 Processing helix chain 'A' and resid 1296 through 1309 removed outlier: 3.597A pdb=" N CYS A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1316 Processing helix chain 'A' and resid 1317 through 1326 removed outlier: 4.156A pdb=" N ALA A1321 " --> pdb=" O LEU A1317 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A1322 " --> pdb=" O PHE A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1349 Processing helix chain 'A' and resid 1352 through 1369 Processing helix chain 'A' and resid 1377 through 1385 Processing helix chain 'A' and resid 1393 through 1407 Processing helix chain 'A' and resid 1409 through 1423 removed outlier: 3.658A pdb=" N SER A1418 " --> pdb=" O GLU A1414 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A1421 " --> pdb=" O ILE A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.588A pdb=" N LYS A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1454 Processing helix chain 'A' and resid 1455 through 1470 Processing helix chain 'A' and resid 1473 through 1487 Processing helix chain 'A' and resid 1490 through 1500 removed outlier: 3.611A pdb=" N CYS A1497 " --> pdb=" O LEU A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1523 removed outlier: 3.778A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1536 removed outlier: 3.547A pdb=" N TYR A1532 " --> pdb=" O SER A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 removed outlier: 3.608A pdb=" N TYR A1546 " --> pdb=" O ASP A1542 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1576 removed outlier: 3.912A pdb=" N THR A1576 " --> pdb=" O ASP A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 4.265A pdb=" N GLY A1580 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1603 Processing helix chain 'A' and resid 1610 through 1613 Processing helix chain 'A' and resid 1614 through 1625 Processing helix chain 'A' and resid 1629 through 1644 removed outlier: 4.229A pdb=" N TRP A1633 " --> pdb=" O ILE A1629 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A1643 " --> pdb=" O VAL A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1663 removed outlier: 3.516A pdb=" N ASP A1649 " --> pdb=" O SER A1645 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG A1651 " --> pdb=" O HIS A1647 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N THR A1652 " --> pdb=" O GLU A1648 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A1655 " --> pdb=" O ARG A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 removed outlier: 4.113A pdb=" N ALA A1669 " --> pdb=" O ARG A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1707 Processing helix chain 'A' and resid 1710 through 1732 removed outlier: 3.598A pdb=" N MET A1717 " --> pdb=" O ALA A1713 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A1718 " --> pdb=" O PHE A1714 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A1729 " --> pdb=" O GLN A1725 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS A1730 " --> pdb=" O GLN A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1763 removed outlier: 3.873A pdb=" N LEU A1743 " --> pdb=" O HIS A1739 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A1745 " --> pdb=" O GLN A1741 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A1755 " --> pdb=" O PHE A1751 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A1763 " --> pdb=" O LEU A1759 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1783 Processing helix chain 'A' and resid 1788 through 1809 removed outlier: 3.629A pdb=" N ALA A1794 " --> pdb=" O TRP A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1896 Proline residue: A1883 - end of helix removed outlier: 3.846A pdb=" N LEU A1894 " --> pdb=" O ARG A1890 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A1896 " --> pdb=" O ILE A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1911 Processing helix chain 'A' and resid 1916 through 1930 removed outlier: 3.926A pdb=" N VAL A1927 " --> pdb=" O LEU A1923 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS A1928 " --> pdb=" O VAL A1924 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A1929 " --> pdb=" O GLU A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1945 removed outlier: 3.954A pdb=" N VAL A1938 " --> pdb=" O THR A1934 " (cutoff:3.500A) Proline residue: A1940 - end of helix Processing helix chain 'A' and resid 1946 through 1948 No H-bonds generated for 'chain 'A' and resid 1946 through 1948' Processing helix chain 'A' and resid 1950 through 1965 removed outlier: 4.256A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1980 removed outlier: 4.201A pdb=" N LEU A1972 " --> pdb=" O HIS A1968 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR A1974 " --> pdb=" O GLN A1970 " (cutoff:3.500A) Proline residue: A1975 - end of helix Processing helix chain 'A' and resid 1984 through 2021 removed outlier: 4.358A pdb=" N HIS A1988 " --> pdb=" O THR A1984 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A2002 " --> pdb=" O MET A1998 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR A2004 " --> pdb=" O GLU A2000 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A2005 " --> pdb=" O HIS A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2040 Processing helix chain 'A' and resid 2044 through 2060 removed outlier: 3.998A pdb=" N GLU A2049 " --> pdb=" O LYS A2045 " (cutoff:3.500A) Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2064 through 2074 Processing helix chain 'A' and resid 2074 through 2092 removed outlier: 3.968A pdb=" N LEU A2078 " --> pdb=" O TYR A2074 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A2083 " --> pdb=" O MET A2079 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP A2084 " --> pdb=" O GLU A2080 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2115 removed outlier: 3.750A pdb=" N LEU A2097 " --> pdb=" O ASN A2093 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A2113 " --> pdb=" O ARG A2109 " (cutoff:3.500A) Processing helix chain 'A' and resid 2127 through 2133 removed outlier: 3.727A pdb=" N CYS A2133 " --> pdb=" O LYS A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2212 removed outlier: 3.902A pdb=" N GLN A2200 " --> pdb=" O GLU A2196 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A2203 " --> pdb=" O MET A2199 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A2204 " --> pdb=" O GLN A2200 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A2212 " --> pdb=" O LEU A2208 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2219 Processing helix chain 'A' and resid 2245 through 2257 removed outlier: 3.655A pdb=" N LEU A2249 " --> pdb=" O THR A2245 " (cutoff:3.500A) Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2274 through 2278 Processing helix chain 'A' and resid 2279 through 2293 Processing helix chain 'A' and resid 2297 through 2307 removed outlier: 3.845A pdb=" N LEU A2302 " --> pdb=" O ASP A2298 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2334 removed outlier: 3.739A pdb=" N MET A2327 " --> pdb=" O SER A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2363 through 2368 Processing helix chain 'A' and resid 2380 through 2387 removed outlier: 3.737A pdb=" N MET A2387 " --> pdb=" O LEU A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2423 removed outlier: 3.597A pdb=" N ARG A2408 " --> pdb=" O MET A2404 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A2409 " --> pdb=" O GLU A2405 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP A2412 " --> pdb=" O ARG A2408 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER A2413 " --> pdb=" O GLU A2409 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A2416 " --> pdb=" O ASP A2412 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A2417 " --> pdb=" O SER A2413 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A2421 " --> pdb=" O VAL A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2424 through 2429 Processing helix chain 'A' and resid 2429 through 2435 Processing helix chain 'A' and resid 2493 through 2510 removed outlier: 4.263A pdb=" N ILE A2500 " --> pdb=" O LYS A2496 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A2501 " --> pdb=" O ALA A2497 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN A2502 " --> pdb=" O ILE A2498 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A2503 " --> pdb=" O GLN A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2534 removed outlier: 3.510A pdb=" N GLN A2524 " --> pdb=" O ASP A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2534 through 2541 Processing helix chain 'B' and resid 98 through 113 removed outlier: 3.782A pdb=" N GLY B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.861A pdb=" N ASP B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 345 through 351 removed outlier: 4.276A pdb=" N LEU B 351 " --> pdb=" O PHE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 382 through 402 removed outlier: 4.113A pdb=" N VAL B 386 " --> pdb=" O TRP B 382 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 4.167A pdb=" N ILE B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 removed outlier: 3.785A pdb=" N LEU B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 removed outlier: 3.733A pdb=" N VAL B 424 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 466 removed outlier: 3.672A pdb=" N GLY B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Proline residue: B 461 - end of helix removed outlier: 3.800A pdb=" N SER B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 removed outlier: 4.572A pdb=" N SER B 482 " --> pdb=" O LYS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.977A pdb=" N SER B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 524 Processing helix chain 'B' and resid 529 through 537 Processing helix chain 'B' and resid 537 through 546 removed outlier: 3.878A pdb=" N ASN B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 601 removed outlier: 3.846A pdb=" N SER B 590 " --> pdb=" O GLN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 609 Processing helix chain 'B' and resid 610 through 621 removed outlier: 4.322A pdb=" N ALA B 618 " --> pdb=" O GLU B 614 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B 621 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 629 through 636 removed outlier: 4.021A pdb=" N THR B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N HIS B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.953A pdb=" N ILE B 640 " --> pdb=" O HIS B 636 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 666 removed outlier: 3.839A pdb=" N ASP B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Proline residue: B 657 - end of helix removed outlier: 3.691A pdb=" N LYS B 661 " --> pdb=" O PRO B 657 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 663 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 664 " --> pdb=" O ARG B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 680 removed outlier: 3.749A pdb=" N SER B 676 " --> pdb=" O VAL B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 694 removed outlier: 4.678A pdb=" N ALA B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 694 " --> pdb=" O LYS B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 704 Processing helix chain 'B' and resid 709 through 724 Proline residue: B 715 - end of helix removed outlier: 3.833A pdb=" N SER B 719 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 741 removed outlier: 3.624A pdb=" N SER B 734 " --> pdb=" O ALA B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 758 removed outlier: 4.968A pdb=" N SER B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Proline residue: B 756 - end of helix Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.562A pdb=" N SER C 269 " --> pdb=" O GLY C 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 211 through 216 removed outlier: 4.011A pdb=" N CYS a 216 " --> pdb=" O ALA a 212 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 222 removed outlier: 3.653A pdb=" N GLN a 222 " --> pdb=" O ILE a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 229 through 242 removed outlier: 4.053A pdb=" N TRP a 233 " --> pdb=" O GLN a 229 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR a 237 " --> pdb=" O TRP a 233 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE a 238 " --> pdb=" O TYR a 234 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU a 239 " --> pdb=" O ARG a 235 " (cutoff:3.500A) Processing helix chain 'a' and resid 247 through 254 Processing helix chain 'a' and resid 265 through 278 removed outlier: 3.893A pdb=" N GLU a 270 " --> pdb=" O LEU a 266 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU a 278 " --> pdb=" O ILE a 274 " (cutoff:3.500A) Processing helix chain 'a' and resid 285 through 294 removed outlier: 4.239A pdb=" N ILE a 289 " --> pdb=" O GLU a 285 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN a 292 " --> pdb=" O GLU a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 300 through 305 removed outlier: 3.532A pdb=" N MET a 304 " --> pdb=" O CYS a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 314 removed outlier: 3.568A pdb=" N THR a 314 " --> pdb=" O PRO a 310 " (cutoff:3.500A) Processing helix chain 'a' and resid 318 through 326 Proline residue: a 324 - end of helix Processing helix chain 'a' and resid 336 through 341 Processing helix chain 'a' and resid 341 through 346 removed outlier: 4.442A pdb=" N GLY a 346 " --> pdb=" O LEU a 342 " (cutoff:3.500A) Processing helix chain 'a' and resid 355 through 367 removed outlier: 4.787A pdb=" N CYS a 361 " --> pdb=" O VAL a 357 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS a 362 " --> pdb=" O GLU a 358 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP a 364 " --> pdb=" O ARG a 360 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU a 365 " --> pdb=" O CYS a 361 " (cutoff:3.500A) Processing helix chain 'a' and resid 377 through 382 Processing helix chain 'a' and resid 382 through 389 removed outlier: 4.091A pdb=" N SER a 386 " --> pdb=" O ASN a 382 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU a 387 " --> pdb=" O SER a 383 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE a 388 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN a 389 " --> pdb=" O ASN a 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 382 through 389' Processing helix chain 'a' and resid 394 through 400 removed outlier: 3.538A pdb=" N ARG a 398 " --> pdb=" O ASN a 394 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 422 Processing helix chain 'a' and resid 521 through 532 removed outlier: 5.306A pdb=" N ARG a 526 " --> pdb=" O TYR a 522 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN a 527 " --> pdb=" O ASP a 523 " (cutoff:3.500A) Proline residue: a 529 - end of helix removed outlier: 4.158A pdb=" N LYS a 532 " --> pdb=" O ILE a 528 " (cutoff:3.500A) Processing helix chain 'a' and resid 539 through 548 removed outlier: 3.665A pdb=" N LEU a 543 " --> pdb=" O LEU a 539 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER a 544 " --> pdb=" O LEU a 540 " (cutoff:3.500A) Processing helix chain 'a' and resid 549 through 554 Processing helix chain 'a' and resid 558 through 565 Processing helix chain 'a' and resid 575 through 587 removed outlier: 4.389A pdb=" N THR a 583 " --> pdb=" O VAL a 579 " (cutoff:3.500A) Processing helix chain 'a' and resid 593 through 604 Processing helix chain 'a' and resid 609 through 619 removed outlier: 3.509A pdb=" N LYS a 616 " --> pdb=" O ASN a 612 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU a 617 " --> pdb=" O SER a 613 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE a 618 " --> pdb=" O GLU a 614 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG a 619 " --> pdb=" O HIS a 615 " (cutoff:3.500A) Processing helix chain 'a' and resid 619 through 626 Processing helix chain 'a' and resid 631 through 638 Processing helix chain 'a' and resid 646 through 656 removed outlier: 4.165A pdb=" N GLN a 650 " --> pdb=" O GLN a 646 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU a 656 " --> pdb=" O VAL a 652 " (cutoff:3.500A) Processing helix chain 'a' and resid 666 through 676 removed outlier: 4.601A pdb=" N TYR a 673 " --> pdb=" O PRO a 669 " (cutoff:3.500A) Processing helix chain 'a' and resid 682 through 697 Processing helix chain 'a' and resid 701 through 711 removed outlier: 3.650A pdb=" N ARG a 708 " --> pdb=" O VAL a 704 " (cutoff:3.500A) Processing helix chain 'a' and resid 720 through 731 removed outlier: 3.749A pdb=" N ALA a 724 " --> pdb=" O SER a 720 " (cutoff:3.500A) Proline residue: a 728 - end of helix Processing helix chain 'a' and resid 735 through 748 removed outlier: 3.808A pdb=" N THR a 739 " --> pdb=" O ILE a 735 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU a 742 " --> pdb=" O LEU a 738 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER a 744 " --> pdb=" O GLU a 740 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG a 748 " --> pdb=" O SER a 744 " (cutoff:3.500A) Processing helix chain 'a' and resid 749 through 752 Processing helix chain 'a' and resid 756 through 769 Proline residue: a 765 - end of helix Processing helix chain 'a' and resid 770 through 773 Processing helix chain 'a' and resid 779 through 785 Processing helix chain 'a' and resid 794 through 801 Processing helix chain 'a' and resid 802 through 813 removed outlier: 3.658A pdb=" N GLU a 812 " --> pdb=" O VAL a 808 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET a 813 " --> pdb=" O SER a 809 " (cutoff:3.500A) Processing helix chain 'a' and resid 821 through 836 removed outlier: 3.784A pdb=" N MET a 825 " --> pdb=" O PHE a 821 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP a 826 " --> pdb=" O ILE a 822 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET a 827 " --> pdb=" O ILE a 823 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU a 828 " --> pdb=" O ILE a 824 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN a 829 " --> pdb=" O MET a 825 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU a 834 " --> pdb=" O ASP a 830 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA a 835 " --> pdb=" O SER a 831 " (cutoff:3.500A) Processing helix chain 'a' and resid 837 through 842 Processing helix chain 'a' and resid 843 through 855 Processing helix chain 'a' and resid 861 through 874 removed outlier: 3.633A pdb=" N LEU a 865 " --> pdb=" O TYR a 861 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU a 866 " --> pdb=" O PRO a 862 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU a 869 " --> pdb=" O LEU a 865 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN a 870 " --> pdb=" O GLU a 866 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE a 871 " --> pdb=" O VAL a 867 " (cutoff:3.500A) Processing helix chain 'a' and resid 879 through 884 Processing helix chain 'a' and resid 886 through 898 Proline residue: a 896 - end of helix Processing helix chain 'a' and resid 901 through 915 removed outlier: 4.177A pdb=" N GLN a 908 " --> pdb=" O GLY a 904 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER a 909 " --> pdb=" O MET a 905 " (cutoff:3.500A) Processing helix chain 'a' and resid 920 through 925 Processing helix chain 'a' and resid 935 through 941 Processing helix chain 'a' and resid 941 through 946 removed outlier: 4.054A pdb=" N GLU a 945 " --> pdb=" O LEU a 941 " (cutoff:3.500A) Processing helix chain 'a' and resid 947 through 966 removed outlier: 3.703A pdb=" N ARG a 957 " --> pdb=" O VAL a 953 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE a 958 " --> pdb=" O ALA a 954 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE a 959 " --> pdb=" O LEU a 955 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG a 960 " --> pdb=" O MET a 956 " (cutoff:3.500A) Processing helix chain 'a' and resid 972 through 987 Processing helix chain 'a' and resid 990 through 992 No H-bonds generated for 'chain 'a' and resid 990 through 992' Processing helix chain 'a' and resid 993 through 1007 removed outlier: 3.822A pdb=" N PHE a 997 " --> pdb=" O VAL a 993 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU a 998 " --> pdb=" O MET a 994 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN a 999 " --> pdb=" O PRO a 995 " (cutoff:3.500A) Processing helix chain 'a' and resid 1008 through 1026 removed outlier: 3.758A pdb=" N LEU a1012 " --> pdb=" O ILE a1008 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER a1021 " --> pdb=" O GLY a1017 " (cutoff:3.500A) Processing helix chain 'a' and resid 1030 through 1046 removed outlier: 5.382A pdb=" N THR a1036 " --> pdb=" O ASP a1032 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU a1037 " --> pdb=" O GLU a1033 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET a1038 " --> pdb=" O ILE a1034 " (cutoff:3.500A) Processing helix chain 'a' and resid 1049 through 1065 Processing helix chain 'a' and resid 1069 through 1074 Processing helix chain 'a' and resid 1076 through 1085 removed outlier: 4.090A pdb=" N ARG a1080 " --> pdb=" O PRO a1076 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE a1082 " --> pdb=" O MET a1078 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET a1083 " --> pdb=" O LEU a1079 " (cutoff:3.500A) Processing helix chain 'a' and resid 1089 through 1091 No H-bonds generated for 'chain 'a' and resid 1089 through 1091' Processing helix chain 'a' and resid 1092 through 1105 removed outlier: 3.636A pdb=" N PHE a1103 " --> pdb=" O ALA a1099 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY a1104 " --> pdb=" O ILE a1100 " (cutoff:3.500A) Processing helix chain 'a' and resid 1110 through 1121 Proline residue: a1116 - end of helix Processing helix chain 'a' and resid 1127 through 1144 removed outlier: 3.909A pdb=" N SER a1131 " --> pdb=" O ALA a1127 " (cutoff:3.500A) Processing helix chain 'a' and resid 1152 through 1165 Proline residue: a1158 - end of helix removed outlier: 3.712A pdb=" N ARG a1161 " --> pdb=" O HIS a1157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU a1163 " --> pdb=" O ILE a1159 " (cutoff:3.500A) Processing helix chain 'a' and resid 1167 through 1184 removed outlier: 4.343A pdb=" N SER a1171 " --> pdb=" O PRO a1167 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR a1172 " --> pdb=" O GLU a1168 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN a1183 " --> pdb=" O SER a1179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU a1184 " --> pdb=" O LEU a1180 " (cutoff:3.500A) Processing helix chain 'a' and resid 1184 through 1189 removed outlier: 3.953A pdb=" N TYR a1188 " --> pdb=" O LEU a1184 " (cutoff:3.500A) Processing helix chain 'a' and resid 1191 through 1202 removed outlier: 3.809A pdb=" N VAL a1195 " --> pdb=" O PHE a1191 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL a1200 " --> pdb=" O ASN a1196 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG a1201 " --> pdb=" O LYS a1197 " (cutoff:3.500A) Processing helix chain 'a' and resid 1207 through 1222 Processing helix chain 'a' and resid 1256 through 1268 Processing helix chain 'a' and resid 1274 through 1291 Processing helix chain 'a' and resid 1296 through 1309 removed outlier: 3.597A pdb=" N CYS a1303 " --> pdb=" O SER a1299 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP a1304 " --> pdb=" O LEU a1300 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA a1305 " --> pdb=" O ARG a1301 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA a1309 " --> pdb=" O ALA a1305 " (cutoff:3.500A) Processing helix chain 'a' and resid 1310 through 1316 Processing helix chain 'a' and resid 1317 through 1326 removed outlier: 4.156A pdb=" N ALA a1321 " --> pdb=" O LEU a1317 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE a1322 " --> pdb=" O PHE a1318 " (cutoff:3.500A) Processing helix chain 'a' and resid 1329 through 1349 Processing helix chain 'a' and resid 1352 through 1369 Processing helix chain 'a' and resid 1377 through 1385 Processing helix chain 'a' and resid 1393 through 1407 Processing helix chain 'a' and resid 1409 through 1423 removed outlier: 3.658A pdb=" N SER a1418 " --> pdb=" O GLU a1414 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN a1421 " --> pdb=" O ILE a1417 " (cutoff:3.500A) Processing helix chain 'a' and resid 1425 through 1440 removed outlier: 3.588A pdb=" N LYS a1438 " --> pdb=" O GLU a1434 " (cutoff:3.500A) Processing helix chain 'a' and resid 1445 through 1454 Processing helix chain 'a' and resid 1455 through 1470 Processing helix chain 'a' and resid 1473 through 1487 Processing helix chain 'a' and resid 1490 through 1500 removed outlier: 3.612A pdb=" N CYS a1497 " --> pdb=" O LEU a1493 " (cutoff:3.500A) Processing helix chain 'a' and resid 1505 through 1523 removed outlier: 3.778A pdb=" N ARG a1514 " --> pdb=" O ALA a1510 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET a1515 " --> pdb=" O LYS a1511 " (cutoff:3.500A) Processing helix chain 'a' and resid 1526 through 1536 removed outlier: 3.546A pdb=" N TYR a1532 " --> pdb=" O SER a1528 " (cutoff:3.500A) Processing helix chain 'a' and resid 1540 through 1554 removed outlier: 3.608A pdb=" N TYR a1546 " --> pdb=" O ASP a1542 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG a1547 " --> pdb=" O GLY a1543 " (cutoff:3.500A) Processing helix chain 'a' and resid 1557 through 1576 removed outlier: 3.911A pdb=" N THR a1576 " --> pdb=" O ASP a1572 " (cutoff:3.500A) Processing helix chain 'a' and resid 1577 through 1581 removed outlier: 4.265A pdb=" N GLY a1580 " --> pdb=" O ALA a1577 " (cutoff:3.500A) Processing helix chain 'a' and resid 1585 through 1603 Processing helix chain 'a' and resid 1610 through 1613 Processing helix chain 'a' and resid 1614 through 1625 Processing helix chain 'a' and resid 1629 through 1644 removed outlier: 4.228A pdb=" N TRP a1633 " --> pdb=" O ILE a1629 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL a1643 " --> pdb=" O VAL a1639 " (cutoff:3.500A) Processing helix chain 'a' and resid 1645 through 1663 removed outlier: 3.516A pdb=" N ASP a1649 " --> pdb=" O SER a1645 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG a1651 " --> pdb=" O HIS a1647 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N THR a1652 " --> pdb=" O GLU a1648 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS a1655 " --> pdb=" O ARG a1651 " (cutoff:3.500A) Processing helix chain 'a' and resid 1665 through 1678 removed outlier: 4.113A pdb=" N ALA a1669 " --> pdb=" O ARG a1665 " (cutoff:3.500A) Processing helix chain 'a' and resid 1693 through 1707 Processing helix chain 'a' and resid 1710 through 1732 removed outlier: 3.598A pdb=" N MET a1717 " --> pdb=" O ALA a1713 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN a1718 " --> pdb=" O PHE a1714 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN a1729 " --> pdb=" O GLN a1725 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS a1730 " --> pdb=" O GLN a1726 " (cutoff:3.500A) Processing helix chain 'a' and resid 1737 through 1763 removed outlier: 3.873A pdb=" N LEU a1743 " --> pdb=" O HIS a1739 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS a1745 " --> pdb=" O GLN a1741 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY a1755 " --> pdb=" O PHE a1751 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY a1763 " --> pdb=" O LEU a1759 " (cutoff:3.500A) Processing helix chain 'a' and resid 1767 through 1783 Processing helix chain 'a' and resid 1788 through 1809 removed outlier: 3.630A pdb=" N ALA a1794 " --> pdb=" O TRP a1790 " (cutoff:3.500A) Processing helix chain 'a' and resid 1868 through 1896 Proline residue: a1883 - end of helix removed outlier: 3.847A pdb=" N LEU a1894 " --> pdb=" O ARG a1890 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG a1896 " --> pdb=" O ILE a1892 " (cutoff:3.500A) Processing helix chain 'a' and resid 1899 through 1911 Processing helix chain 'a' and resid 1916 through 1930 removed outlier: 3.926A pdb=" N VAL a1927 " --> pdb=" O LEU a1923 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS a1928 " --> pdb=" O VAL a1924 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA a1929 " --> pdb=" O GLU a1925 " (cutoff:3.500A) Processing helix chain 'a' and resid 1934 through 1945 removed outlier: 3.954A pdb=" N VAL a1938 " --> pdb=" O THR a1934 " (cutoff:3.500A) Proline residue: a1940 - end of helix Processing helix chain 'a' and resid 1946 through 1948 No H-bonds generated for 'chain 'a' and resid 1946 through 1948' Processing helix chain 'a' and resid 1950 through 1965 removed outlier: 4.256A pdb=" N LEU a1956 " --> pdb=" O LEU a1952 " (cutoff:3.500A) Processing helix chain 'a' and resid 1968 through 1980 removed outlier: 4.201A pdb=" N LEU a1972 " --> pdb=" O HIS a1968 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR a1974 " --> pdb=" O GLN a1970 " (cutoff:3.500A) Proline residue: a1975 - end of helix Processing helix chain 'a' and resid 1984 through 2021 removed outlier: 4.358A pdb=" N HIS a1988 " --> pdb=" O THR a1984 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS a2001 " --> pdb=" O ASN a1997 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER a2002 " --> pdb=" O MET a1998 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR a2004 " --> pdb=" O GLU a2000 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU a2005 " --> pdb=" O HIS a2001 " (cutoff:3.500A) Processing helix chain 'a' and resid 2022 through 2040 Processing helix chain 'a' and resid 2044 through 2060 removed outlier: 3.998A pdb=" N GLU a2049 " --> pdb=" O LYS a2045 " (cutoff:3.500A) Proline residue: a2053 - end of helix Processing helix chain 'a' and resid 2064 through 2074 Processing helix chain 'a' and resid 2074 through 2092 removed outlier: 3.969A pdb=" N LEU a2078 " --> pdb=" O TYR a2074 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU a2083 " --> pdb=" O MET a2079 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP a2084 " --> pdb=" O GLU a2080 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS a2090 " --> pdb=" O ARG a2086 " (cutoff:3.500A) Processing helix chain 'a' and resid 2093 through 2115 removed outlier: 3.750A pdb=" N LEU a2097 " --> pdb=" O ASN a2093 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS a2113 " --> pdb=" O ARG a2109 " (cutoff:3.500A) Processing helix chain 'a' and resid 2127 through 2133 removed outlier: 3.727A pdb=" N CYS a2133 " --> pdb=" O LYS a2129 " (cutoff:3.500A) Processing helix chain 'a' and resid 2192 through 2212 removed outlier: 3.902A pdb=" N GLN a2200 " --> pdb=" O GLU a2196 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY a2203 " --> pdb=" O MET a2199 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU a2204 " --> pdb=" O GLN a2200 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP a2212 " --> pdb=" O LEU a2208 " (cutoff:3.500A) Processing helix chain 'a' and resid 2212 through 2219 Processing helix chain 'a' and resid 2245 through 2257 removed outlier: 3.655A pdb=" N LEU a2249 " --> pdb=" O THR a2245 " (cutoff:3.500A) Processing helix chain 'a' and resid 2262 through 2272 Processing helix chain 'a' and resid 2274 through 2278 Processing helix chain 'a' and resid 2279 through 2293 Processing helix chain 'a' and resid 2297 through 2307 removed outlier: 3.845A pdb=" N LEU a2302 " --> pdb=" O ASP a2298 " (cutoff:3.500A) Processing helix chain 'a' and resid 2309 through 2334 removed outlier: 3.738A pdb=" N MET a2327 " --> pdb=" O SER a2323 " (cutoff:3.500A) Processing helix chain 'a' and resid 2363 through 2368 Processing helix chain 'a' and resid 2380 through 2387 removed outlier: 3.738A pdb=" N MET a2387 " --> pdb=" O LEU a2383 " (cutoff:3.500A) Processing helix chain 'a' and resid 2394 through 2423 removed outlier: 3.597A pdb=" N ARG a2408 " --> pdb=" O MET a2404 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU a2409 " --> pdb=" O GLU a2405 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP a2412 " --> pdb=" O ARG a2408 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER a2413 " --> pdb=" O GLU a2409 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA a2416 " --> pdb=" O ASP a2412 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL a2417 " --> pdb=" O SER a2413 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE a2421 " --> pdb=" O VAL a2417 " (cutoff:3.500A) Processing helix chain 'a' and resid 2424 through 2429 Processing helix chain 'a' and resid 2429 through 2435 Processing helix chain 'a' and resid 2493 through 2510 removed outlier: 4.263A pdb=" N ILE a2500 " --> pdb=" O LYS a2496 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE a2501 " --> pdb=" O ALA a2497 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN a2502 " --> pdb=" O ILE a2498 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG a2503 " --> pdb=" O GLN a2499 " (cutoff:3.500A) Processing helix chain 'a' and resid 2520 through 2534 removed outlier: 3.510A pdb=" N GLN a2524 " --> pdb=" O ASP a2520 " (cutoff:3.500A) Processing helix chain 'a' and resid 2534 through 2541 Processing helix chain 'b' and resid 98 through 113 removed outlier: 3.783A pdb=" N GLY b 103 " --> pdb=" O LEU b 99 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA b 104 " --> pdb=" O GLU b 100 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN b 105 " --> pdb=" O THR b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 124 through 138 removed outlier: 3.860A pdb=" N ASP b 128 " --> pdb=" O ASP b 124 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS b 131 " --> pdb=" O VAL b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 167 Processing helix chain 'b' and resid 198 through 216 Processing helix chain 'b' and resid 217 through 221 Processing helix chain 'b' and resid 345 through 351 removed outlier: 4.276A pdb=" N LEU b 351 " --> pdb=" O PHE b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 353 through 363 Processing helix chain 'b' and resid 366 through 370 Processing helix chain 'b' and resid 382 through 402 removed outlier: 4.113A pdb=" N VAL b 386 " --> pdb=" O TRP b 382 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE b 388 " --> pdb=" O LEU b 384 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN b 392 " --> pdb=" O ILE b 388 " (cutoff:3.500A) Proline residue: b 394 - end of helix removed outlier: 4.166A pdb=" N ILE b 397 " --> pdb=" O LEU b 393 " (cutoff:3.500A) Processing helix chain 'b' and resid 409 through 420 removed outlier: 3.786A pdb=" N LEU b 420 " --> pdb=" O PHE b 416 " (cutoff:3.500A) Processing helix chain 'b' and resid 421 through 425 removed outlier: 3.733A pdb=" N VAL b 424 " --> pdb=" O THR b 421 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 466 removed outlier: 3.672A pdb=" N GLY b 454 " --> pdb=" O LEU b 450 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG b 455 " --> pdb=" O ASP b 451 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP b 458 " --> pdb=" O GLY b 454 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY b 460 " --> pdb=" O PHE b 456 " (cutoff:3.500A) Proline residue: b 461 - end of helix removed outlier: 3.800A pdb=" N SER b 465 " --> pdb=" O PRO b 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU b 466 " --> pdb=" O TRP b 462 " (cutoff:3.500A) Processing helix chain 'b' and resid 474 through 482 removed outlier: 4.572A pdb=" N SER b 482 " --> pdb=" O LYS b 478 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 488 Processing helix chain 'b' and resid 499 through 508 removed outlier: 3.976A pdb=" N SER b 504 " --> pdb=" O ALA b 500 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA b 507 " --> pdb=" O SER b 503 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP b 508 " --> pdb=" O SER b 504 " (cutoff:3.500A) Processing helix chain 'b' and resid 511 through 524 Processing helix chain 'b' and resid 529 through 537 Processing helix chain 'b' and resid 537 through 546 removed outlier: 3.878A pdb=" N ASN b 544 " --> pdb=" O ALA b 540 " (cutoff:3.500A) Processing helix chain 'b' and resid 585 through 601 removed outlier: 3.846A pdb=" N SER b 590 " --> pdb=" O GLN b 586 " (cutoff:3.500A) Processing helix chain 'b' and resid 606 through 609 Processing helix chain 'b' and resid 610 through 621 removed outlier: 4.322A pdb=" N ALA b 618 " --> pdb=" O GLU b 614 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE b 621 " --> pdb=" O CYS b 617 " (cutoff:3.500A) Processing helix chain 'b' and resid 622 through 624 No H-bonds generated for 'chain 'b' and resid 622 through 624' Processing helix chain 'b' and resid 626 through 628 No H-bonds generated for 'chain 'b' and resid 626 through 628' Processing helix chain 'b' and resid 629 through 636 removed outlier: 4.021A pdb=" N THR b 634 " --> pdb=" O SER b 630 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N HIS b 636 " --> pdb=" O GLU b 632 " (cutoff:3.500A) Processing helix chain 'b' and resid 636 through 643 removed outlier: 3.953A pdb=" N ILE b 640 " --> pdb=" O HIS b 636 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP b 641 " --> pdb=" O SER b 637 " (cutoff:3.500A) Processing helix chain 'b' and resid 648 through 666 removed outlier: 3.839A pdb=" N ASP b 654 " --> pdb=" O GLN b 650 " (cutoff:3.500A) Proline residue: b 657 - end of helix removed outlier: 3.691A pdb=" N LYS b 661 " --> pdb=" O PRO b 657 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU b 663 " --> pdb=" O VAL b 659 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL b 664 " --> pdb=" O ARG b 660 " (cutoff:3.500A) Processing helix chain 'b' and resid 667 through 680 removed outlier: 3.748A pdb=" N SER b 676 " --> pdb=" O VAL b 672 " (cutoff:3.500A) Processing helix chain 'b' and resid 687 through 694 removed outlier: 4.678A pdb=" N ALA b 693 " --> pdb=" O GLU b 689 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU b 694 " --> pdb=" O LYS b 690 " (cutoff:3.500A) Processing helix chain 'b' and resid 694 through 704 Processing helix chain 'b' and resid 709 through 724 Proline residue: b 715 - end of helix removed outlier: 3.833A pdb=" N SER b 719 " --> pdb=" O PRO b 715 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER b 722 " --> pdb=" O ARG b 718 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR b 723 " --> pdb=" O SER b 719 " (cutoff:3.500A) Processing helix chain 'b' and resid 729 through 741 removed outlier: 3.624A pdb=" N SER b 734 " --> pdb=" O ALA b 730 " (cutoff:3.500A) Processing helix chain 'b' and resid 748 through 758 removed outlier: 4.969A pdb=" N SER b 755 " --> pdb=" O ALA b 751 " (cutoff:3.500A) Proline residue: b 756 - end of helix Processing helix chain 'b' and resid 1098 through 1103 Processing helix chain 'c' and resid 202 through 206 Processing helix chain 'c' and resid 266 through 270 removed outlier: 3.562A pdb=" N SER c 269 " --> pdb=" O GLY c 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 8.466A pdb=" N SER A2159 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR A2173 " --> pdb=" O SER A2159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2243 through 2244 Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 148 Processing sheet with id=AA5, first strand: chain 'B' and resid 779 through 782 Processing sheet with id=AA6, first strand: chain 'B' and resid 788 through 793 Processing sheet with id=AA7, first strand: chain 'B' and resid 891 through 892 Processing sheet with id=AA8, first strand: chain 'B' and resid 954 through 956 Processing sheet with id=AA9, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AB1, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.023A pdb=" N ILE B1093 " --> pdb=" O MET B1118 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B1118 " --> pdb=" O ILE B1093 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL B1095 " --> pdb=" O SER B1116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1138 through 1141 Processing sheet with id=AB3, first strand: chain 'B' and resid 1169 through 1171 removed outlier: 6.584A pdb=" N VAL B1192 " --> pdb=" O ALA B1217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.566A pdb=" N ILE C 14 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.940A pdb=" N GLU C 49 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 90 through 93 Processing sheet with id=AB7, first strand: chain 'C' and resid 135 through 136 Processing sheet with id=AB8, first strand: chain 'C' and resid 173 through 177 removed outlier: 4.225A pdb=" N ALA C 186 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N CYS C 194 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS C 215 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 196 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 226 through 228 Processing sheet with id=AC1, first strand: chain 'C' and resid 285 through 288 removed outlier: 3.796A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 2120 through 2122 removed outlier: 8.466A pdb=" N SER a2159 " --> pdb=" O THR a2173 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR a2173 " --> pdb=" O SER a2159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 2243 through 2244 Processing sheet with id=AC4, first strand: chain 'b' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'b' and resid 146 through 148 Processing sheet with id=AC6, first strand: chain 'b' and resid 779 through 782 Processing sheet with id=AC7, first strand: chain 'b' and resid 788 through 793 Processing sheet with id=AC8, first strand: chain 'b' and resid 891 through 892 Processing sheet with id=AC9, first strand: chain 'b' and resid 954 through 956 Processing sheet with id=AD1, first strand: chain 'b' and resid 1049 through 1050 Processing sheet with id=AD2, first strand: chain 'b' and resid 1085 through 1086 removed outlier: 6.024A pdb=" N ILE b1093 " --> pdb=" O MET b1118 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET b1118 " --> pdb=" O ILE b1093 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL b1095 " --> pdb=" O SER b1116 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 1138 through 1141 Processing sheet with id=AD4, first strand: chain 'b' and resid 1169 through 1171 removed outlier: 6.584A pdb=" N VAL b1192 " --> pdb=" O ALA b1217 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 34 through 38 removed outlier: 3.566A pdb=" N ILE c 14 " --> pdb=" O ASN c 321 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 48 through 50 removed outlier: 3.940A pdb=" N GLU c 49 " --> pdb=" O ALA c 58 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 90 through 93 Processing sheet with id=AD8, first strand: chain 'c' and resid 135 through 136 Processing sheet with id=AD9, first strand: chain 'c' and resid 173 through 177 removed outlier: 4.226A pdb=" N ALA c 186 " --> pdb=" O HIS c 177 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N CYS c 194 " --> pdb=" O LYS c 215 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS c 215 " --> pdb=" O CYS c 194 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL c 196 " --> pdb=" O LYS c 213 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 226 through 228 Processing sheet with id=AE2, first strand: chain 'c' and resid 285 through 288 removed outlier: 3.796A pdb=" N ARG c 306 " --> pdb=" O LEU c 296 " (cutoff:3.500A) 2415 hydrogen bonds defined for protein. 7035 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: 24.04 Time building geometry restraints manager: 22.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10716 1.33 - 1.45: 10561 1.45 - 1.58: 24309 1.58 - 1.70: 2 1.70 - 1.83: 394 Bond restraints: 45982 Sorted by residual: bond pdb=" CA ARG A 886 " pdb=" C ARG A 886 " ideal model delta sigma weight residual 1.523 1.430 0.093 1.41e-02 5.03e+03 4.31e+01 bond pdb=" CA ARG a 886 " pdb=" C ARG a 886 " ideal model delta sigma weight residual 1.523 1.430 0.092 1.41e-02 5.03e+03 4.30e+01 bond pdb=" N PRO b 115 " pdb=" CD PRO b 115 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.71e+01 bond pdb=" N PRO B 115 " pdb=" CD PRO B 115 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.69e+01 bond pdb=" CA TYR A1151 " pdb=" CB TYR A1151 " ideal model delta sigma weight residual 1.532 1.454 0.078 1.62e-02 3.81e+03 2.32e+01 ... (remaining 45977 not shown) Histogram of bond angle deviations from ideal: 81.41 - 93.26: 4 93.26 - 105.10: 1031 105.10 - 116.95: 32563 116.95 - 128.80: 28498 128.80 - 140.64: 458 Bond angle restraints: 62554 Sorted by residual: angle pdb=" C SER A1087 " pdb=" N PRO A1088 " pdb=" CA PRO A1088 " ideal model delta sigma weight residual 119.84 140.64 -20.80 1.25e+00 6.40e-01 2.77e+02 angle pdb=" C SER a1087 " pdb=" N PRO a1088 " pdb=" CA PRO a1088 " ideal model delta sigma weight residual 119.84 140.59 -20.75 1.25e+00 6.40e-01 2.75e+02 angle pdb=" C THR b 363 " pdb=" N PRO b 364 " pdb=" CA PRO b 364 " ideal model delta sigma weight residual 119.84 139.66 -19.82 1.25e+00 6.40e-01 2.51e+02 angle pdb=" C THR B 363 " pdb=" N PRO B 364 " pdb=" CA PRO B 364 " ideal model delta sigma weight residual 119.84 139.63 -19.79 1.25e+00 6.40e-01 2.51e+02 angle pdb=" C ARG b 157 " pdb=" N PRO b 158 " pdb=" CA PRO b 158 " ideal model delta sigma weight residual 119.84 136.53 -16.69 1.25e+00 6.40e-01 1.78e+02 ... (remaining 62549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 27248 26.56 - 53.12: 444 53.12 - 79.68: 28 79.68 - 106.24: 14 106.24 - 132.81: 8 Dihedral angle restraints: 27742 sinusoidal: 8988 harmonic: 18754 Sorted by residual: dihedral pdb=" CA SER A1087 " pdb=" C SER A1087 " pdb=" N PRO A1088 " pdb=" CA PRO A1088 " ideal model delta harmonic sigma weight residual -180.00 -47.19 -132.81 0 5.00e+00 4.00e-02 7.05e+02 dihedral pdb=" CA SER a1087 " pdb=" C SER a1087 " pdb=" N PRO a1088 " pdb=" CA PRO a1088 " ideal model delta harmonic sigma weight residual -180.00 -47.21 -132.79 0 5.00e+00 4.00e-02 7.05e+02 dihedral pdb=" CA THR A 714 " pdb=" C THR A 714 " pdb=" N VAL A 715 " pdb=" CA VAL A 715 " ideal model delta harmonic sigma weight residual 180.00 51.22 128.78 0 5.00e+00 4.00e-02 6.63e+02 ... (remaining 27739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 5888 0.078 - 0.157: 1282 0.157 - 0.235: 159 0.235 - 0.314: 39 0.314 - 0.392: 8 Chirality restraints: 7376 Sorted by residual: chirality pdb=" CA GLN B 114 " pdb=" N GLN B 114 " pdb=" C GLN B 114 " pdb=" CB GLN B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA GLN b 114 " pdb=" N GLN b 114 " pdb=" C GLN b 114 " pdb=" CB GLN b 114 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CB ILE c 285 " pdb=" CA ILE c 285 " pdb=" CG1 ILE c 285 " pdb=" CG2 ILE c 285 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 7373 not shown) Planarity restraints: 8162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN b 114 " 0.173 5.00e-02 4.00e+02 2.16e-01 7.46e+01 pdb=" N PRO b 115 " -0.361 5.00e-02 4.00e+02 pdb=" CA PRO b 115 " 0.160 5.00e-02 4.00e+02 pdb=" CD PRO b 115 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 114 " -0.173 5.00e-02 4.00e+02 2.16e-01 7.45e+01 pdb=" N PRO B 115 " 0.360 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.160 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 112 " -0.027 2.00e-02 2.50e+03 5.85e-02 3.43e+01 pdb=" C ASN B 112 " 0.101 2.00e-02 2.50e+03 pdb=" O ASN B 112 " -0.041 2.00e-02 2.50e+03 pdb=" N TRP B 113 " -0.034 2.00e-02 2.50e+03 ... (remaining 8159 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.90: 14 1.90 - 2.65: 2409 2.65 - 3.40: 79207 3.40 - 4.15: 125506 4.15 - 4.90: 200774 Nonbonded interactions: 407910 Sorted by model distance: nonbonded pdb=" O TYR B 110 " pdb=" N GLN B 114 " model vdw 1.144 2.520 nonbonded pdb=" O TYR b 110 " pdb=" N GLN b 114 " model vdw 1.145 2.520 nonbonded pdb=" O VAL B 424 " pdb=" N ASN B 426 " model vdw 1.307 2.520 nonbonded pdb=" O VAL b 424 " pdb=" N ASN b 426 " model vdw 1.307 2.520 nonbonded pdb=" CB PRO B 80 " pdb=" CG GLN B 114 " model vdw 1.594 3.840 ... (remaining 407905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.440 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: 0.040 Extract box with map and model: 8.170 Check model and map are aligned: 0.670 Set scattering table: 0.420 Process input model: 126.090 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.330 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 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 : 0.011 0.133 45982 Z= 0.709 Angle : 1.567 43.591 62554 Z= 0.890 Chirality : 0.066 0.392 7376 Planarity : 0.009 0.216 8162 Dihedral : 11.971 132.806 15498 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 72.33 Ramachandran Plot: Outliers : 2.43 % Allowed : 17.33 % Favored : 80.24 % Rotamer: Outliers : 0.80 % Allowed : 1.69 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 1.94 % Twisted Proline : 8.33 % Twisted General : 1.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.08), residues: 6342 helix: -4.50 (0.05), residues: 2686 sheet: -2.94 (0.18), residues: 522 loop : -3.59 (0.09), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP a1490 HIS 0.026 0.005 HIS a 759 PHE 0.052 0.005 PHE A 705 TYR 0.041 0.005 TYR A 673 ARG 0.020 0.002 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12684 Ramachandran restraints generated. 6342 Oldfield, 0 Emsley, 6342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12684 Ramachandran restraints generated. 6342 Oldfield, 0 Emsley, 6342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 615 time to evaluate : 5.343 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: 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 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable