Starting phenix.real_space_refine on Wed Nov 15 10:51:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/11_2023/7k0t_22616_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/11_2023/7k0t_22616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/11_2023/7k0t_22616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/11_2023/7k0t_22616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/11_2023/7k0t_22616_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/11_2023/7k0t_22616_neut_updated.pdb" } resolution = 4.3 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= 0.001 sd= 0.006 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 12 5.49 5 S 628 5.16 5 C 73396 2.51 5 N 20527 2.21 5 O 21338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1114": "OE1" <-> "OE2" Residue "A GLU 2449": "OE1" <-> "OE2" Residue "A GLU 2779": "OE1" <-> "OE2" Residue "A GLU 3665": "OE1" <-> "OE2" Residue "A GLU 3754": "OE1" <-> "OE2" Residue "A GLU 3755": "OE1" <-> "OE2" Residue "A GLU 3759": "OE1" <-> "OE2" Residue "A GLU 4011": "OE1" <-> "OE2" Residue "A GLU 4172": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A GLU 4227": "OE1" <-> "OE2" Residue "A GLU 4871": "OE1" <-> "OE2" Residue "A GLU 4942": "OE1" <-> "OE2" Residue "A GLU 4976": "OE1" <-> "OE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 2205": "OE1" <-> "OE2" Residue "B GLU 2348": "OE1" <-> "OE2" Residue "B GLU 3655": "OE1" <-> "OE2" Residue "B GLU 3755": "OE1" <-> "OE2" Residue "B GLU 4011": "OE1" <-> "OE2" Residue "B PHE 4141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4244": "OE1" <-> "OE2" Residue "B GLU 4942": "OE1" <-> "OE2" Residue "B GLU 4976": "OE1" <-> "OE2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D GLU 700": "OE1" <-> "OE2" Residue "D GLU 2205": "OE1" <-> "OE2" Residue "D GLU 2348": "OE1" <-> "OE2" Residue "D GLU 4011": "OE1" <-> "OE2" Residue "D GLU 4244": "OE1" <-> "OE2" Residue "D GLU 4867": "OE1" <-> "OE2" Residue "D PHE 4922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4981": "OE1" <-> "OE2" Residue "D GLU 5016": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C GLU 2209": "OE1" <-> "OE2" Residue "C GLU 2449": "OE1" <-> "OE2" Residue "C GLU 3665": "OE1" <-> "OE2" Residue "C GLU 4050": "OE1" <-> "OE2" Residue "C GLU 4168": "OE1" <-> "OE2" Residue "C GLU 4232": "OE1" <-> "OE2" Residue "C GLU 4676": "OE1" <-> "OE2" Residue "C GLU 4867": "OE1" <-> "OE2" Residue "C GLU 4942": "OE1" <-> "OE2" Residue "C GLU 4948": "OE1" <-> "OE2" Time to flip residues: 0.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 115905 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 28962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4105, 28962 Classifications: {'peptide': 4105} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1220} Link IDs: {'PTRANS': 147, 'TRANS': 3957} Chain breaks: 25 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 2939 Unresolved non-hydrogen angles: 4113 Unresolved non-hydrogen dihedrals: 1813 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 42, 'TYR:plan': 1, 'ASN:plan1': 13, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 79, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 1701 Chain: "B" Number of atoms: 28934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4105, 28934 Classifications: {'peptide': 4105} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1229} Link IDs: {'PTRANS': 147, 'TRANS': 3957} Chain breaks: 25 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 2968 Unresolved non-hydrogen angles: 4151 Unresolved non-hydrogen dihedrals: 1835 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 45, 'TYR:plan': 1, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 80, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1717 Chain: "D" Number of atoms: 28933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4105, 28933 Classifications: {'peptide': 4105} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1229} Link IDs: {'PTRANS': 147, 'TRANS': 3957} Chain breaks: 25 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 2969 Unresolved non-hydrogen angles: 4151 Unresolved non-hydrogen dihedrals: 1837 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 44, 'TYR:plan': 1, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 81, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1718 Chain: "C" Number of atoms: 28948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4105, 28948 Classifications: {'peptide': 4105} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1225} Link IDs: {'PTRANS': 147, 'TRANS': 3957} Chain breaks: 25 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 2954 Unresolved non-hydrogen angles: 4135 Unresolved non-hydrogen dihedrals: 1823 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 43, 'TYR:plan': 1, 'ASN:plan1': 13, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 81, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1712 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28287 SG CYS A4958 178.654 206.106 90.539 1.00 48.38 S ATOM 28312 SG CYS A4961 181.122 207.311 93.254 1.00 51.33 S ATOM 57224 SG CYS B4958 205.322 206.002 90.660 1.00 48.74 S ATOM 57249 SG CYS B4961 207.536 205.810 93.850 1.00 58.42 S ATOM 86154 SG CYS D4958 180.481 179.613 90.617 1.00 50.83 S ATOM 86179 SG CYS D4961 179.233 182.093 93.348 1.00 50.76 S ATOM A0BNI SG CYS C4958 206.723 181.536 90.705 1.00 44.99 S ATOM A0BO7 SG CYS C4961 203.951 180.366 93.338 1.00 48.51 S Time building chain proxies: 43.19, per 1000 atoms: 0.37 Number of scatterers: 115905 At special positions: 0 Unit cell: (386.27, 387.34, 212.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 628 16.00 P 12 15.00 O 21338 8.00 N 20527 7.00 C 73396 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: 32.35 Conformation dependent library (CDL) restraints added in 13.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 6 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31136 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 472 helices and 64 sheets defined 54.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 29.17 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.628A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 4.053A pdb=" N MET A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.072A pdb=" N CYS A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 256' Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.342A pdb=" N ALA A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N HIS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.438A pdb=" N LEU A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 422 removed outlier: 3.949A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 4.831A pdb=" N VAL A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 480 removed outlier: 3.785A pdb=" N GLN A 465 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 496 removed outlier: 6.833A pdb=" N LEU A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 removed outlier: 4.788A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 3.796A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 4.020A pdb=" N VAL A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.351A pdb=" N LEU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.268A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.759A pdb=" N LYS A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 4.223A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 4.164A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 890 removed outlier: 5.972A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 removed outlier: 3.837A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1005 removed outlier: 4.026A pdb=" N THR A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1050 removed outlier: 4.978A pdb=" N LYS A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN A1041 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG A1044 " --> pdb=" O CYS A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1581 removed outlier: 3.729A pdb=" N MET A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 3.821A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1657' Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 3.991A pdb=" N PHE A1662 " --> pdb=" O ASP A1658 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1689 removed outlier: 4.324A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS A1688 " --> pdb=" O ALA A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1701 removed outlier: 3.902A pdb=" N HIS A1696 " --> pdb=" O ALA A1692 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A1698 " --> pdb=" O LEU A1694 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA A1701 " --> pdb=" O ALA A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1707 through 1720 removed outlier: 4.029A pdb=" N TYR A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR A1712 " --> pdb=" O ARG A1708 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP A1713 " --> pdb=" O ALA A1709 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A1714 " --> pdb=" O GLY A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1723 through 1731 removed outlier: 4.118A pdb=" N ARG A1727 " --> pdb=" O ALA A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.794A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.523A pdb=" N GLN A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 removed outlier: 3.787A pdb=" N VAL A1839 " --> pdb=" O GLU A1835 " (cutoff:3.500A) Proline residue: A1840 - end of helix removed outlier: 4.802A pdb=" N LYS A1843 " --> pdb=" O VAL A1839 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET A1851 " --> pdb=" O THR A1847 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1855 through 1865 removed outlier: 4.046A pdb=" N MET A1865 " --> pdb=" O GLN A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1871 Processing helix chain 'A' and resid 1934 through 1977 removed outlier: 3.784A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1988 through 1999 removed outlier: 3.975A pdb=" N ALA A1992 " --> pdb=" O ALA A1988 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A1993 " --> pdb=" O ALA A1989 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A1996 " --> pdb=" O ALA A1992 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2015 removed outlier: 4.359A pdb=" N GLU A2015 " --> pdb=" O HIS A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2024 through 2043 removed outlier: 5.100A pdb=" N ARG A2028 " --> pdb=" O PRO A2024 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLN A2029 " --> pdb=" O GLU A2025 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP A2030 " --> pdb=" O ASP A2026 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU A2031 " --> pdb=" O ILE A2027 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN A2032 " --> pdb=" O ARG A2028 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 5.170A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.519A pdb=" N VAL A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A2128 " --> pdb=" O LEU A2124 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2142 Proline residue: A2139 - end of helix removed outlier: 5.640A pdb=" N TYR A2142 " --> pdb=" O LEU A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 4.327A pdb=" N THR A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2188 removed outlier: 4.289A pdb=" N ASN A2176 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET A2186 " --> pdb=" O ILE A2182 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A2187 " --> pdb=" O GLY A2183 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2194 removed outlier: 4.227A pdb=" N GLN A2193 " --> pdb=" O LYS A2189 " (cutoff:3.500A) Processing helix chain 'A' and resid 2195 through 2202 removed outlier: 4.059A pdb=" N ARG A2199 " --> pdb=" O PRO A2195 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A2200 " --> pdb=" O ASN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2215 Processing helix chain 'A' and resid 2227 through 2243 removed outlier: 5.430A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A2232 " --> pdb=" O MET A2228 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A2242 " --> pdb=" O TYR A2238 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2252 removed outlier: 4.533A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) Processing helix chain 'A' and resid 2253 through 2264 removed outlier: 3.593A pdb=" N LEU A2257 " --> pdb=" O HIS A2253 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A2259 " --> pdb=" O SER A2255 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2281 removed outlier: 3.502A pdb=" N SER A2279 " --> pdb=" O VAL A2275 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A2281 " --> pdb=" O ALA A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2291 removed outlier: 3.502A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN A2291 " --> pdb=" O ALA A2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2286 through 2291' Processing helix chain 'A' and resid 2294 through 2309 removed outlier: 5.226A pdb=" N SER A2309 " --> pdb=" O CYS A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2315 removed outlier: 4.495A pdb=" N ALA A2315 " --> pdb=" O PRO A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2340 removed outlier: 3.932A pdb=" N GLY A2328 " --> pdb=" O ASN A2324 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A2332 " --> pdb=" O GLY A2328 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASP A2333 " --> pdb=" O GLU A2329 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A2335 " --> pdb=" O TYR A2331 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A2336 " --> pdb=" O LEU A2332 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.837A pdb=" N ALA A2350 " --> pdb=" O VAL A2346 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A2353 " --> pdb=" O ASN A2349 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A2360 " --> pdb=" O LEU A2356 " (cutoff:3.500A) Proline residue: A2361 - end of helix Processing helix chain 'A' and resid 2365 through 2370 removed outlier: 3.583A pdb=" N GLY A2370 " --> pdb=" O PRO A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2375 through 2389 Processing helix chain 'A' and resid 2417 through 2437 removed outlier: 4.709A pdb=" N ALA A2421 " --> pdb=" O HIS A2417 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A2422 " --> pdb=" O LEU A2418 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A2437 " --> pdb=" O LEU A2433 " (cutoff:3.500A) Processing helix chain 'A' and resid 2441 through 2446 removed outlier: 5.046A pdb=" N ALA A2445 " --> pdb=" O HIS A2441 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY A2446 " --> pdb=" O LEU A2442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2441 through 2446' Processing helix chain 'A' and resid 2447 through 2462 removed outlier: 4.132A pdb=" N LEU A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A2461 " --> pdb=" O LEU A2457 " (cutoff:3.500A) Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2465 through 2472 removed outlier: 3.744A pdb=" N SER A2471 " --> pdb=" O VAL A2467 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A2472 " --> pdb=" O GLY A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2748 through 2774 removed outlier: 4.510A pdb=" N SER A2753 " --> pdb=" O GLU A2749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE A2754 " --> pdb=" O LYS A2750 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2814 removed outlier: 3.617A pdb=" N TYR A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TRP A2807 " --> pdb=" O GLU A2803 " (cutoff:3.500A) Proline residue: A2808 - end of helix removed outlier: 5.233A pdb=" N GLU A2811 " --> pdb=" O TRP A2807 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER A2812 " --> pdb=" O PRO A2808 " (cutoff:3.500A) Processing helix chain 'A' and resid 2815 through 2820 Processing helix chain 'A' and resid 2870 through 2896 removed outlier: 3.900A pdb=" N TRP A2886 " --> pdb=" O TYR A2882 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA A2896 " --> pdb=" O GLN A2892 " (cutoff:3.500A) Processing helix chain 'A' and resid 2907 through 2912 removed outlier: 5.495A pdb=" N THR A2912 " --> pdb=" O TYR A2908 " (cutoff:3.500A) Processing helix chain 'A' and resid 2915 through 2932 removed outlier: 4.538A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3657 removed outlier: 3.675A pdb=" N TYR A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3667 through 3684 removed outlier: 4.921A pdb=" N ASP A3671 " --> pdb=" O HIS A3667 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG A3672 " --> pdb=" O SER A3668 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE A3674 " --> pdb=" O GLU A3670 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASP A3675 " --> pdb=" O ASP A3671 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A3677 " --> pdb=" O MET A3673 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A3681 " --> pdb=" O LEU A3677 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU A3684 " --> pdb=" O ALA A3680 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3712 removed outlier: 6.073A pdb=" N GLU A3712 " --> pdb=" O THR A3708 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3735 removed outlier: 3.837A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3771 removed outlier: 3.899A pdb=" N GLN A3766 " --> pdb=" O ARG A3762 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN A3767 " --> pdb=" O LEU A3763 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A3768 " --> pdb=" O LEU A3764 " (cutoff:3.500A) Processing helix chain 'A' and resid 3776 through 3786 removed outlier: 4.690A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A3781 " --> pdb=" O GLU A3777 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N CYS A3786 " --> pdb=" O MET A3782 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 4.449A pdb=" N LYS A3799 " --> pdb=" O SER A3795 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A3800 " --> pdb=" O SER A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3824 removed outlier: 3.551A pdb=" N GLN A3813 " --> pdb=" O ASN A3809 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A3814 " --> pdb=" O ALA A3810 " (cutoff:3.500A) Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 7.050A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3857 removed outlier: 3.931A pdb=" N PHE A3847 " --> pdb=" O ASP A3843 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A3855 " --> pdb=" O ASN A3851 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY A3857 " --> pdb=" O ALA A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3893 removed outlier: 4.738A pdb=" N ASP A3883 " --> pdb=" O GLU A3879 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 6.404A pdb=" N GLN A3900 " --> pdb=" O ASN A3896 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN A3901 " --> pdb=" O ASN A3897 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.824A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A3935 " --> pdb=" O SER A3931 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A3936 " --> pdb=" O ASP A3932 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A3937 " --> pdb=" O PHE A3933 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 4.249A pdb=" N LYS A3953 " --> pdb=" O ARG A3949 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A3954 " --> pdb=" O ASN A3950 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A3958 " --> pdb=" O ALA A3954 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A3968 " --> pdb=" O SER A3964 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 3.595A pdb=" N GLN A3977 " --> pdb=" O CYS A3973 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A3983 " --> pdb=" O SER A3979 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4003 removed outlier: 4.042A pdb=" N GLY A3991 " --> pdb=" O ASP A3987 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A3999 " --> pdb=" O VAL A3995 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET A4000 " --> pdb=" O PHE A3996 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.973A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4052 removed outlier: 6.401A pdb=" N ARG A4042 " --> pdb=" O GLY A4038 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A4043 " --> pdb=" O MET A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4053 through 4075 removed outlier: 4.511A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A4058 " --> pdb=" O ASN A4054 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A4068 " --> pdb=" O MET A4064 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS A4069 " --> pdb=" O PHE A4065 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A4071 " --> pdb=" O LYS A4067 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A4072 " --> pdb=" O LEU A4068 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A4074 " --> pdb=" O ASP A4070 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLU A4075 " --> pdb=" O ILE A4071 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 4.248A pdb=" N PHE A4093 " --> pdb=" O SER A4089 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A4094 " --> pdb=" O LYS A4090 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4115 Processing helix chain 'A' and resid 4124 through 4155 removed outlier: 3.899A pdb=" N ASN A4130 " --> pdb=" O GLU A4126 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A4131 " --> pdb=" O GLU A4127 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Proline residue: A4135 - end of helix Proline residue: A4155 - end of helix Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 3.532A pdb=" N ALA A4167 " --> pdb=" O PHE A4163 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A4168 " --> pdb=" O LEU A4164 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4179 Proline residue: A4176 - end of helix removed outlier: 5.578A pdb=" N GLY A4179 " --> pdb=" O ARG A4175 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4207 removed outlier: 5.435A pdb=" N ARG A4202 " --> pdb=" O SER A4198 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA A4203 " --> pdb=" O GLU A4199 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A4206 " --> pdb=" O ARG A4202 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4224 removed outlier: 3.509A pdb=" N GLU A4224 " --> pdb=" O ASP A4220 " (cutoff:3.500A) Processing helix chain 'A' and resid 4229 through 4252 removed outlier: 4.090A pdb=" N GLN A4250 " --> pdb=" O GLN A4246 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A4251 " --> pdb=" O ILE A4247 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A4252 " --> pdb=" O ALA A4248 " (cutoff:3.500A) Processing helix chain 'A' and resid 4540 through 4559 removed outlier: 4.375A pdb=" N LEU A4544 " --> pdb=" O PHE A4540 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A4545 " --> pdb=" O TRP A4541 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A4558 " --> pdb=" O TYR A4554 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A4559 " --> pdb=" O LEU A4555 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4579 removed outlier: 3.967A pdb=" N LEU A4578 " --> pdb=" O ASN A4574 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4642 through 4664 removed outlier: 3.979A pdb=" N LEU A4646 " --> pdb=" O ALA A4642 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A4659 " --> pdb=" O PHE A4655 " (cutoff:3.500A) Processing helix chain 'A' and resid 4666 through 4684 removed outlier: 4.881A pdb=" N ILE A4670 " --> pdb=" O VAL A4666 " (cutoff:3.500A) Processing helix chain 'A' and resid 4696 through 4707 removed outlier: 4.448A pdb=" N ASP A4702 " --> pdb=" O LYS A4698 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4728 removed outlier: 4.334A pdb=" N LEU A4725 " --> pdb=" O LYS A4721 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 removed outlier: 3.530A pdb=" N ILE A4737 " --> pdb=" O GLY A4733 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A4738 " --> pdb=" O ARG A4734 " (cutoff:3.500A) Processing helix chain 'A' and resid 4745 through 4750 removed outlier: 3.999A pdb=" N ILE A4750 " --> pdb=" O ALA A4746 " (cutoff:3.500A) Processing helix chain 'A' and resid 4772 through 4787 removed outlier: 5.984A pdb=" N ASN A4787 " --> pdb=" O ILE A4783 " (cutoff:3.500A) Processing helix chain 'A' and resid 4788 through 4803 removed outlier: 3.722A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4820 removed outlier: 4.478A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLY A4819 " --> pdb=" O ASP A4815 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A4820 " --> pdb=" O ILE A4816 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 4.132A pdb=" N THR A4825 " --> pdb=" O LYS A4821 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE A4826 " --> pdb=" O THR A4822 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 removed outlier: 3.627A pdb=" N MET A4839 " --> pdb=" O LYS A4835 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A4853 " --> pdb=" O TYR A4849 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A4854 " --> pdb=" O LEU A4850 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A4855 " --> pdb=" O TYR A4851 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 5.170A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4897 through 4902 removed outlier: 4.427A pdb=" N ILE A4901 " --> pdb=" O ILE A4897 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4897 through 4902' Processing helix chain 'A' and resid 4909 through 4925 removed outlier: 3.744A pdb=" N VAL A4914 " --> pdb=" O GLU A4910 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A4923 " --> pdb=" O THR A4919 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A4924 " --> pdb=" O PHE A4920 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A4925 " --> pdb=" O PHE A4921 " (cutoff:3.500A) Processing helix chain 'A' and resid 4928 through 4957 removed outlier: 4.283A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A4933 " --> pdb=" O LEU A4929 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A4936 " --> pdb=" O ILE A4932 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG A4944 " --> pdb=" O PHE A4940 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A4945 " --> pdb=" O GLY A4941 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A4951 " --> pdb=" O GLN A4947 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR A4956 " --> pdb=" O GLU A4952 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A4957 " --> pdb=" O ASP A4953 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4970 removed outlier: 3.997A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4999 removed outlier: 6.465A pdb=" N TYR A4988 " --> pdb=" O ASN A4984 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A4990 " --> pdb=" O ALA A4986 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP A4999 " --> pdb=" O LEU A4995 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'A' and resid 5027 through 5033 removed outlier: 6.305A pdb=" N GLN A5031 " --> pdb=" O CYS A5027 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR A5032 " --> pdb=" O PHE A5028 " (cutoff:3.500A) Processing helix chain 'A' and resid 3870 through 3875 removed outlier: 3.674A pdb=" N LYS A3873 " --> pdb=" O ASN A3870 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL A3874 " --> pdb=" O GLY A3871 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET A3875 " --> pdb=" O GLU A3872 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3870 through 3875' Processing helix chain 'A' and resid 1978 through 1984 removed outlier: 3.842A pdb=" N ALA A1983 " --> pdb=" O ALA A1978 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A1984 " --> pdb=" O LEU A1979 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1978 through 1984' Processing helix chain 'A' and resid 3861 through 3868 removed outlier: 6.627A pdb=" N ILE A3866 " --> pdb=" O GLU A3861 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN A3867 " --> pdb=" O ASP A3862 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG A3868 " --> pdb=" O GLY A3863 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3861 through 3868' Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.802A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 4.393A pdb=" N MET B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 4.515A pdb=" N CYS B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 256' Processing helix chain 'B' and resid 303 through 308 removed outlier: 4.488A pdb=" N ALA B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.457A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 422 removed outlier: 3.666A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 4.837A pdb=" N VAL B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 480 removed outlier: 3.772A pdb=" N GLN B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 496 removed outlier: 6.761A pdb=" N LEU B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 531 removed outlier: 4.860A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.736A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 4.035A pdb=" N VAL B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.501A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 562 " --> pdb=" O SER B 558 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 4.201A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.808A pdb=" N LYS B 584 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 4.115A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 removed outlier: 4.174A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 890 removed outlier: 6.334A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG B 871 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA B 883 " --> pdb=" O HIS B 879 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ARG B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 removed outlier: 3.837A pdb=" N LEU B 935 " --> pdb=" O THR B 931 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1005 removed outlier: 4.715A pdb=" N THR B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN B1003 " --> pdb=" O ASP B 999 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1050 removed outlier: 4.746A pdb=" N LYS B1032 " --> pdb=" O ASP B1028 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B1033 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN B1041 " --> pdb=" O ASP B1037 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B1042 " --> pdb=" O SER B1038 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ARG B1044 " --> pdb=" O CYS B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1574 through 1581 removed outlier: 4.295A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B1581 " --> pdb=" O ALA B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1649 through 1657 removed outlier: 3.964A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B1656 " --> pdb=" O GLU B1652 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 4.027A pdb=" N PHE B1662 " --> pdb=" O ASP B1658 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1689 removed outlier: 4.228A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1692 through 1701 removed outlier: 3.916A pdb=" N HIS B1696 " --> pdb=" O ALA B1692 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA B1701 " --> pdb=" O ALA B1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 1707 through 1720 removed outlier: 4.451A pdb=" N TYR B1711 " --> pdb=" O LEU B1707 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B1712 " --> pdb=" O ARG B1708 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP B1713 " --> pdb=" O ALA B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1723 through 1731 removed outlier: 4.036A pdb=" N ARG B1727 " --> pdb=" O ALA B1723 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.827A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.576A pdb=" N GLN B1824 " --> pdb=" O ARG B1820 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 removed outlier: 3.951A pdb=" N GLN B1837 " --> pdb=" O SER B1833 " (cutoff:3.500A) Proline residue: B1840 - end of helix removed outlier: 4.321A pdb=" N LYS B1843 " --> pdb=" O VAL B1839 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1865 removed outlier: 4.026A pdb=" N MET B1865 " --> pdb=" O GLN B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1871 Processing helix chain 'B' and resid 1934 through 1977 removed outlier: 4.179A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) Processing helix chain 'B' and resid 1988 through 1999 removed outlier: 4.710A pdb=" N ALA B1992 " --> pdb=" O ALA B1988 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B1993 " --> pdb=" O ALA B1989 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG B1996 " --> pdb=" O ALA B1992 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B1999 " --> pdb=" O THR B1995 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2015 removed outlier: 4.336A pdb=" N GLU B2015 " --> pdb=" O HIS B2011 " (cutoff:3.500A) Processing helix chain 'B' and resid 2024 through 2043 removed outlier: 5.094A pdb=" N ARG B2028 " --> pdb=" O PRO B2024 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLN B2029 " --> pdb=" O GLU B2025 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP B2030 " --> pdb=" O ASP B2026 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B2031 " --> pdb=" O ILE B2027 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 5.204A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.536A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B2128 " --> pdb=" O LEU B2124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2142 Proline residue: B2139 - end of helix removed outlier: 5.625A pdb=" N TYR B2142 " --> pdb=" O LEU B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2169 removed outlier: 4.335A pdb=" N THR B2152 " --> pdb=" O SER B2148 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2188 removed outlier: 4.135A pdb=" N ASN B2176 " --> pdb=" O PRO B2172 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN B2187 " --> pdb=" O GLY B2183 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2194 removed outlier: 4.376A pdb=" N GLN B2193 " --> pdb=" O LYS B2189 " (cutoff:3.500A) Processing helix chain 'B' and resid 2195 through 2202 removed outlier: 3.626A pdb=" N ARG B2199 " --> pdb=" O PRO B2195 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B2200 " --> pdb=" O ASN B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2215 Processing helix chain 'B' and resid 2227 through 2243 removed outlier: 4.532A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2252 removed outlier: 4.064A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2264 removed outlier: 3.838A pdb=" N LEU B2257 " --> pdb=" O HIS B2253 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B2259 " --> pdb=" O SER B2255 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2281 removed outlier: 4.243A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE B2281 " --> pdb=" O ALA B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2286 through 2291 removed outlier: 4.407A pdb=" N GLN B2291 " --> pdb=" O ALA B2287 " (cutoff:3.500A) Processing helix chain 'B' and resid 2294 through 2309 removed outlier: 5.289A pdb=" N SER B2309 " --> pdb=" O CYS B2305 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 4.744A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2340 removed outlier: 3.888A pdb=" N GLY B2328 " --> pdb=" O ASN B2324 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP B2333 " --> pdb=" O GLU B2329 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU B2335 " --> pdb=" O TYR B2331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B2336 " --> pdb=" O LEU B2332 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 3.863A pdb=" N ALA B2350 " --> pdb=" O VAL B2346 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B2353 " --> pdb=" O ASN B2349 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B2359 " --> pdb=" O ARG B2355 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B2360 " --> pdb=" O LEU B2356 " (cutoff:3.500A) Proline residue: B2361 - end of helix Processing helix chain 'B' and resid 2365 through 2370 removed outlier: 3.640A pdb=" N GLY B2370 " --> pdb=" O PRO B2366 " (cutoff:3.500A) Processing helix chain 'B' and resid 2375 through 2389 Processing helix chain 'B' and resid 2417 through 2437 removed outlier: 4.760A pdb=" N ALA B2421 " --> pdb=" O HIS B2417 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B2422 " --> pdb=" O LEU B2418 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B2437 " --> pdb=" O LEU B2433 " (cutoff:3.500A) Processing helix chain 'B' and resid 2441 through 2446 removed outlier: 5.087A pdb=" N ALA B2445 " --> pdb=" O HIS B2441 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY B2446 " --> pdb=" O LEU B2442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2441 through 2446' Processing helix chain 'B' and resid 2447 through 2462 removed outlier: 4.057A pdb=" N LEU B2451 " --> pdb=" O LYS B2447 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B2461 " --> pdb=" O LEU B2457 " (cutoff:3.500A) Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2465 through 2472 removed outlier: 3.912A pdb=" N SER B2471 " --> pdb=" O VAL B2467 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B2472 " --> pdb=" O GLY B2468 " (cutoff:3.500A) Processing helix chain 'B' and resid 2748 through 2774 removed outlier: 4.045A pdb=" N SER B2753 " --> pdb=" O GLU B2749 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2814 removed outlier: 3.551A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP B2807 " --> pdb=" O GLU B2803 " (cutoff:3.500A) Proline residue: B2808 - end of helix removed outlier: 5.232A pdb=" N GLU B2811 " --> pdb=" O TRP B2807 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER B2812 " --> pdb=" O PRO B2808 " (cutoff:3.500A) Processing helix chain 'B' and resid 2815 through 2820 Processing helix chain 'B' and resid 2870 through 2896 removed outlier: 4.706A pdb=" N ALA B2896 " --> pdb=" O GLN B2892 " (cutoff:3.500A) Processing helix chain 'B' and resid 2907 through 2912 removed outlier: 5.458A pdb=" N THR B2912 " --> pdb=" O TYR B2908 " (cutoff:3.500A) Processing helix chain 'B' and resid 2915 through 2932 removed outlier: 4.949A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B2931 " --> pdb=" O LEU B2927 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET B2932 " --> pdb=" O LYS B2928 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3657 Processing helix chain 'B' and resid 3667 through 3684 removed outlier: 4.916A pdb=" N ASP B3671 " --> pdb=" O HIS B3667 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ARG B3672 " --> pdb=" O SER B3668 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE B3674 " --> pdb=" O GLU B3670 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP B3675 " --> pdb=" O ASP B3671 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B3681 " --> pdb=" O LEU B3677 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU B3684 " --> pdb=" O ALA B3680 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3712 removed outlier: 6.068A pdb=" N GLU B3712 " --> pdb=" O THR B3708 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3735 removed outlier: 4.019A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3771 removed outlier: 4.046A pdb=" N LYS B3756 " --> pdb=" O SER B3752 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B3771 " --> pdb=" O GLN B3767 " (cutoff:3.500A) Processing helix chain 'B' and resid 3776 through 3786 removed outlier: 4.653A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B3785 " --> pdb=" O GLN B3781 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N CYS B3786 " --> pdb=" O MET B3782 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 removed outlier: 3.513A pdb=" N SER B3795 " --> pdb=" O GLY B3791 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS B3799 " --> pdb=" O SER B3795 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3826 through 3839 removed outlier: 7.278A pdb=" N GLN B3830 " --> pdb=" O VAL B3826 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B3831 " --> pdb=" O GLY B3827 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS B3839 " --> pdb=" O LEU B3835 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3857 removed outlier: 3.888A pdb=" N PHE B3847 " --> pdb=" O ASP B3843 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B3855 " --> pdb=" O ASN B3851 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU B3856 " --> pdb=" O LYS B3852 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY B3857 " --> pdb=" O ALA B3853 " (cutoff:3.500A) Processing helix chain 'B' and resid 3879 through 3893 removed outlier: 5.344A pdb=" N ASP B3883 " --> pdb=" O GLU B3879 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B3884 " --> pdb=" O PHE B3880 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 6.518A pdb=" N GLN B3900 " --> pdb=" O ASN B3896 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN B3901 " --> pdb=" O ASN B3897 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 3.830A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP B3935 " --> pdb=" O SER B3931 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.682A pdb=" N LYS B3953 " --> pdb=" O ARG B3949 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B3954 " --> pdb=" O ASN B3950 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR B3968 " --> pdb=" O SER B3964 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3984 removed outlier: 3.853A pdb=" N GLN B3977 " --> pdb=" O CYS B3973 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B3983 " --> pdb=" O SER B3979 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ARG B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4003 removed outlier: 4.120A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 4.037A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4052 removed outlier: 6.361A pdb=" N ARG B4042 " --> pdb=" O GLY B4038 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B4043 " --> pdb=" O MET B4039 " (cutoff:3.500A) Processing helix chain 'B' and resid 4053 through 4075 removed outlier: 4.174A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B4058 " --> pdb=" O ASN B4054 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B4067 " --> pdb=" O ASP B4063 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B4068 " --> pdb=" O MET B4064 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B4069 " --> pdb=" O PHE B4065 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE B4071 " --> pdb=" O LYS B4067 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B4072 " --> pdb=" O LEU B4068 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLY B4073 " --> pdb=" O LYS B4069 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N SER B4074 " --> pdb=" O ASP B4070 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU B4075 " --> pdb=" O ILE B4071 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 4.055A pdb=" N PHE B4093 " --> pdb=" O SER B4089 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4124 through 4155 removed outlier: 4.080A pdb=" N ASN B4130 " --> pdb=" O GLU B4126 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B4131 " --> pdb=" O GLU B4127 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Proline residue: B4135 - end of helix removed outlier: 4.161A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) Proline residue: B4155 - end of helix Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 3.697A pdb=" N ALA B4167 " --> pdb=" O PHE B4163 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU B4168 " --> pdb=" O LEU B4164 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4179 Proline residue: B4176 - end of helix removed outlier: 5.587A pdb=" N GLY B4179 " --> pdb=" O ARG B4175 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4207 removed outlier: 5.083A pdb=" N ARG B4202 " --> pdb=" O SER B4198 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B4203 " --> pdb=" O GLU B4199 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU B4206 " --> pdb=" O ARG B4202 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N MET B4207 " --> pdb=" O ALA B4203 " (cutoff:3.500A) Processing helix chain 'B' and resid 4208 through 4224 removed outlier: 3.741A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASN B4223 " --> pdb=" O PHE B4219 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU B4224 " --> pdb=" O ASP B4220 " (cutoff:3.500A) Processing helix chain 'B' and resid 4229 through 4252 removed outlier: 5.425A pdb=" N LEU B4233 " --> pdb=" O GLU B4229 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B4250 " --> pdb=" O GLN B4246 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B4251 " --> pdb=" O ILE B4247 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B4252 " --> pdb=" O ALA B4248 " (cutoff:3.500A) Processing helix chain 'B' and resid 4540 through 4559 removed outlier: 4.054A pdb=" N LEU B4544 " --> pdb=" O PHE B4540 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU B4545 " --> pdb=" O TRP B4541 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL B4546 " --> pdb=" O GLY B4542 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE B4559 " --> pdb=" O LEU B4555 " (cutoff:3.500A) Processing helix chain 'B' and resid 4560 through 4579 removed outlier: 4.886A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4642 through 4664 removed outlier: 4.073A pdb=" N LEU B4646 " --> pdb=" O ALA B4642 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B4658 " --> pdb=" O ALA B4654 " (cutoff:3.500A) Processing helix chain 'B' and resid 4666 through 4684 removed outlier: 3.793A pdb=" N ILE B4670 " --> pdb=" O VAL B4666 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B4682 " --> pdb=" O ALA B4678 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE B4683 " --> pdb=" O ARG B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4707 removed outlier: 4.388A pdb=" N ASP B4702 " --> pdb=" O LYS B4698 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ARG B4703 " --> pdb=" O GLY B4699 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4728 removed outlier: 3.943A pdb=" N LEU B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 removed outlier: 3.551A pdb=" N ILE B4737 " --> pdb=" O GLY B4733 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B4739 " --> pdb=" O GLU B4735 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B4740 " --> pdb=" O ARG B4736 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B4742 " --> pdb=" O ALA B4738 " (cutoff:3.500A) Processing helix chain 'B' and resid 4745 through 4750 removed outlier: 4.506A pdb=" N ILE B4750 " --> pdb=" O ALA B4746 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4787 removed outlier: 3.678A pdb=" N PHE B4784 " --> pdb=" O PHE B4780 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR B4785 " --> pdb=" O GLY B4781 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN B4787 " --> pdb=" O ILE B4783 " (cutoff:3.500A) Processing helix chain 'B' and resid 4788 through 4803 removed outlier: 3.807A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) Processing helix chain 'B' and resid 4808 through 4820 removed outlier: 4.191A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B4817 " --> pdb=" O LEU B4813 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLY B4819 " --> pdb=" O ASP B4815 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B4820 " --> pdb=" O ILE B4816 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 4.085A pdb=" N THR B4825 " --> pdb=" O LYS B4821 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 removed outlier: 4.139A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B4842 " --> pdb=" O VAL B4838 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B4843 " --> pdb=" O MET B4839 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B4848 " --> pdb=" O LEU B4844 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR B4849 " --> pdb=" O ALA B4845 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B4853 " --> pdb=" O TYR B4849 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B4854 " --> pdb=" O LEU B4850 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B4855 " --> pdb=" O TYR B4851 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 5.431A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4897 through 4902 removed outlier: 4.332A pdb=" N ILE B4901 " --> pdb=" O ILE B4897 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLU B4902 " --> pdb=" O GLY B4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4897 through 4902' Processing helix chain 'B' and resid 4909 through 4925 removed outlier: 4.226A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B4916 " --> pdb=" O TYR B4912 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B4923 " --> pdb=" O THR B4919 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B4924 " --> pdb=" O PHE B4920 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B4925 " --> pdb=" O PHE B4921 " (cutoff:3.500A) Processing helix chain 'B' and resid 4928 through 4957 removed outlier: 3.875A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B4933 " --> pdb=" O LEU B4929 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE B4937 " --> pdb=" O GLN B4933 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS B4951 " --> pdb=" O GLN B4947 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B4955 " --> pdb=" O LYS B4951 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B4956 " --> pdb=" O GLU B4952 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS B4957 " --> pdb=" O ASP B4953 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4970 removed outlier: 4.151A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 removed outlier: 3.574A pdb=" N LEU B4980 " --> pdb=" O GLU B4976 " (cutoff:3.500A) Processing helix chain 'B' and resid 4984 through 4999 removed outlier: 6.698A pdb=" N TYR B4988 " --> pdb=" O ASN B4984 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N MET B4989 " --> pdb=" O LEU B4985 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B4990 " --> pdb=" O ALA B4986 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP B4999 " --> pdb=" O LEU B4995 " (cutoff:3.500A) Processing helix chain 'B' and resid 5004 through 5017 removed outlier: 3.592A pdb=" N TYR B5009 " --> pdb=" O GLY B5005 " (cutoff:3.500A) Processing helix chain 'B' and resid 5027 through 5033 removed outlier: 6.594A pdb=" N GLN B5031 " --> pdb=" O CYS B5027 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR B5032 " --> pdb=" O PHE B5028 " (cutoff:3.500A) Processing helix chain 'B' and resid 3870 through 3875 removed outlier: 3.706A pdb=" N LYS B3873 " --> pdb=" O ASN B3870 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B3874 " --> pdb=" O GLY B3871 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N MET B3875 " --> pdb=" O GLU B3872 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3870 through 3875' Processing helix chain 'B' and resid 1978 through 1984 removed outlier: 3.887A pdb=" N ALA B1983 " --> pdb=" O ALA B1978 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B1984 " --> pdb=" O LEU B1979 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1978 through 1984' Processing helix chain 'B' and resid 3861 through 3868 removed outlier: 6.952A pdb=" N ILE B3866 " --> pdb=" O GLU B3861 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN B3867 " --> pdb=" O ASP B3862 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG B3868 " --> pdb=" O GLY B3863 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3861 through 3868' Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.907A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 84 removed outlier: 4.116A pdb=" N MET D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 256 removed outlier: 4.070A pdb=" N CYS D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 256' Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.493A pdb=" N ALA D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N HIS D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 364 through 371 removed outlier: 4.358A pdb=" N LEU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 422 removed outlier: 3.924A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 removed outlier: 4.885A pdb=" N VAL D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 480 removed outlier: 3.766A pdb=" N GLN D 465 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 478 " --> pdb=" O ARG D 474 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLN D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 496 removed outlier: 6.346A pdb=" N LEU D 486 " --> pdb=" O GLY D 482 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 removed outlier: 4.691A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE D 518 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 531 " --> pdb=" O ALA D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 541 removed outlier: 3.765A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.735A pdb=" N VAL D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.542A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 562 " --> pdb=" O SER D 558 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 4.255A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 594 removed outlier: 3.789A pdb=" N LYS D 584 " --> pdb=" O GLU D 580 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 4.017A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 626 removed outlier: 4.218A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 890 removed outlier: 4.797A pdb=" N ILE D 870 " --> pdb=" O HIS D 866 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 871 " --> pdb=" O LEU D 867 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 936 removed outlier: 3.838A pdb=" N LEU D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 1005 removed outlier: 4.443A pdb=" N THR D 982 " --> pdb=" O THR D 978 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR D 983 " --> pdb=" O PRO D 979 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN D1003 " --> pdb=" O ASP D 999 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY D1004 " --> pdb=" O ARG D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1050 removed outlier: 4.528A pdb=" N GLN D1041 " --> pdb=" O ASP D1037 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA D1042 " --> pdb=" O SER D1038 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL D1043 " --> pdb=" O LEU D1039 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG D1044 " --> pdb=" O CYS D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1574 through 1581 removed outlier: 4.130A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET D1579 " --> pdb=" O LEU D1575 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU D1581 " --> pdb=" O ALA D1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1574 through 1581' Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 3.897A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG D1656 " --> pdb=" O GLU D1652 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1649 through 1657' Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 3.940A pdb=" N PHE D1662 " --> pdb=" O ASP D1658 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA D1675 " --> pdb=" O ARG D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1689 removed outlier: 4.273A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1692 through 1701 removed outlier: 4.018A pdb=" N HIS D1696 " --> pdb=" O ALA D1692 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA D1701 " --> pdb=" O ALA D1697 " (cutoff:3.500A) Processing helix chain 'D' and resid 1707 through 1720 removed outlier: 4.444A pdb=" N TYR D1711 " --> pdb=" O LEU D1707 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D1712 " --> pdb=" O ARG D1708 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP D1713 " --> pdb=" O ALA D1709 " (cutoff:3.500A) Processing helix chain 'D' and resid 1723 through 1731 removed outlier: 4.778A pdb=" N ARG D1727 " --> pdb=" O ALA D1723 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET D1730 " --> pdb=" O SER D1726 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.550A pdb=" N ALA D1744 " --> pdb=" O PRO D1740 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 4.021A pdb=" N LEU D1807 " --> pdb=" O PRO D1803 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D1824 " --> pdb=" O ARG D1820 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 removed outlier: 3.526A pdb=" N VAL D1839 " --> pdb=" O GLU D1835 " (cutoff:3.500A) Proline residue: D1840 - end of helix removed outlier: 4.875A pdb=" N LYS D1843 " --> pdb=" O VAL D1839 " (cutoff:3.500A) Processing helix chain 'D' and resid 1855 through 1865 removed outlier: 3.815A pdb=" N MET D1865 " --> pdb=" O GLN D1861 " (cutoff:3.500A) Processing helix chain 'D' and resid 1866 through 1871 Processing helix chain 'D' and resid 1934 through 1977 removed outlier: 4.187A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D1946 " --> pdb=" O LEU D1942 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D1964 " --> pdb=" O ALA D1960 " (cutoff:3.500A) Processing helix chain 'D' and resid 1988 through 1999 removed outlier: 4.566A pdb=" N ALA D1992 " --> pdb=" O ALA D1988 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D1993 " --> pdb=" O ALA D1989 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG D1996 " --> pdb=" O ALA D1992 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2015 removed outlier: 4.342A pdb=" N GLU D2015 " --> pdb=" O HIS D2011 " (cutoff:3.500A) Processing helix chain 'D' and resid 2024 through 2043 removed outlier: 4.835A pdb=" N ARG D2028 " --> pdb=" O PRO D2024 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLN D2029 " --> pdb=" O GLU D2025 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASP D2030 " --> pdb=" O ASP D2026 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU D2031 " --> pdb=" O ILE D2027 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN D2032 " --> pdb=" O ARG D2028 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY D2043 " --> pdb=" O LEU D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 5.201A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.570A pdb=" N VAL D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2142 Proline residue: D2139 - end of helix removed outlier: 5.622A pdb=" N TYR D2142 " --> pdb=" O LEU D2138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 4.267A pdb=" N THR D2152 " --> pdb=" O SER D2148 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2172 through 2188 removed outlier: 3.872A pdb=" N ASN D2176 " --> pdb=" O PRO D2172 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN D2187 " --> pdb=" O GLY D2183 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2194 removed outlier: 4.659A pdb=" N GLN D2193 " --> pdb=" O LYS D2189 " (cutoff:3.500A) Processing helix chain 'D' and resid 2195 through 2202 removed outlier: 3.621A pdb=" N ALA D2200 " --> pdb=" O ASN D2196 " (cutoff:3.500A) Processing helix chain 'D' and resid 2203 through 2215 Processing helix chain 'D' and resid 2227 through 2243 removed outlier: 4.581A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2252 removed outlier: 4.132A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) Processing helix chain 'D' and resid 2253 through 2264 removed outlier: 3.818A pdb=" N GLU D2259 " --> pdb=" O SER D2255 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2281 removed outlier: 3.916A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE D2281 " --> pdb=" O ALA D2277 " (cutoff:3.500A) Processing helix chain 'D' and resid 2286 through 2291 removed outlier: 4.283A pdb=" N GLN D2291 " --> pdb=" O ALA D2287 " (cutoff:3.500A) Processing helix chain 'D' and resid 2294 through 2309 removed outlier: 5.352A pdb=" N SER D2309 " --> pdb=" O CYS D2305 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2315 removed outlier: 4.780A pdb=" N ALA D2315 " --> pdb=" O PRO D2311 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2340 removed outlier: 4.114A pdb=" N GLY D2328 " --> pdb=" O ASN D2324 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU D2332 " --> pdb=" O GLY D2328 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP D2333 " --> pdb=" O GLU D2329 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU D2335 " --> pdb=" O TYR D2331 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.542A pdb=" N ALA D2350 " --> pdb=" O VAL D2346 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL D2353 " --> pdb=" O ASN D2349 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2365 through 2370 removed outlier: 3.609A pdb=" N GLY D2370 " --> pdb=" O PRO D2366 " (cutoff:3.500A) Processing helix chain 'D' and resid 2375 through 2389 Processing helix chain 'D' and resid 2417 through 2437 removed outlier: 4.790A pdb=" N ALA D2421 " --> pdb=" O HIS D2417 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D2422 " --> pdb=" O LEU D2418 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D2437 " --> pdb=" O LEU D2433 " (cutoff:3.500A) Processing helix chain 'D' and resid 2441 through 2446 removed outlier: 5.165A pdb=" N ALA D2445 " --> pdb=" O HIS D2441 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY D2446 " --> pdb=" O LEU D2442 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2441 through 2446' Processing helix chain 'D' and resid 2447 through 2462 removed outlier: 4.214A pdb=" N LEU D2451 " --> pdb=" O LYS D2447 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D2461 " --> pdb=" O LEU D2457 " (cutoff:3.500A) Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2465 through 2472 removed outlier: 3.863A pdb=" N SER D2471 " --> pdb=" O VAL D2467 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D2472 " --> pdb=" O GLY D2468 " (cutoff:3.500A) Processing helix chain 'D' and resid 2748 through 2774 removed outlier: 4.419A pdb=" N SER D2753 " --> pdb=" O GLU D2749 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE D2754 " --> pdb=" O LYS D2750 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN D2774 " --> pdb=" O LYS D2770 " (cutoff:3.500A) Processing helix chain 'D' and resid 2798 through 2814 removed outlier: 3.709A pdb=" N TYR D2805 " --> pdb=" O ASP D2801 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP D2807 " --> pdb=" O GLU D2803 " (cutoff:3.500A) Proline residue: D2808 - end of helix removed outlier: 5.225A pdb=" N GLU D2811 " --> pdb=" O TRP D2807 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER D2812 " --> pdb=" O PRO D2808 " (cutoff:3.500A) Processing helix chain 'D' and resid 2815 through 2820 Processing helix chain 'D' and resid 2870 through 2896 removed outlier: 3.635A pdb=" N TRP D2886 " --> pdb=" O TYR D2882 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA D2896 " --> pdb=" O GLN D2892 " (cutoff:3.500A) Processing helix chain 'D' and resid 2907 through 2912 removed outlier: 5.549A pdb=" N THR D2912 " --> pdb=" O TYR D2908 " (cutoff:3.500A) Processing helix chain 'D' and resid 2915 through 2932 removed outlier: 4.429A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D2931 " --> pdb=" O LEU D2927 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N MET D2932 " --> pdb=" O LYS D2928 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3657 removed outlier: 3.722A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) Processing helix chain 'D' and resid 3667 through 3684 removed outlier: 5.013A pdb=" N ASP D3671 " --> pdb=" O HIS D3667 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ARG D3672 " --> pdb=" O SER D3668 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE D3674 " --> pdb=" O GLU D3670 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP D3675 " --> pdb=" O ASP D3671 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP D3676 " --> pdb=" O ARG D3672 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU D3677 " --> pdb=" O MET D3673 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY D3681 " --> pdb=" O LEU D3677 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU D3684 " --> pdb=" O ALA D3680 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3712 removed outlier: 6.123A pdb=" N GLU D3712 " --> pdb=" O THR D3708 " (cutoff:3.500A) Processing helix chain 'D' and resid 3719 through 3735 removed outlier: 3.839A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3771 removed outlier: 3.874A pdb=" N GLU D3759 " --> pdb=" O GLU D3755 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS D3760 " --> pdb=" O LYS D3756 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN D3761 " --> pdb=" O GLU D3757 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS D3771 " --> pdb=" O GLN D3767 " (cutoff:3.500A) Processing helix chain 'D' and resid 3776 through 3786 removed outlier: 4.565A pdb=" N LEU D3780 " --> pdb=" O ALA D3776 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D3785 " --> pdb=" O GLN D3781 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N CYS D3786 " --> pdb=" O MET D3782 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 removed outlier: 3.534A pdb=" N SER D3795 " --> pdb=" O GLY D3791 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS D3799 " --> pdb=" O SER D3795 " (cutoff:3.500A) Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3826 through 3839 removed outlier: 7.291A pdb=" N GLN D3830 " --> pdb=" O VAL D3826 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER D3831 " --> pdb=" O GLY D3827 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR D3838 " --> pdb=" O ALA D3834 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3857 removed outlier: 3.640A pdb=" N GLY D3855 " --> pdb=" O ASN D3851 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU D3856 " --> pdb=" O LYS D3852 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY D3857 " --> pdb=" O ALA D3853 " (cutoff:3.500A) Processing helix chain 'D' and resid 3879 through 3893 removed outlier: 5.439A pdb=" N ASP D3883 " --> pdb=" O GLU D3879 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D3884 " --> pdb=" O PHE D3880 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS D3892 " --> pdb=" O LEU D3888 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 6.470A pdb=" N GLN D3900 " --> pdb=" O ASN D3896 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN D3901 " --> pdb=" O ASN D3897 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.783A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP D3935 " --> pdb=" O SER D3931 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR D3936 " --> pdb=" O ASP D3932 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR D3937 " --> pdb=" O PHE D3933 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 4.240A pdb=" N LYS D3953 " --> pdb=" O ARG D3949 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA D3954 " --> pdb=" O ASN D3950 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D3958 " --> pdb=" O ALA D3954 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D3968 " --> pdb=" O SER D3964 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 3.846A pdb=" N GLN D3977 " --> pdb=" O CYS D3973 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D3983 " --> pdb=" O SER D3979 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4003 removed outlier: 4.076A pdb=" N GLY D3991 " --> pdb=" O ASP D3987 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET D3999 " --> pdb=" O VAL D3995 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET D4000 " --> pdb=" O PHE D3996 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 4.021A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4052 removed outlier: 6.375A pdb=" N ARG D4042 " --> pdb=" O GLY D4038 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN D4043 " --> pdb=" O MET D4039 " (cutoff:3.500A) Processing helix chain 'D' and resid 4053 through 4075 removed outlier: 4.247A pdb=" N MET D4057 " --> pdb=" O SER D4053 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE D4058 " --> pdb=" O ASN D4054 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU D4068 " --> pdb=" O MET D4064 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS D4069 " --> pdb=" O PHE D4065 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE D4071 " --> pdb=" O LYS D4067 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D4072 " --> pdb=" O LEU D4068 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY D4073 " --> pdb=" O LYS D4069 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER D4074 " --> pdb=" O ASP D4070 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU D4075 " --> pdb=" O ILE D4071 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 3.952A pdb=" N PHE D4093 " --> pdb=" O SER D4089 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4115 Processing helix chain 'D' and resid 4124 through 4155 removed outlier: 3.893A pdb=" N ASN D4130 " --> pdb=" O GLU D4126 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Proline residue: D4135 - end of helix removed outlier: 4.300A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY D4140 " --> pdb=" O ALA D4136 " (cutoff:3.500A) Proline residue: D4155 - end of helix Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 3.671A pdb=" N ALA D4167 " --> pdb=" O PHE D4163 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU D4168 " --> pdb=" O LEU D4164 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4179 Proline residue: D4176 - end of helix removed outlier: 5.542A pdb=" N GLY D4179 " --> pdb=" O ARG D4175 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4207 removed outlier: 4.790A pdb=" N ARG D4202 " --> pdb=" O SER D4198 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D4203 " --> pdb=" O GLU D4199 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU D4206 " --> pdb=" O ARG D4202 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4224 Processing helix chain 'D' and resid 4229 through 4252 removed outlier: 3.909A pdb=" N ILE D4251 " --> pdb=" O ILE D4247 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D4252 " --> pdb=" O ALA D4248 " (cutoff:3.500A) Processing helix chain 'D' and resid 4540 through 4559 removed outlier: 3.871A pdb=" N LEU D4544 " --> pdb=" O PHE D4540 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLU D4545 " --> pdb=" O TRP D4541 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL D4546 " --> pdb=" O GLY D4542 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN D4558 " --> pdb=" O TYR D4554 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE D4559 " --> pdb=" O LEU D4555 " (cutoff:3.500A) Processing helix chain 'D' and resid 4560 through 4579 removed outlier: 3.575A pdb=" N LEU D4578 " --> pdb=" O ASN D4574 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4642 through 4664 removed outlier: 3.930A pdb=" N LEU D4646 " --> pdb=" O ALA D4642 " (cutoff:3.500A) Processing helix chain 'D' and resid 4666 through 4684 removed outlier: 3.993A pdb=" N ILE D4670 " --> pdb=" O VAL D4666 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS D4680 " --> pdb=" O GLU D4676 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE D4683 " --> pdb=" O ARG D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4696 through 4707 removed outlier: 4.336A pdb=" N ASP D4702 " --> pdb=" O LYS D4698 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4728 removed outlier: 4.016A pdb=" N LEU D4725 " --> pdb=" O LYS D4721 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP D4726 " --> pdb=" O ARG D4722 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D4727 " --> pdb=" O LYS D4723 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 removed outlier: 3.777A pdb=" N ILE D4737 " --> pdb=" O GLY D4733 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D4738 " --> pdb=" O ARG D4734 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D4739 " --> pdb=" O GLU D4735 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU D4740 " --> pdb=" O ARG D4736 " (cutoff:3.500A) Processing helix chain 'D' and resid 4745 through 4750 removed outlier: 4.104A pdb=" N ILE D4750 " --> pdb=" O ALA D4746 " (cutoff:3.500A) Processing helix chain 'D' and resid 4772 through 4787 removed outlier: 3.523A pdb=" N GLN D4776 " --> pdb=" O ASP D4772 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D4785 " --> pdb=" O GLY D4781 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP D4786 " --> pdb=" O VAL D4782 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN D4787 " --> pdb=" O ILE D4783 " (cutoff:3.500A) Processing helix chain 'D' and resid 4788 through 4803 Processing helix chain 'D' and resid 4808 through 4820 removed outlier: 4.142A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLY D4819 " --> pdb=" O ASP D4815 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL D4820 " --> pdb=" O ILE D4816 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.935A pdb=" N THR D4825 " --> pdb=" O LYS D4821 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D4826 " --> pdb=" O THR D4822 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS D4832 " --> pdb=" O SER D4828 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 removed outlier: 3.634A pdb=" N GLY D4842 " --> pdb=" O VAL D4838 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D4848 " --> pdb=" O LEU D4844 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR D4849 " --> pdb=" O ALA D4845 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU D4850 " --> pdb=" O VAL D4846 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR D4851 " --> pdb=" O VAL D4847 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D4853 " --> pdb=" O TYR D4849 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D4855 " --> pdb=" O TYR D4851 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.499A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4897 through 4902 removed outlier: 5.066A pdb=" N ILE D4901 " --> pdb=" O ILE D4897 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU D4902 " --> pdb=" O GLY D4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4897 through 4902' Processing helix chain 'D' and resid 4909 through 4925 removed outlier: 3.898A pdb=" N VAL D4914 " --> pdb=" O GLU D4910 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE D4923 " --> pdb=" O THR D4919 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D4924 " --> pdb=" O PHE D4920 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D4925 " --> pdb=" O PHE D4921 " (cutoff:3.500A) Processing helix chain 'D' and resid 4928 through 4957 removed outlier: 4.083A pdb=" N ILE D4936 " --> pdb=" O ILE D4932 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D4937 " --> pdb=" O GLN D4933 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D4940 " --> pdb=" O ILE D4936 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D4941 " --> pdb=" O ILE D4937 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS D4951 " --> pdb=" O GLN D4947 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET D4954 " --> pdb=" O VAL D4950 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D4955 " --> pdb=" O LYS D4951 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR D4956 " --> pdb=" O GLU D4952 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4970 removed outlier: 4.033A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 removed outlier: 3.709A pdb=" N HIS D4978 " --> pdb=" O GLY D4974 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D4979 " --> pdb=" O PHE D4975 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D4980 " --> pdb=" O GLU D4976 " (cutoff:3.500A) Processing helix chain 'D' and resid 4984 through 4999 removed outlier: 6.671A pdb=" N TYR D4988 " --> pdb=" O ASN D4984 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N MET D4989 " --> pdb=" O LEU D4985 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D4996 " --> pdb=" O LEU D4992 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP D4999 " --> pdb=" O LEU D4995 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 removed outlier: 3.674A pdb=" N TYR D5009 " --> pdb=" O GLY D5005 " (cutoff:3.500A) Processing helix chain 'D' and resid 5027 through 5033 removed outlier: 6.069A pdb=" N GLN D5031 " --> pdb=" O CYS D5027 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR D5032 " --> pdb=" O PHE D5028 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D5033 " --> pdb=" O ARG D5029 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5027 through 5033' Processing helix chain 'D' and resid 3870 through 3875 removed outlier: 3.868A pdb=" N LYS D3873 " --> pdb=" O ASN D3870 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL D3874 " --> pdb=" O GLY D3871 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N MET D3875 " --> pdb=" O GLU D3872 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3870 through 3875' Processing helix chain 'D' and resid 1978 through 1984 removed outlier: 3.829A pdb=" N ALA D1983 " --> pdb=" O ALA D1978 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D1984 " --> pdb=" O LEU D1979 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1978 through 1984' Processing helix chain 'D' and resid 3861 through 3868 removed outlier: 6.823A pdb=" N ILE D3866 " --> pdb=" O GLU D3861 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN D3867 " --> pdb=" O ASP D3862 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG D3868 " --> pdb=" O GLY D3863 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3861 through 3868' Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.729A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 84 removed outlier: 4.056A pdb=" N MET C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 256 removed outlier: 4.655A pdb=" N CYS C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 256' Processing helix chain 'C' and resid 303 through 308 removed outlier: 4.354A pdb=" N ALA C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.386A pdb=" N LEU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 422 removed outlier: 3.602A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 4.866A pdb=" N VAL C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 480 removed outlier: 3.736A pdb=" N GLN C 465 " --> pdb=" O HIS C 461 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 478 " --> pdb=" O ARG C 474 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 496 removed outlier: 6.755A pdb=" N LEU C 486 " --> pdb=" O GLY C 482 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 removed outlier: 5.378A pdb=" N SER C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 529 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 531 " --> pdb=" O ALA C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 3.741A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 551 removed outlier: 3.835A pdb=" N VAL C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 4.803A pdb=" N LEU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER C 571 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 4.258A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 594 removed outlier: 3.785A pdb=" N LYS C 584 " --> pdb=" O GLU C 580 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 4.011A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 removed outlier: 4.223A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 890 removed outlier: 6.221A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 871 " --> pdb=" O LEU C 867 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 removed outlier: 3.924A pdb=" N LEU C 935 " --> pdb=" O THR C 931 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1005 removed outlier: 3.964A pdb=" N THR C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN C1003 " --> pdb=" O ASP C 999 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1050 removed outlier: 4.907A pdb=" N LYS C1032 " --> pdb=" O ASP C1028 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN C1041 " --> pdb=" O ASP C1037 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C1042 " --> pdb=" O SER C1038 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C1043 " --> pdb=" O LEU C1039 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG C1044 " --> pdb=" O CYS C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1574 through 1581 removed outlier: 4.042A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C1580 " --> pdb=" O SER C1576 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU C1581 " --> pdb=" O ALA C1577 " (cutoff:3.500A) Processing helix chain 'C' and resid 1649 through 1657 removed outlier: 4.191A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU C1655 " --> pdb=" O LEU C1651 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C1656 " --> pdb=" O GLU C1652 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C1657 " --> pdb=" O LEU C1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1649 through 1657' Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 3.867A pdb=" N PHE C1662 " --> pdb=" O ASP C1658 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1689 removed outlier: 3.972A pdb=" N SER C1687 " --> pdb=" O HIS C1683 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C1688 " --> pdb=" O ALA C1684 " (cutoff:3.500A) Processing helix chain 'C' and resid 1692 through 1701 removed outlier: 4.104A pdb=" N HIS C1696 " --> pdb=" O ALA C1692 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP C1700 " --> pdb=" O HIS C1696 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA C1701 " --> pdb=" O ALA C1697 " (cutoff:3.500A) Processing helix chain 'C' and resid 1707 through 1720 removed outlier: 3.767A pdb=" N TYR C1711 " --> pdb=" O LEU C1707 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP C1713 " --> pdb=" O ALA C1709 " (cutoff:3.500A) Processing helix chain 'C' and resid 1723 through 1731 removed outlier: 4.104A pdb=" N ARG C1727 " --> pdb=" O ALA C1723 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 3.787A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.628A pdb=" N GLN C1824 " --> pdb=" O ARG C1820 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix removed outlier: 4.781A pdb=" N LYS C1843 " --> pdb=" O VAL C1839 " (cutoff:3.500A) Processing helix chain 'C' and resid 1855 through 1865 removed outlier: 3.809A pdb=" N MET C1865 " --> pdb=" O GLN C1861 " (cutoff:3.500A) Processing helix chain 'C' and resid 1866 through 1871 Processing helix chain 'C' and resid 1934 through 1977 removed outlier: 3.695A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C1946 " --> pdb=" O LEU C1942 " (cutoff:3.500A) Processing helix chain 'C' and resid 1988 through 1999 removed outlier: 3.816A pdb=" N ALA C1992 " --> pdb=" O ALA C1988 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C1993 " --> pdb=" O ALA C1989 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG C1996 " --> pdb=" O ALA C1992 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2015 removed outlier: 4.038A pdb=" N GLU C2015 " --> pdb=" O HIS C2011 " (cutoff:3.500A) Processing helix chain 'C' and resid 2024 through 2043 removed outlier: 5.029A pdb=" N ARG C2028 " --> pdb=" O PRO C2024 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN C2029 " --> pdb=" O GLU C2025 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP C2030 " --> pdb=" O ASP C2026 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU C2031 " --> pdb=" O ILE C2027 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN C2032 " --> pdb=" O ARG C2028 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 5.181A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.513A pdb=" N VAL C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR C2128 " --> pdb=" O LEU C2124 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2142 Proline residue: C2139 - end of helix removed outlier: 5.665A pdb=" N TYR C2142 " --> pdb=" O LEU C2138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2148 through 2169 removed outlier: 4.300A pdb=" N THR C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2172 through 2188 removed outlier: 4.207A pdb=" N ASN C2176 " --> pdb=" O PRO C2172 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU C2177 " --> pdb=" O GLN C2173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C2186 " --> pdb=" O ILE C2182 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN C2187 " --> pdb=" O GLY C2183 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2194 removed outlier: 3.987A pdb=" N GLN C2193 " --> pdb=" O LYS C2189 " (cutoff:3.500A) Processing helix chain 'C' and resid 2195 through 2202 removed outlier: 3.953A pdb=" N ARG C2199 " --> pdb=" O PRO C2195 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA C2200 " --> pdb=" O ASN C2196 " (cutoff:3.500A) Processing helix chain 'C' and resid 2203 through 2215 Processing helix chain 'C' and resid 2227 through 2243 removed outlier: 4.531A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C2242 " --> pdb=" O TYR C2238 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2252 removed outlier: 4.376A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) Processing helix chain 'C' and resid 2253 through 2264 removed outlier: 3.892A pdb=" N LEU C2257 " --> pdb=" O HIS C2253 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C2259 " --> pdb=" O SER C2255 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2281 removed outlier: 4.273A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE C2281 " --> pdb=" O ALA C2277 " (cutoff:3.500A) Processing helix chain 'C' and resid 2286 through 2291 removed outlier: 3.611A pdb=" N LEU C2290 " --> pdb=" O LEU C2286 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN C2291 " --> pdb=" O ALA C2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2286 through 2291' Processing helix chain 'C' and resid 2294 through 2309 removed outlier: 5.294A pdb=" N SER C2309 " --> pdb=" O CYS C2305 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2315 removed outlier: 4.604A pdb=" N ALA C2315 " --> pdb=" O PRO C2311 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2340 removed outlier: 3.921A pdb=" N GLY C2328 " --> pdb=" O ASN C2324 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU C2332 " --> pdb=" O GLY C2328 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP C2333 " --> pdb=" O GLU C2329 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C2335 " --> pdb=" O TYR C2331 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C2336 " --> pdb=" O LEU C2332 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 3.688A pdb=" N ALA C2350 " --> pdb=" O VAL C2346 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C2353 " --> pdb=" O ASN C2349 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS C2360 " --> pdb=" O LEU C2356 " (cutoff:3.500A) Proline residue: C2361 - end of helix Processing helix chain 'C' and resid 2365 through 2370 removed outlier: 3.646A pdb=" N GLY C2370 " --> pdb=" O PRO C2366 " (cutoff:3.500A) Processing helix chain 'C' and resid 2375 through 2389 Processing helix chain 'C' and resid 2417 through 2437 removed outlier: 4.635A pdb=" N ALA C2421 " --> pdb=" O HIS C2417 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C2422 " --> pdb=" O LEU C2418 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C2437 " --> pdb=" O LEU C2433 " (cutoff:3.500A) Processing helix chain 'C' and resid 2441 through 2446 removed outlier: 5.162A pdb=" N ALA C2445 " --> pdb=" O HIS C2441 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C2446 " --> pdb=" O LEU C2442 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2441 through 2446' Processing helix chain 'C' and resid 2447 through 2462 removed outlier: 4.116A pdb=" N LEU C2451 " --> pdb=" O LYS C2447 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C2461 " --> pdb=" O LEU C2457 " (cutoff:3.500A) Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2465 through 2472 removed outlier: 3.828A pdb=" N SER C2471 " --> pdb=" O VAL C2467 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C2472 " --> pdb=" O GLY C2468 " (cutoff:3.500A) Processing helix chain 'C' and resid 2748 through 2774 removed outlier: 4.197A pdb=" N SER C2753 " --> pdb=" O GLU C2749 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C2754 " --> pdb=" O LYS C2750 " (cutoff:3.500A) Processing helix chain 'C' and resid 2798 through 2814 removed outlier: 3.716A pdb=" N TYR C2805 " --> pdb=" O ASP C2801 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP C2807 " --> pdb=" O GLU C2803 " (cutoff:3.500A) Proline residue: C2808 - end of helix removed outlier: 5.008A pdb=" N GLU C2811 " --> pdb=" O TRP C2807 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER C2812 " --> pdb=" O PRO C2808 " (cutoff:3.500A) Processing helix chain 'C' and resid 2815 through 2820 Processing helix chain 'C' and resid 2870 through 2896 removed outlier: 3.753A pdb=" N MET C2874 " --> pdb=" O GLU C2870 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA C2896 " --> pdb=" O GLN C2892 " (cutoff:3.500A) Processing helix chain 'C' and resid 2907 through 2912 removed outlier: 3.501A pdb=" N LEU C2911 " --> pdb=" O PRO C2907 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N THR C2912 " --> pdb=" O TYR C2908 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2907 through 2912' Processing helix chain 'C' and resid 2915 through 2932 removed outlier: 4.261A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN C2931 " --> pdb=" O LEU C2927 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N MET C2932 " --> pdb=" O LYS C2928 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3657 removed outlier: 3.510A pdb=" N TYR C3657 " --> pdb=" O PHE C3653 " (cutoff:3.500A) Processing helix chain 'C' and resid 3667 through 3684 removed outlier: 4.879A pdb=" N ASP C3671 " --> pdb=" O HIS C3667 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ARG C3672 " --> pdb=" O SER C3668 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE C3674 " --> pdb=" O GLU C3670 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP C3675 " --> pdb=" O ASP C3671 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP C3676 " --> pdb=" O ARG C3672 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU C3677 " --> pdb=" O MET C3673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY C3681 " --> pdb=" O LEU C3677 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU C3684 " --> pdb=" O ALA C3680 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3712 removed outlier: 6.018A pdb=" N GLU C3712 " --> pdb=" O THR C3708 " (cutoff:3.500A) Processing helix chain 'C' and resid 3719 through 3735 removed outlier: 3.862A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3771 removed outlier: 4.041A pdb=" N LYS C3760 " --> pdb=" O LYS C3756 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS C3771 " --> pdb=" O GLN C3767 " (cutoff:3.500A) Processing helix chain 'C' and resid 3776 through 3786 removed outlier: 4.764A pdb=" N LEU C3780 " --> pdb=" O ALA C3776 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C3781 " --> pdb=" O GLU C3777 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C3785 " --> pdb=" O GLN C3781 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N CYS C3786 " --> pdb=" O MET C3782 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 3.673A pdb=" N SER C3795 " --> pdb=" O GLY C3791 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS C3799 " --> pdb=" O SER C3795 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C3800 " --> pdb=" O SER C3796 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3826 through 3839 removed outlier: 7.264A pdb=" N GLN C3830 " --> pdb=" O VAL C3826 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER C3831 " --> pdb=" O GLY C3827 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N CYS C3839 " --> pdb=" O LEU C3835 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3857 removed outlier: 3.776A pdb=" N PHE C3847 " --> pdb=" O ASP C3843 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY C3855 " --> pdb=" O ASN C3851 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU C3856 " --> pdb=" O LYS C3852 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLY C3857 " --> pdb=" O ALA C3853 " (cutoff:3.500A) Processing helix chain 'C' and resid 3879 through 3893 removed outlier: 5.126A pdb=" N ASP C3883 " --> pdb=" O GLU C3879 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C3884 " --> pdb=" O PHE C3880 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3905 removed outlier: 6.473A pdb=" N GLN C3900 " --> pdb=" O ASN C3896 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASN C3901 " --> pdb=" O ASN C3897 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 3.859A pdb=" N CYS C3918 " --> pdb=" O ASN C3914 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP C3935 " --> pdb=" O SER C3931 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR C3936 " --> pdb=" O ASP C3932 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR C3937 " --> pdb=" O PHE C3933 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 4.355A pdb=" N LYS C3953 " --> pdb=" O ARG C3949 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA C3954 " --> pdb=" O ASN C3950 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA C3958 " --> pdb=" O ALA C3954 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C3968 " --> pdb=" O SER C3964 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3984 removed outlier: 3.572A pdb=" N GLN C3977 " --> pdb=" O CYS C3973 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C3983 " --> pdb=" O SER C3979 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG C3984 " --> pdb=" O LEU C3980 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4003 removed outlier: 4.104A pdb=" N GLY C3991 " --> pdb=" O ASP C3987 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET C4000 " --> pdb=" O PHE C3996 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 4.004A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4052 removed outlier: 6.313A pdb=" N ARG C4042 " --> pdb=" O GLY C4038 " (cutoff:3.500A) Processing helix chain 'C' and resid 4053 through 4075 removed outlier: 4.215A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C4058 " --> pdb=" O ASN C4054 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C4069 " --> pdb=" O PHE C4065 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE C4071 " --> pdb=" O LYS C4067 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C4072 " --> pdb=" O LEU C4068 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY C4073 " --> pdb=" O LYS C4069 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER C4074 " --> pdb=" O ASP C4070 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU C4075 " --> pdb=" O ILE C4071 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 4.234A pdb=" N PHE C4093 " --> pdb=" O SER C4089 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4115 Processing helix chain 'C' and resid 4124 through 4155 removed outlier: 4.703A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Proline residue: C4135 - end of helix removed outlier: 4.546A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C4140 " --> pdb=" O ALA C4136 " (cutoff:3.500A) Proline residue: C4155 - end of helix Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 3.580A pdb=" N ARG C4161 " --> pdb=" O ASP C4157 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN C4162 " --> pdb=" O PRO C4158 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C4168 " --> pdb=" O LEU C4164 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4179 Proline residue: C4176 - end of helix removed outlier: 5.670A pdb=" N GLY C4179 " --> pdb=" O ARG C4175 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4207 removed outlier: 4.943A pdb=" N ARG C4202 " --> pdb=" O SER C4198 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C4203 " --> pdb=" O GLU C4199 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C4206 " --> pdb=" O ARG C4202 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N MET C4207 " --> pdb=" O ALA C4203 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4224 removed outlier: 3.535A pdb=" N GLU C4224 " --> pdb=" O ASP C4220 " (cutoff:3.500A) Processing helix chain 'C' and resid 4229 through 4252 removed outlier: 3.519A pdb=" N GLN C4250 " --> pdb=" O GLN C4246 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE C4251 " --> pdb=" O ILE C4247 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER C4252 " --> pdb=" O ALA C4248 " (cutoff:3.500A) Processing helix chain 'C' and resid 4540 through 4559 removed outlier: 3.965A pdb=" N LEU C4544 " --> pdb=" O PHE C4540 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLU C4545 " --> pdb=" O TRP C4541 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL C4546 " --> pdb=" O GLY C4542 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C4558 " --> pdb=" O TYR C4554 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE C4559 " --> pdb=" O LEU C4555 " (cutoff:3.500A) Processing helix chain 'C' and resid 4560 through 4579 removed outlier: 3.757A pdb=" N LEU C4578 " --> pdb=" O ASN C4574 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4642 through 4664 removed outlier: 3.632A pdb=" N LEU C4646 " --> pdb=" O ALA C4642 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C4659 " --> pdb=" O PHE C4655 " (cutoff:3.500A) Processing helix chain 'C' and resid 4666 through 4684 Processing helix chain 'C' and resid 4696 through 4707 removed outlier: 3.621A pdb=" N ARG C4703 " --> pdb=" O GLY C4699 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4728 removed outlier: 3.583A pdb=" N LYS C4723 " --> pdb=" O PHE C4719 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C4725 " --> pdb=" O LYS C4721 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 removed outlier: 3.595A pdb=" N ALA C4738 " --> pdb=" O ARG C4734 " (cutoff:3.500A) Processing helix chain 'C' and resid 4745 through 4750 removed outlier: 4.085A pdb=" N ILE C4750 " --> pdb=" O ALA C4746 " (cutoff:3.500A) Processing helix chain 'C' and resid 4772 through 4787 removed outlier: 5.943A pdb=" N ASN C4787 " --> pdb=" O ILE C4783 " (cutoff:3.500A) Processing helix chain 'C' and resid 4788 through 4803 removed outlier: 3.806A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) Processing helix chain 'C' and resid 4808 through 4820 removed outlier: 4.073A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY C4819 " --> pdb=" O ASP C4815 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL C4820 " --> pdb=" O ILE C4816 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.957A pdb=" N THR C4825 " --> pdb=" O LYS C4821 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C4826 " --> pdb=" O THR C4822 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 removed outlier: 4.034A pdb=" N MET C4839 " --> pdb=" O LYS C4835 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C4842 " --> pdb=" O VAL C4838 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C4853 " --> pdb=" O TYR C4849 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C4854 " --> pdb=" O LEU C4850 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C4855 " --> pdb=" O TYR C4851 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C4859 " --> pdb=" O ALA C4855 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.810A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4897 through 4902 removed outlier: 4.325A pdb=" N ILE C4901 " --> pdb=" O ILE C4897 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU C4902 " --> pdb=" O GLY C4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4897 through 4902' Processing helix chain 'C' and resid 4909 through 4925 removed outlier: 3.594A pdb=" N VAL C4914 " --> pdb=" O GLU C4910 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C4925 " --> pdb=" O PHE C4921 " (cutoff:3.500A) Processing helix chain 'C' and resid 4928 through 4957 removed outlier: 4.267A pdb=" N ILE C4936 " --> pdb=" O ILE C4932 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE C4937 " --> pdb=" O GLN C4933 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C4950 " --> pdb=" O GLN C4946 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C4951 " --> pdb=" O GLN C4947 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU C4955 " --> pdb=" O LYS C4951 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR C4956 " --> pdb=" O GLU C4952 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C4957 " --> pdb=" O ASP C4953 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4970 removed outlier: 3.933A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4999 removed outlier: 6.686A pdb=" N TYR C4988 " --> pdb=" O ASN C4984 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP C4999 " --> pdb=" O LEU C4995 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'C' and resid 5027 through 5033 removed outlier: 6.211A pdb=" N GLN C5031 " --> pdb=" O CYS C5027 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR C5032 " --> pdb=" O PHE C5028 " (cutoff:3.500A) Processing helix chain 'C' and resid 3870 through 3875 removed outlier: 3.661A pdb=" N LYS C3873 " --> pdb=" O ASN C3870 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL C3874 " --> pdb=" O GLY C3871 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET C3875 " --> pdb=" O GLU C3872 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3870 through 3875' Processing helix chain 'C' and resid 1978 through 1984 removed outlier: 3.848A pdb=" N ALA C1983 " --> pdb=" O ALA C1978 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C1984 " --> pdb=" O LEU C1979 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1978 through 1984' Processing helix chain 'C' and resid 3861 through 3868 removed outlier: 6.719A pdb=" N ILE C3866 " --> pdb=" O GLU C3861 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN C3867 " --> pdb=" O ASP C3862 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG C3868 " --> pdb=" O GLY C3863 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3861 through 3868' Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.538A pdb=" N CYS A 36 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.619A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 71 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 118 through 122 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'A' and resid 148 through 152 Processing sheet with id= 5, first strand: chain 'A' and resid 180 through 183 Processing sheet with id= 6, first strand: chain 'A' and resid 217 through 221 removed outlier: 3.998A pdb=" N HIS A 218 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 230 through 233 No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'A' and resid 314 through 318 removed outlier: 3.562A pdb=" N CYS A 315 " --> pdb=" O GLN A 349 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 355 through 359 Processing sheet with id= 10, first strand: chain 'A' and resid 660 through 667 removed outlier: 7.300A pdb=" N GLY A 660 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP A 662 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 748 " --> pdb=" O TRP A 662 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS A 746 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 666 " --> pdb=" O VAL A 744 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 713 through 716 removed outlier: 6.501A pdb=" N HIS A 681 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1099 through 1104 removed outlier: 6.696A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N VAL A1072 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER A1241 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1122 through 1126 removed outlier: 3.684A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY A1129 " --> pdb=" O PRO A1138 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG A1131 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER A1136 " --> pdb=" O ARG A1131 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS A1133 " --> pdb=" O LEU A1134 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1158 through 1164 removed outlier: 3.516A pdb=" N THR A1159 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A1154 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A1161 " --> pdb=" O MET A1152 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP A1147 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A1093 " --> pdb=" O HIS A1201 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 4180 through 4184 Processing sheet with id= 16, first strand: chain 'A' and resid 4580 through 4584 Processing sheet with id= 17, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.697A pdb=" N CYS B 36 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 67 through 70 removed outlier: 3.674A pdb=" N GLU B 70 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN B 71 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 118 through 122 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'B' and resid 148 through 152 Processing sheet with id= 21, first strand: chain 'B' and resid 180 through 183 Processing sheet with id= 22, first strand: chain 'B' and resid 217 through 221 removed outlier: 3.943A pdb=" N HIS B 218 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 230 through 233 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'B' and resid 314 through 318 removed outlier: 3.733A pdb=" N CYS B 315 " --> pdb=" O GLN B 349 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 355 through 359 removed outlier: 3.533A pdb=" N THR B 358 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 660 through 667 removed outlier: 7.128A pdb=" N GLY B 660 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP B 662 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 748 " --> pdb=" O TRP B 662 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS B 746 " --> pdb=" O PHE B 664 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 713 through 716 removed outlier: 6.440A pdb=" N HIS B 681 " --> pdb=" O SER B 784 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 1099 through 1104 removed outlier: 6.625A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B1073 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL B1072 " --> pdb=" O SER B1241 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N SER B1241 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 1122 through 1126 removed outlier: 3.733A pdb=" N VAL B1123 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLY B1129 " --> pdb=" O PRO B1138 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG B1131 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER B1136 " --> pdb=" O ARG B1131 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS B1133 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 1158 through 1164 removed outlier: 3.556A pdb=" N ASP B1154 " --> pdb=" O THR B1159 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B1161 " --> pdb=" O MET B1152 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B1152 " --> pdb=" O ILE B1161 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP B1147 " --> pdb=" O ALA B1094 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 4180 through 4184 removed outlier: 3.621A pdb=" N ILE B4183 " --> pdb=" O GLU B4191 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 4580 through 4584 Processing sheet with id= 33, first strand: chain 'D' and resid 47 through 52 removed outlier: 3.583A pdb=" N CYS D 36 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.565A pdb=" N LEU D 108 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 71 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 118 through 122 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'D' and resid 148 through 152 Processing sheet with id= 37, first strand: chain 'D' and resid 180 through 183 Processing sheet with id= 38, first strand: chain 'D' and resid 217 through 221 removed outlier: 4.210A pdb=" N HIS D 218 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 230 through 233 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'D' and resid 314 through 318 removed outlier: 3.698A pdb=" N CYS D 315 " --> pdb=" O GLN D 349 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 355 through 359 removed outlier: 3.570A pdb=" N THR D 358 " --> pdb=" O ILE D 377 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 660 through 667 removed outlier: 7.345A pdb=" N GLY D 660 " --> pdb=" O LEU D 750 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 748 " --> pdb=" O TRP D 662 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS D 746 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 666 " --> pdb=" O VAL D 744 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 713 through 716 removed outlier: 6.553A pdb=" N HIS D 681 " --> pdb=" O SER D 784 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'D' and resid 1099 through 1104 removed outlier: 6.272A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG D1073 " --> pdb=" O LEU D1194 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N VAL D1072 " --> pdb=" O SER D1241 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N SER D1241 " --> pdb=" O VAL D1072 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'D' and resid 1122 through 1126 removed outlier: 3.992A pdb=" N VAL D1123 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLY D1129 " --> pdb=" O PRO D1138 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG D1131 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER D1136 " --> pdb=" O ARG D1131 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N HIS D1133 " --> pdb=" O LEU D1134 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'D' and resid 1158 through 1164 removed outlier: 4.490A pdb=" N ASP D1147 " --> pdb=" O ALA D1094 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D1094 " --> pdb=" O ASP D1147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE D1090 " --> pdb=" O CYS D1151 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D1091 " --> pdb=" O ASN D1203 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D1093 " --> pdb=" O HIS D1201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS D1201 " --> pdb=" O GLU D1093 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D1095 " --> pdb=" O VAL D1199 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'D' and resid 4180 through 4184 removed outlier: 3.541A pdb=" N ILE D4193 " --> pdb=" O ILE D4181 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D4183 " --> pdb=" O GLU D4191 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'D' and resid 4580 through 4584 Processing sheet with id= 49, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.571A pdb=" N CYS C 36 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.667A pdb=" N LEU C 108 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN C 71 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 118 through 122 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'C' and resid 148 through 152 Processing sheet with id= 53, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.518A pdb=" N ASP C 192 " --> pdb=" O HIS C 181 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 217 through 221 removed outlier: 3.995A pdb=" N HIS C 218 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 230 through 233 No H-bonds generated for sheet with id= 55 Processing sheet with id= 56, first strand: chain 'C' and resid 314 through 318 removed outlier: 3.742A pdb=" N CYS C 315 " --> pdb=" O GLN C 349 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 355 through 359 removed outlier: 3.507A pdb=" N THR C 358 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 660 through 667 removed outlier: 7.374A pdb=" N GLY C 660 " --> pdb=" O LEU C 750 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 748 " --> pdb=" O TRP C 662 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS C 746 " --> pdb=" O PHE C 664 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 713 through 716 removed outlier: 6.654A pdb=" N HIS C 681 " --> pdb=" O SER C 784 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 1099 through 1104 removed outlier: 6.809A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C1077 " --> pdb=" O PRO C1190 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N VAL C1072 " --> pdb=" O SER C1241 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N SER C1241 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'C' and resid 1122 through 1126 removed outlier: 3.682A pdb=" N VAL C1123 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLY C1129 " --> pdb=" O PRO C1138 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C1131 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C1136 " --> pdb=" O ARG C1131 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N HIS C1133 " --> pdb=" O LEU C1134 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 1158 through 1164 removed outlier: 3.755A pdb=" N ILE C1161 " --> pdb=" O MET C1152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C1152 " --> pdb=" O ILE C1161 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP C1147 " --> pdb=" O ALA C1094 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C1094 " --> pdb=" O ASP C1147 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 4180 through 4184 removed outlier: 3.582A pdb=" N ILE C4183 " --> pdb=" O GLU C4191 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'C' and resid 4580 through 4584 4109 hydrogen bonds defined for protein. 12303 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: 54.20 Time building geometry restraints manager: 36.03 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: 30272 1.33 - 1.45: 20719 1.45 - 1.58: 66039 1.58 - 1.70: 24 1.70 - 1.82: 1004 Bond restraints: 118058 Sorted by residual: bond pdb=" C GLN D 889 " pdb=" N GLY D 890 " ideal model delta sigma weight residual 1.331 1.456 -0.125 1.40e-02 5.10e+03 8.00e+01 bond pdb=" C PRO B 967 " pdb=" N ALA B 968 " ideal model delta sigma weight residual 1.331 1.485 -0.154 2.07e-02 2.33e+03 5.50e+01 bond pdb=" O2B ACP B5101 " pdb=" PB ACP B5101 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O2B ACP C5101 " pdb=" PB ACP C5101 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O2B ACP D5101 " pdb=" PB ACP D5101 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.67e+01 ... (remaining 118053 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.66: 2217 105.66 - 113.48: 65309 113.48 - 121.29: 59938 121.29 - 129.11: 32823 129.11 - 136.92: 727 Bond angle restraints: 161014 Sorted by residual: angle pdb=" O PRO B 967 " pdb=" C PRO B 967 " pdb=" N ALA B 968 " ideal model delta sigma weight residual 122.86 136.92 -14.06 1.24e+00 6.50e-01 1.29e+02 angle pdb=" CA PRO B 967 " pdb=" C PRO B 967 " pdb=" N ALA B 968 " ideal model delta sigma weight residual 114.75 98.31 16.44 1.45e+00 4.76e-01 1.28e+02 angle pdb=" N PRO D4872 " pdb=" CA PRO D4872 " pdb=" C PRO D4872 " ideal model delta sigma weight residual 113.98 102.24 11.74 1.29e+00 6.01e-01 8.29e+01 angle pdb=" CA GLN D 889 " pdb=" C GLN D 889 " pdb=" N GLY D 890 " ideal model delta sigma weight residual 118.59 105.50 13.09 1.63e+00 3.76e-01 6.45e+01 angle pdb=" C ASP B4868 " pdb=" CA ASP B4868 " pdb=" CB ASP B4868 " ideal model delta sigma weight residual 109.71 120.52 -10.81 1.39e+00 5.18e-01 6.05e+01 ... (remaining 161009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 64055 17.84 - 35.67: 5133 35.67 - 53.51: 906 53.51 - 71.35: 175 71.35 - 89.18: 67 Dihedral angle restraints: 70336 sinusoidal: 22484 harmonic: 47852 Sorted by residual: dihedral pdb=" CA ALA B 883 " pdb=" C ALA B 883 " pdb=" N LEU B 884 " pdb=" CA LEU B 884 " ideal model delta harmonic sigma weight residual 180.00 92.82 87.18 0 5.00e+00 4.00e-02 3.04e+02 dihedral pdb=" CA TRP B2807 " pdb=" C TRP B2807 " pdb=" N PRO B2808 " pdb=" CA PRO B2808 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA VAL A4666 " pdb=" C VAL A4666 " pdb=" N PRO A4667 " pdb=" CA PRO A4667 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 70333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 17891 0.077 - 0.155: 932 0.155 - 0.232: 30 0.232 - 0.309: 2 0.309 - 0.387: 1 Chirality restraints: 18856 Sorted by residual: chirality pdb=" CA ASP B4868 " pdb=" N ASP B4868 " pdb=" C ASP B4868 " pdb=" CB ASP B4868 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA ASN D4864 " pdb=" N ASN D4864 " pdb=" C ASN D4864 " pdb=" CB ASN D4864 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL B1839 " pdb=" CA VAL B1839 " pdb=" CG1 VAL B1839 " pdb=" CG2 VAL B1839 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 18853 not shown) Planarity restraints: 21167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 889 " -0.033 2.00e-02 2.50e+03 7.22e-02 5.21e+01 pdb=" C GLN D 889 " 0.124 2.00e-02 2.50e+03 pdb=" O GLN D 889 " -0.052 2.00e-02 2.50e+03 pdb=" N GLY D 890 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 967 " 0.026 2.00e-02 2.50e+03 6.19e-02 3.83e+01 pdb=" C PRO B 967 " -0.106 2.00e-02 2.50e+03 pdb=" O PRO B 967 " 0.047 2.00e-02 2.50e+03 pdb=" N ALA B 968 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D4869 " -0.026 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C GLU D4869 " 0.094 2.00e-02 2.50e+03 pdb=" O GLU D4869 " -0.036 2.00e-02 2.50e+03 pdb=" N ASP D4870 " -0.033 2.00e-02 2.50e+03 ... (remaining 21164 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 534 2.51 - 3.11: 82548 3.11 - 3.70: 173661 3.70 - 4.30: 220704 4.30 - 4.90: 358792 Nonbonded interactions: 836239 Sorted by model distance: nonbonded pdb=" NE2 HIS B 879 " pdb=" O VAL B 908 " model vdw 1.909 2.520 nonbonded pdb=" OE2 GLU D 880 " pdb=" OH TYR D 965 " model vdw 2.022 2.440 nonbonded pdb=" OE2 GLU B 880 " pdb=" OH TYR B 965 " model vdw 2.063 2.440 nonbonded pdb=" OE2 GLU B 880 " pdb=" CE2 TYR B 965 " model vdw 2.125 3.340 nonbonded pdb=" O LYS B4875 " pdb=" N ASP B4877 " model vdw 2.133 2.520 ... (remaining 836234 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' and (resid 12 through 1027 or (resid 1028 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1029 through 1031 or (resid 1032 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1033 through 3755 or ( \ resid 3756 and (name N or name CA or name C or name O or name CB )) or resid 375 \ 7 through 4542 or (resid 4543 through 4545 and (name N or name CA or name C or n \ ame O or name CB )) or resid 4546 through 4747 or (resid 4748 through 4749 and ( \ name N or name CA or name C or name O or name CB )) or resid 4750 or (resid 4751 \ through 4757 and (name N or name CA or name C or name O or name CB )) or resid \ 4758 or (resid 4759 and (name N or name CA or name C or name O or name CB )) or \ resid 4760 through 4763 or (resid 4764 through 4765 and (name N or name CA or na \ me C or name O or name CB )) or resid 4766 through 4870 or (resid 4871 and (name \ N or name CA or name C or name O or name CB )) or resid 4872 or (resid 4873 and \ (name N or name CA or name C or name O or name CB )) or resid 4874 through 5033 \ or (resid 5034 and (name N or name CA or name C or name O or name CB )) or resi \ d 5035 through 5037 or resid 5101 through 5102)) selection = (chain 'B' and (resid 12 through 1027 or (resid 1028 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1029 through 1679 or (resid 1680 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1681 through 3755 or ( \ resid 3756 and (name N or name CA or name C or name O or name CB )) or resid 375 \ 7 through 4750 or (resid 4751 through 4757 and (name N or name CA or name C or n \ ame O or name CB )) or resid 4758 through 4866 or (resid 4867 and (name N or nam \ e CA or name C or name O or name CB )) or resid 4868 through 4870 or (resid 4871 \ and (name N or name CA or name C or name O or name CB )) or resid 4872 through \ 5037 or resid 5101 through 5102)) selection = (chain 'C' and (resid 12 through 1027 or (resid 1028 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1029 through 1031 or (resid 1032 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1033 through 1679 or ( \ resid 1680 and (name N or name CA or name C or name O or name CB )) or resid 168 \ 1 through 3755 or (resid 3756 and (name N or name CA or name C or name O or name \ CB )) or resid 3757 through 4753 or (resid 4754 through 4757 and (name N or nam \ e CA or name C or name O or name CB )) or resid 4758 through 4763 or (resid 4764 \ through 4765 and (name N or name CA or name C or name O or name CB )) or resid \ 4766 through 4864 or (resid 4865 and (name N or name CA or name C or name O or n \ ame CB )) or resid 4866 or (resid 4867 and (name N or name CA or name C or name \ O or name CB )) or resid 4868 through 4872 or (resid 4873 and (name N or name CA \ or name C or name O or name CB )) or resid 4874 through 5033 or (resid 5034 and \ (name N or name CA or name C or name O or name CB )) or resid 5035 through 5037 \ or resid 5101 through 5102)) selection = (chain 'D' and (resid 12 through 1679 or (resid 1680 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1681 through 4763 or (resid 4764 through \ 4765 and (name N or name CA or name C or name O or name CB )) or resid 4766 thro \ ugh 4866 or (resid 4867 and (name N or name CA or name C or name O or name CB )) \ or resid 4868 through 4872 or (resid 4873 and (name N or name CA or name C or n \ ame O or name CB )) or resid 4874 through 5033 or (resid 5034 and (name N or nam \ e CA or name C or name O or name CB )) or resid 5035 through 5037 or resid 5101 \ through 5102)) } 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: 3.130 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: 0.090 Extract box with map and model: 19.360 Check model and map are aligned: 1.220 Set scattering table: 0.750 Process input model: 261.180 Find NCS groups from input model: 5.940 Set up NCS constraints: 0.370 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 294.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 118058 Z= 0.187 Angle : 0.646 17.941 161014 Z= 0.380 Chirality : 0.036 0.387 18856 Planarity : 0.004 0.109 21167 Dihedral : 13.799 89.183 39200 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.45 % Favored : 92.39 % Rotamer: Outliers : 0.63 % Allowed : 0.50 % Favored : 98.87 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.19 (0.08), residues: 12684 helix: 1.70 (0.08), residues: 5628 sheet: 0.08 (0.18), residues: 1012 loop : -2.07 (0.08), residues: 6044 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 862 time to evaluate : 8.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 16 residues processed: 907 average time/residue: 0.8964 time to fit residues: 1488.7952 Evaluate side-chains 696 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 680 time to evaluate : 9.080 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.9165 time to fit residues: 38.0304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 HIS A 949 ASN ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 GLN A1611 HIS A1928 GLN A1949 GLN A1973 GLN A2011 HIS A2125 HIS A3845 ASN ** A3850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3895 HIS ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3998 HIS A4102 GLN ** A4109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4130 ASN ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS A4886 HIS ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B 113 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 HIS B 949 ASN ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1611 HIS B1660 GLN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1949 GLN B1972 ASN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2011 HIS ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS B2169 GLN B2247 GLN B2260 ASN B2744 ASN B2763 HIS ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2884 ASN ** B3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3767 GLN B3781 GLN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3845 ASN B3895 HIS ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4156 HIS ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4947 GLN D 105 HIS ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN D 681 HIS D 866 HIS ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 ASN ** D1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1165 ASN D1206 GLN ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1611 HIS D1663 HIS ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1775 HIS D1928 GLN D1949 GLN D1972 ASN ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2011 HIS ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2884 ASN D2931 GLN ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3761 GLN ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3845 ASN D3895 HIS ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3946 GLN D3994 HIS D3998 HIS ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4803 HIS D4857 ASN D4886 HIS ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5015 GLN ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN C 904 HIS ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 GLN ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1611 HIS C1660 GLN ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1775 HIS C1928 GLN C1949 GLN C1972 ASN ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2011 HIS C2035 HIS C2125 HIS C2193 GLN C2763 HIS ** C3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3895 HIS ** C3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3998 HIS ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4102 GLN C4153 HIS C4574 ASN C4803 HIS ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.481 118058 Z= 2.307 Angle : 2.561 37.789 161014 Z= 1.285 Chirality : 0.098 0.581 18856 Planarity : 0.016 0.228 21167 Dihedral : 9.862 108.398 17355 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 81.81 Ramachandran Plot: Outliers : 2.24 % Allowed : 20.85 % Favored : 76.92 % Rotamer: Outliers : 6.76 % Allowed : 18.78 % Favored : 74.45 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.08 % Twisted General : 0.92 % 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: -5.38 (0.06), residues: 12684 helix: -3.51 (0.05), residues: 5760 sheet: -1.79 (0.17), residues: 880 loop : -3.94 (0.07), residues: 6044 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 665 poor density : 499 time to evaluate : 8.488 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 outliers start: 665 outliers final: 416 residues processed: 1149 average time/residue: 0.8763 time to fit residues: 1854.8356 Evaluate side-chains 873 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 457 time to evaluate : 8.746 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 416 outliers final: 7 residues processed: 416 average time/residue: 0.8055 time to fit residues: 654.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 ASN ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1663 HIS ** A1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2011 HIS ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3946 GLN ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN ** A4109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4156 HIS ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS A4933 GLN ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN B 624 ASN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 HIS ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1702 HIS B1775 HIS B1949 GLN ** B1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2169 GLN ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3809 ASN ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3998 HIS ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4142 ASN ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4728 HIS ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN D1203 ASN ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1696 HIS D1949 GLN ** D2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2011 HIS ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2169 GLN ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2881 ASN ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3896 ASN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4886 HIS ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 HIS C 974 HIS C1158 ASN ** C1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1949 GLN ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2169 GLN ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3814 GLN C3994 HIS ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4102 GLN ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4156 HIS ** C4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.035 0.484 118058 Z= 2.282 Angle : 2.548 38.172 161014 Z= 1.276 Chirality : 0.099 0.779 18856 Planarity : 0.016 0.194 21167 Dihedral : 11.605 145.933 17355 Min Nonbonded Distance : 1.233 Molprobity Statistics. All-atom Clashscore : 97.16 Ramachandran Plot: Outliers : 1.89 % Allowed : 31.56 % Favored : 66.55 % Rotamer: Outliers : 6.54 % Allowed : 18.96 % Favored : 74.50 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.65 % Twisted General : 2.13 % 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: -6.62 (0.05), residues: 12684 helix: -4.37 (0.04), residues: 5724 sheet: -2.80 (0.16), residues: 896 loop : -4.73 (0.06), residues: 6064 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 643 poor density : 474 time to evaluate : 8.901 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 outliers start: 643 outliers final: 437 residues processed: 1109 average time/residue: 0.8918 time to fit residues: 1824.6962 Evaluate side-chains 891 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 437 poor density : 454 time to evaluate : 8.699 Switching outliers to nearest non-outliers outliers start: 437 outliers final: 2 residues processed: 437 average time/residue: 0.8080 time to fit residues: 688.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 HIS ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1928 GLN A1949 GLN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2035 HIS ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5031 GLN B 44 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1127 HIS ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1775 HIS ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 HIS ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2194 HIS ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2881 ASN D3761 GLN ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3946 GLN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 765 GLN C 812 HIS C 909 ASN C 921 ASN ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1678 ASN ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1928 GLN ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2169 GLN C2763 HIS ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4707 ASN ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.7877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.494 118058 Z= 2.322 Angle : 2.589 38.109 161014 Z= 1.295 Chirality : 0.101 0.566 18856 Planarity : 0.017 0.248 21167 Dihedral : 12.202 159.779 17355 Min Nonbonded Distance : 1.286 Molprobity Statistics. All-atom Clashscore : 102.80 Ramachandran Plot: Outliers : 1.57 % Allowed : 36.68 % Favored : 61.75 % Rotamer: Outliers : 4.94 % Allowed : 18.89 % Favored : 76.17 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.68 % Twisted General : 2.71 % 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: -7.03 (0.05), residues: 12684 helix: -4.56 (0.04), residues: 5760 sheet: -3.18 (0.16), residues: 828 loop : -5.09 (0.06), residues: 6096 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 486 poor density : 460 time to evaluate : 8.744 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 outliers start: 486 outliers final: 384 residues processed: 946 average time/residue: 0.8857 time to fit residues: 1548.1314 Evaluate side-chains 827 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 443 time to evaluate : 8.657 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 384 outliers final: 2 residues processed: 384 average time/residue: 0.7674 time to fit residues: 577.1620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN A2884 ASN ** A3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3946 GLN ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4707 ASN ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2035 HIS ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2169 GLN ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4805 ASN ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 ASN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2035 HIS ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3781 GLN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4142 ASN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 765 GLN ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2193 GLN ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3946 GLN ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4574 ASN ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.8293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.492 118058 Z= 2.325 Angle : 2.595 39.056 161014 Z= 1.298 Chirality : 0.101 0.591 18856 Planarity : 0.017 0.236 21167 Dihedral : 12.538 155.673 17355 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 104.55 Ramachandran Plot: Outliers : 1.45 % Allowed : 38.75 % Favored : 59.80 % Rotamer: Outliers : 3.61 % Allowed : 15.30 % Favored : 81.09 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.02 % Twisted General : 2.99 % 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: -7.17 (0.05), residues: 12684 helix: -4.63 (0.03), residues: 5844 sheet: -3.33 (0.16), residues: 796 loop : -5.19 (0.06), residues: 6044 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 455 time to evaluate : 8.884 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 outliers start: 355 outliers final: 294 residues processed: 806 average time/residue: 0.8900 time to fit residues: 1329.4951 Evaluate side-chains 733 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 439 time to evaluate : 8.729 Switching outliers to nearest non-outliers outliers start: 294 outliers final: 3 residues processed: 294 average time/residue: 0.8229 time to fit residues: 474.9520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 GLN ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 ASN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3994 HIS ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN A4142 ASN ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1127 HIS ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2035 HIS ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3850 GLN ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 ASN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2035 HIS ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4806 ASN D4947 GLN ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.8578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.472 118058 Z= 2.329 Angle : 2.600 38.804 161014 Z= 1.301 Chirality : 0.102 0.628 18856 Planarity : 0.017 0.210 21167 Dihedral : 12.770 157.449 17355 Min Nonbonded Distance : 1.305 Molprobity Statistics. All-atom Clashscore : 105.91 Ramachandran Plot: Outliers : 1.55 % Allowed : 40.48 % Favored : 57.97 % Rotamer: Outliers : 2.27 % Allowed : 12.73 % Favored : 85.00 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.53 % Twisted General : 3.25 % 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: -7.27 (0.05), residues: 12684 helix: -4.65 (0.03), residues: 5896 sheet: -3.75 (0.16), residues: 828 loop : -5.24 (0.06), residues: 5960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 451 time to evaluate : 8.989 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 outliers start: 223 outliers final: 186 residues processed: 672 average time/residue: 0.9121 time to fit residues: 1127.7177 Evaluate side-chains 623 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 437 time to evaluate : 8.635 Switching outliers to nearest non-outliers outliers start: 186 outliers final: 1 residues processed: 186 average time/residue: 0.8110 time to fit residues: 300.8364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 ASN ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN ** A4109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS B 921 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1696 HIS ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3896 ASN ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4204 GLN ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 ASN ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4574 ASN ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2193 GLN ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3850 GLN ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4574 ASN ** C4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.8792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.459 118058 Z= 2.334 Angle : 2.607 36.108 161014 Z= 1.306 Chirality : 0.103 0.717 18856 Planarity : 0.017 0.240 21167 Dihedral : 12.948 161.792 17355 Min Nonbonded Distance : 1.310 Molprobity Statistics. All-atom Clashscore : 106.66 Ramachandran Plot: Outliers : 1.55 % Allowed : 41.31 % Favored : 57.13 % Rotamer: Outliers : 1.19 % Allowed : 10.56 % Favored : 88.25 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.88 % Twisted General : 3.53 % 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: -7.33 (0.05), residues: 12684 helix: -4.68 (0.03), residues: 5844 sheet: -3.72 (0.16), residues: 788 loop : -5.31 (0.06), residues: 6052 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 448 time to evaluate : 8.703 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 outliers start: 117 outliers final: 101 residues processed: 565 average time/residue: 0.9213 time to fit residues: 959.4564 Evaluate side-chains 534 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 433 time to evaluate : 8.685 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 2 residues processed: 101 average time/residue: 0.8004 time to fit residues: 165.2762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 GLN ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2035 HIS ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 GLN D 405 HIS ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 HIS ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1952 GLN ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2035 HIS C2193 GLN ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.8974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.466 118058 Z= 2.339 Angle : 2.614 35.720 161014 Z= 1.311 Chirality : 0.104 0.771 18856 Planarity : 0.017 0.256 21167 Dihedral : 13.110 162.752 17355 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 108.32 Ramachandran Plot: Outliers : 1.51 % Allowed : 41.93 % Favored : 56.57 % Rotamer: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.56 % Twisted General : 3.62 % 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: -7.39 (0.05), residues: 12684 helix: -4.69 (0.03), residues: 5904 sheet: -3.74 (0.16), residues: 768 loop : -5.39 (0.05), residues: 6012 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 452 time to evaluate : 8.959 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 outliers start: 18 outliers final: 18 residues processed: 470 average time/residue: 0.9567 time to fit residues: 820.6847 Evaluate side-chains 452 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 434 time to evaluate : 8.760 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.8423 time to fit residues: 40.0482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1775 HIS ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 ASN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1201 HIS ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2324 ASN ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2763 HIS ** D3651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4574 ASN ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN C 349 GLN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2881 ASN ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.9113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.460 118058 Z= 2.347 Angle : 2.625 36.015 161014 Z= 1.319 Chirality : 0.105 0.726 18856 Planarity : 0.018 0.248 21167 Dihedral : 13.242 170.256 17355 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 108.75 Ramachandran Plot: Outliers : 1.58 % Allowed : 42.34 % Favored : 56.08 % Rotamer: Outliers : 0.01 % Allowed : 4.80 % Favored : 95.19 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.56 % Twisted General : 3.85 % 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: -7.40 (0.05), residues: 12684 helix: -4.70 (0.03), residues: 5820 sheet: -3.94 (0.17), residues: 700 loop : -5.36 (0.05), residues: 6164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 451 time to evaluate : 8.571 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 outliers start: 1 outliers final: 0 residues processed: 452 average time/residue: 0.9389 time to fit residues: 773.3821 Evaluate side-chains 433 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 8.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.3435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 HIS A1158 ASN ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1775 HIS D1861 GLN ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2127 GLN ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2763 HIS D2773 ASN ** D3651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4574 ASN ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.9266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.478 118058 Z= 2.351 Angle : 2.636 36.182 161014 Z= 1.326 Chirality : 0.106 0.669 18856 Planarity : 0.018 0.249 21167 Dihedral : 13.372 169.178 17355 Min Nonbonded Distance : 1.339 Molprobity Statistics. All-atom Clashscore : 109.52 Ramachandran Plot: Outliers : 1.59 % Allowed : 43.19 % Favored : 55.22 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.90 % Twisted General : 4.11 % 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: -7.42 (0.05), residues: 12684 helix: -4.70 (0.03), residues: 5884 sheet: -3.73 (0.16), residues: 756 loop : -5.42 (0.05), residues: 6044 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25368 Ramachandran restraints generated. 12684 Oldfield, 0 Emsley, 12684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 8.754 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 outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.9450 time to fit residues: 773.9659 Evaluate side-chains 433 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 8.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.3209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2763 HIS D2773 ASN ** D3651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.061729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.046174 restraints weight = 973757.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045483 restraints weight = 797579.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.045383 restraints weight = 962633.842| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.9386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.471 118058 Z= 2.352 Angle : 2.638 36.220 161014 Z= 1.327 Chirality : 0.106 0.891 18856 Planarity : 0.018 0.250 21167 Dihedral : 13.418 155.743 17355 Min Nonbonded Distance : 1.368 Molprobity Statistics. All-atom Clashscore : 109.82 Ramachandran Plot: Outliers : 1.61 % Allowed : 43.44 % Favored : 54.95 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.25 % Twisted General : 4.17 % 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: -7.43 (0.05), residues: 12684 helix: -4.72 (0.03), residues: 5840 sheet: -3.75 (0.16), residues: 756 loop : -5.42 (0.05), residues: 6088 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41037.52 seconds wall clock time: 710 minutes 56.84 seconds (42656.84 seconds total)