Starting phenix.real_space_refine on Tue Mar 12 12:38:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/03_2024/7k0t_22616_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/03_2024/7k0t_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_22616/03_2024/7k0t_22616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/03_2024/7k0t_22616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/03_2024/7k0t_22616_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0t_22616/03_2024/7k0t_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: 0.31s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 43.63, per 1000 atoms: 0.38 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: 31.83 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: 31.14 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: 58.02 Time building geometry restraints manager: 35.24 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: 64078 17.84 - 35.67: 5183 35.67 - 53.51: 942 53.51 - 71.35: 178 71.35 - 89.18: 67 Dihedral angle restraints: 70448 sinusoidal: 22596 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 70445 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 19.190 Check model and map are aligned: 1.260 Set scattering table: 0.740 Process input model: 270.420 Find NCS groups from input model: 6.200 Set up NCS constraints: 0.410 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:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 304.200 ------------------------------------------------------------------------------- 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 : 13.884 89.183 39312 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C3661 HIS 0.005 0.000 HIS B5003 PHE 0.019 0.001 PHE B4920 TYR 0.020 0.001 TYR D3722 ARG 0.003 0.000 ARG C 164 *********************** 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 : 10.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 LEU cc_start: 0.8383 (mm) cc_final: 0.8027 (pp) REVERT: A 1236 THR cc_start: 0.8533 (p) cc_final: 0.8232 (p) REVERT: A 2423 MET cc_start: 0.7295 (ppp) cc_final: 0.6851 (ppp) REVERT: A 2441 HIS cc_start: 0.7636 (t70) cc_final: 0.7255 (t70) REVERT: A 3652 MET cc_start: 0.8480 (mpp) cc_final: 0.8189 (mpp) REVERT: A 4088 ILE cc_start: 0.7735 (tp) cc_final: 0.7484 (tp) REVERT: A 4919 THR cc_start: 0.9082 (t) cc_final: 0.8617 (t) REVERT: A 5026 ASP cc_start: 0.6262 (t0) cc_final: 0.5696 (p0) REVERT: B 139 GLU cc_start: 0.7074 (tp30) cc_final: 0.6360 (mm-30) REVERT: B 196 MET cc_start: 0.6983 (mmp) cc_final: 0.6694 (mmm) REVERT: B 483 MET cc_start: 0.7600 (mmt) cc_final: 0.7030 (mpp) REVERT: B 1236 THR cc_start: 0.8219 (p) cc_final: 0.7861 (p) REVERT: B 2186 MET cc_start: 0.7755 (mmt) cc_final: 0.7521 (mmm) REVERT: B 2423 MET cc_start: 0.7361 (ppp) cc_final: 0.6949 (ppp) REVERT: B 3760 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8894 (mptt) REVERT: B 3768 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8452 (p) REVERT: B 4184 MET cc_start: 0.8845 (ptm) cc_final: 0.8354 (tmm) REVERT: B 4887 MET cc_start: 0.8454 (mmp) cc_final: 0.8210 (mmp) REVERT: B 4989 MET cc_start: 0.8100 (ppp) cc_final: 0.7881 (ppp) REVERT: D 403 MET cc_start: 0.9404 (mtm) cc_final: 0.9037 (mtp) REVERT: D 941 MET cc_start: 0.4170 (mmm) cc_final: 0.0353 (mmt) REVERT: D 1152 MET cc_start: 0.5747 (tpp) cc_final: 0.5187 (tpp) REVERT: D 1236 THR cc_start: 0.8354 (p) cc_final: 0.8003 (p) REVERT: D 2423 MET cc_start: 0.7400 (ppp) cc_final: 0.6875 (ppp) REVERT: D 4019 LEU cc_start: 0.9154 (tt) cc_final: 0.8780 (tt) REVERT: D 4066 LEU cc_start: 0.8770 (tp) cc_final: 0.8568 (tp) REVERT: D 4867 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: D 4870 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.6918 (t70) REVERT: C 1236 THR cc_start: 0.8652 (p) cc_final: 0.8191 (p) REVERT: C 1637 MET cc_start: 0.8247 (ptp) cc_final: 0.7972 (ptp) REVERT: C 2423 MET cc_start: 0.7392 (ppp) cc_final: 0.6885 (ppp) REVERT: C 3652 MET cc_start: 0.8493 (mpp) cc_final: 0.8225 (mpp) REVERT: C 4245 MET cc_start: 0.8213 (mtm) cc_final: 0.7951 (mtm) REVERT: C 4865 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7897 (mmmm) REVERT: C 4867 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: C 4869 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7624 (tm-30) outliers start: 62 outliers final: 16 residues processed: 907 average time/residue: 0.8731 time to fit residues: 1446.4123 Evaluate side-chains 704 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 681 time to evaluate : 8.615 ------------------------------------------------------------------------------- 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 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** 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 A2035 HIS A2125 HIS A3845 ASN ** A3850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3895 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 B3845 ASN B3850 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D3998 HIS ** D4020 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 ** C1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2011 HIS C2125 HIS C2193 GLN ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2763 HIS ** C3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** 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: 90 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5571 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= 2.350 Angle : 2.550 37.874 161014 Z= 1.286 Chirality : 0.101 0.593 18856 Planarity : 0.016 0.235 21167 Dihedral : 10.259 108.711 17467 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 82.26 Ramachandran Plot: Outliers : 2.36 % Allowed : 20.88 % Favored : 76.76 % Rotamer: Outliers : 7.00 % Allowed : 18.81 % Favored : 74.19 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.42 % Twisted General : 0.96 % 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: -5.37 (0.06), residues: 12684 helix: -3.50 (0.05), residues: 5768 sheet: -1.79 (0.17), residues: 880 loop : -3.94 (0.07), residues: 6036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.008 TRP C4716 HIS 0.038 0.007 HIS C4983 PHE 0.073 0.009 PHE A 777 TYR 0.091 0.009 TYR B4851 ARG 0.045 0.003 ARG A3762 *********************** 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 1186 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 688 poor density : 498 time to evaluate : 8.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: A 531 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.9079 (ptp-110) REVERT: A 941 MET cc_start: 0.5132 (tpt) cc_final: 0.4712 (tpt) REVERT: A 1115 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9013 (tt) REVERT: A 1206 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: A 1260 MET cc_start: 0.7664 (mmp) cc_final: 0.7453 (mmp) REVERT: A 1270 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8611 (mt) REVERT: A 2191 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.9048 (t80) REVERT: A 2336 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8788 (ttp-110) REVERT: A 2423 MET cc_start: 0.7907 (ppp) cc_final: 0.7054 (ppp) REVERT: A 3992 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: A 4032 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8309 (pp20) REVERT: A 4686 LEU cc_start: 0.9289 (tp) cc_final: 0.9040 (tp) REVERT: A 4839 MET cc_start: 0.8784 (tmm) cc_final: 0.8088 (tmm) REVERT: A 4989 MET cc_start: 0.9216 (ppp) cc_final: 0.8776 (ppp) REVERT: B 116 MET cc_start: 0.8301 (tpt) cc_final: 0.8059 (tpt) REVERT: B 649 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: B 813 GLU cc_start: 0.2707 (OUTLIER) cc_final: 0.2160 (tt0) REVERT: B 941 MET cc_start: 0.4950 (tpt) cc_final: 0.4525 (tpt) REVERT: B 1201 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.7339 (p90) REVERT: B 2247 GLN cc_start: 0.9528 (OUTLIER) cc_final: 0.9034 (pm20) REVERT: B 2423 MET cc_start: 0.8003 (ppp) cc_final: 0.7292 (ppp) REVERT: B 4064 MET cc_start: 0.9172 (ppp) cc_final: 0.8963 (ppp) REVERT: B 4093 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7754 (t80) REVERT: B 4195 PHE cc_start: 0.9627 (OUTLIER) cc_final: 0.9348 (p90) REVERT: B 4205 TRP cc_start: 0.9285 (OUTLIER) cc_final: 0.7932 (t-100) REVERT: B 4232 GLU cc_start: 0.9554 (OUTLIER) cc_final: 0.9061 (tm-30) REVERT: B 4679 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8330 (mpt180) REVERT: B 4823 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9343 (mm) REVERT: B 4839 MET cc_start: 0.9085 (tmm) cc_final: 0.8599 (tmm) REVERT: B 4916 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.9220 (t80) REVERT: B 4989 MET cc_start: 0.9278 (ppp) cc_final: 0.8965 (ppp) REVERT: D 340 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7287 (ttpp) REVERT: D 797 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7064 (t70) REVERT: D 941 MET cc_start: 0.5791 (mmm) cc_final: 0.1388 (mpp) REVERT: D 1139 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7377 (t80) REVERT: D 1152 MET cc_start: 0.6250 (tpp) cc_final: 0.5909 (tpp) REVERT: D 1186 ASP cc_start: 0.8576 (p0) cc_final: 0.8307 (p0) REVERT: D 1201 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7435 (p-80) REVERT: D 1256 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: D 1270 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8632 (mt) REVERT: D 1636 MET cc_start: 0.9006 (ppp) cc_final: 0.8626 (ppp) REVERT: D 2178 MET cc_start: 0.9107 (ppp) cc_final: 0.8906 (ppp) REVERT: D 2423 MET cc_start: 0.7988 (ppp) cc_final: 0.7163 (ppp) REVERT: D 2441 HIS cc_start: 0.8567 (OUTLIER) cc_final: 0.8273 (t70) REVERT: D 2449 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8822 (pp20) REVERT: D 3652 MET cc_start: 0.9015 (mpp) cc_final: 0.8809 (mpp) REVERT: D 3992 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: D 4093 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7771 (t80) REVERT: D 4232 GLU cc_start: 0.9432 (OUTLIER) cc_final: 0.9054 (tm-30) REVERT: D 4632 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9127 (tt) REVERT: D 4839 MET cc_start: 0.9074 (tmm) cc_final: 0.8577 (tmm) REVERT: D 4954 MET cc_start: 0.9198 (tmm) cc_final: 0.8647 (tmm) REVERT: C 70 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8736 (tp30) REVERT: C 196 MET cc_start: 0.8937 (mpp) cc_final: 0.8708 (mpp) REVERT: C 340 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7791 (ttpp) REVERT: C 483 MET cc_start: 0.8145 (mmp) cc_final: 0.7311 (mmp) REVERT: C 1230 MET cc_start: 0.8053 (mmt) cc_final: 0.7780 (mmt) REVERT: C 1270 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8537 (mt) REVERT: C 1636 MET cc_start: 0.8937 (ppp) cc_final: 0.8528 (ppp) REVERT: C 2250 MET cc_start: 0.9305 (tpp) cc_final: 0.9088 (tmm) REVERT: C 2336 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8826 (ttp-110) REVERT: C 2423 MET cc_start: 0.7966 (ppp) cc_final: 0.7213 (ppp) REVERT: C 2886 TRP cc_start: 0.5213 (OUTLIER) cc_final: 0.4825 (m100) REVERT: C 3875 MET cc_start: 0.8652 (mmm) cc_final: 0.8354 (mmm) REVERT: C 3992 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: C 4023 MET cc_start: 0.8951 (tpt) cc_final: 0.8104 (tpt) REVERT: C 4026 MET cc_start: 0.9503 (tmm) cc_final: 0.8956 (tmm) REVERT: C 4047 MET cc_start: 0.9429 (tmm) cc_final: 0.9199 (tmm) REVERT: C 4227 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 4743 MET cc_start: 0.8280 (ppp) cc_final: 0.7884 (tmm) REVERT: C 4769 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7227 (ppp) REVERT: C 4839 MET cc_start: 0.9119 (tmm) cc_final: 0.8230 (tmm) REVERT: C 4916 PHE cc_start: 0.9520 (OUTLIER) cc_final: 0.9244 (t80) REVERT: C 4954 MET cc_start: 0.9041 (tmm) cc_final: 0.8560 (tmm) outliers start: 688 outliers final: 439 residues processed: 1170 average time/residue: 0.8945 time to fit residues: 1923.3006 Evaluate side-chains 940 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 480 poor density : 460 time to evaluate : 8.690 ------------------------------------------------------------------------------- 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 A1127 HIS ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1663 HIS ** A1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1949 GLN ** 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** ** 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 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 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 624 ASN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1127 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 B1949 GLN ** B1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 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** B3998 HIS ** B4020 GLN ** 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** 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 576 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN D1203 ASN ** 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 D3994 HIS ** D4020 GLN ** 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** D4886 HIS ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** 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 ** C1719 HIS ** 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** C2193 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 ** 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: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.035 0.462 118058 Z= 2.287 Angle : 2.553 38.273 161014 Z= 1.279 Chirality : 0.100 0.761 18856 Planarity : 0.016 0.237 21167 Dihedral : 11.862 146.974 17467 Min Nonbonded Distance : 1.222 Molprobity Statistics. All-atom Clashscore : 96.67 Ramachandran Plot: Outliers : 1.76 % Allowed : 31.43 % Favored : 66.82 % Rotamer: Outliers : 4.48 % Allowed : 19.38 % Favored : 76.13 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.31 % Twisted General : 2.05 % 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: -6.61 (0.05), residues: 12684 helix: -4.38 (0.04), residues: 5848 sheet: -2.85 (0.17), residues: 792 loop : -4.68 (0.06), residues: 6044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.008 TRP C4716 HIS 0.048 0.007 HIS C1133 PHE 0.092 0.009 PHE B2191 TYR 0.087 0.009 TYR A3725 ARG 0.038 0.003 ARG D 493 *********************** 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 910 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 441 poor density : 469 time to evaluate : 8.702 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: A 1636 MET cc_start: 0.8708 (ppp) cc_final: 0.8462 (ppp) REVERT: A 1747 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8032 (mp) REVERT: A 2228 MET cc_start: 0.8636 (mtt) cc_final: 0.8355 (mtt) REVERT: A 2423 MET cc_start: 0.8221 (ppp) cc_final: 0.7255 (ppp) REVERT: A 2440 MET cc_start: 0.8410 (mpp) cc_final: 0.8187 (mpp) REVERT: A 3763 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8797 (tt) REVERT: A 4804 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: A 4839 MET cc_start: 0.8775 (tmm) cc_final: 0.8169 (tmm) REVERT: A 4921 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8289 (t80) REVERT: B 116 MET cc_start: 0.8412 (tpt) cc_final: 0.8065 (tpt) REVERT: B 276 TRP cc_start: 0.7324 (OUTLIER) cc_final: 0.5774 (m100) REVERT: B 479 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8354 (pp30) REVERT: B 1170 MET cc_start: 0.7687 (ppp) cc_final: 0.7448 (ppp) REVERT: B 1661 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8755 (mtp180) REVERT: B 1698 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9286 (mt) REVERT: B 2153 MET cc_start: 0.9216 (mmm) cc_final: 0.8963 (mmm) REVERT: B 2423 MET cc_start: 0.8084 (ppp) cc_final: 0.7164 (ppp) REVERT: B 4064 MET cc_start: 0.9194 (ppp) cc_final: 0.8893 (tmm) REVERT: B 4823 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9334 (mm) REVERT: B 4839 MET cc_start: 0.9002 (tmm) cc_final: 0.8650 (tmm) REVERT: B 4989 MET cc_start: 0.9301 (ppp) cc_final: 0.9058 (ppp) REVERT: D 116 MET cc_start: 0.8612 (tmm) cc_final: 0.8321 (tmm) REVERT: D 276 TRP cc_start: 0.7522 (OUTLIER) cc_final: 0.6227 (m100) REVERT: D 322 LYS cc_start: 0.5193 (mmmt) cc_final: 0.4962 (mmtm) REVERT: D 667 MET cc_start: 0.8098 (tpt) cc_final: 0.7643 (tpt) REVERT: D 813 GLU cc_start: 0.2716 (OUTLIER) cc_final: 0.2097 (tt0) REVERT: D 941 MET cc_start: 0.5801 (mmm) cc_final: -0.0058 (mpp) REVERT: D 1152 MET cc_start: 0.7200 (tpp) cc_final: 0.6797 (tpp) REVERT: D 1256 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: D 1636 MET cc_start: 0.8999 (ppp) cc_final: 0.8691 (ppp) REVERT: D 1661 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8854 (mtp180) REVERT: D 2211 MET cc_start: 0.9346 (tmm) cc_final: 0.9042 (tmm) REVERT: D 2423 MET cc_start: 0.8124 (ppp) cc_final: 0.7155 (ppp) REVERT: D 3652 MET cc_start: 0.9021 (mpp) cc_final: 0.8753 (mpp) REVERT: D 4180 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8332 (ptp90) REVERT: D 4205 TRP cc_start: 0.9412 (OUTLIER) cc_final: 0.7977 (t-100) REVERT: D 4796 MET cc_start: 0.9061 (tpp) cc_final: 0.8700 (tpt) REVERT: D 4839 MET cc_start: 0.9104 (tmm) cc_final: 0.8657 (tmm) REVERT: C 116 MET cc_start: 0.9017 (tmm) cc_final: 0.8752 (tmm) REVERT: C 663 TYR cc_start: 0.3008 (OUTLIER) cc_final: 0.2300 (t80) REVERT: C 1636 MET cc_start: 0.8959 (ppp) cc_final: 0.8681 (ppp) REVERT: C 1702 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.8001 (p-80) REVERT: C 2212 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8881 (p) REVERT: C 2423 MET cc_start: 0.8289 (ppp) cc_final: 0.7365 (ppp) REVERT: C 2440 MET cc_start: 0.8504 (mpp) cc_final: 0.8296 (mpp) REVERT: C 4026 MET cc_start: 0.9465 (tmm) cc_final: 0.9193 (tmm) REVERT: C 4044 MET cc_start: 0.8815 (mmt) cc_final: 0.8596 (mmt) REVERT: C 4180 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8199 (ptp90) REVERT: C 4231 MET cc_start: 0.9451 (mmm) cc_final: 0.9048 (mmm) REVERT: C 4804 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8562 (m-10) REVERT: C 4839 MET cc_start: 0.9097 (tmm) cc_final: 0.8445 (tmm) outliers start: 441 outliers final: 256 residues processed: 905 average time/residue: 0.8558 time to fit residues: 1423.7854 Evaluate side-chains 727 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 451 time to evaluate : 8.644 ------------------------------------------------------------------------------- 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: 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 44 ASN ** 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 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** 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** A1928 GLN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A4754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS A4973 HIS ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 HIS ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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** B3850 GLN ** 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** ** 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 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 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** ** 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 D3946 GLN ** D4020 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 ** 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 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 765 GLN C 812 HIS ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 921 ASN ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1928 GLN ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2035 HIS C2193 GLN C2763 HIS ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3946 GLN ** 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.7834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.479 118058 Z= 2.318 Angle : 2.589 38.120 161014 Z= 1.297 Chirality : 0.101 0.634 18856 Planarity : 0.017 0.331 21167 Dihedral : 12.448 160.991 17467 Min Nonbonded Distance : 1.288 Molprobity Statistics. All-atom Clashscore : 102.28 Ramachandran Plot: Outliers : 1.51 % Allowed : 36.63 % Favored : 61.87 % Rotamer: Outliers : 2.72 % Allowed : 20.03 % Favored : 77.25 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.34 % Twisted General : 2.69 % 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: -7.07 (0.05), residues: 12684 helix: -4.59 (0.03), residues: 5864 sheet: -3.27 (0.15), residues: 868 loop : -5.09 (0.06), residues: 5952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.008 TRP A 356 HIS 0.052 0.007 HIS D 582 PHE 0.091 0.009 PHE D 195 TYR 0.081 0.009 TYR B 103 ARG 0.039 0.003 ARG B 157 *********************** 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 722 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 455 time to evaluate : 8.749 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: A 116 MET cc_start: 0.9044 (tmm) cc_final: 0.8494 (tmm) REVERT: A 196 MET cc_start: 0.8856 (mmp) cc_final: 0.8601 (mmm) REVERT: A 359 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8204 (p90) REVERT: A 1186 ASP cc_start: 0.8321 (p0) cc_final: 0.8112 (p0) REVERT: A 1260 MET cc_start: 0.8464 (mmp) cc_final: 0.8214 (mmm) REVERT: A 2178 MET cc_start: 0.9254 (ppp) cc_final: 0.9009 (ppp) REVERT: A 2423 MET cc_start: 0.8234 (ppp) cc_final: 0.7353 (ppp) REVERT: A 4023 MET cc_start: 0.9168 (tpt) cc_final: 0.8734 (tpt) REVERT: A 4804 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8845 (m-10) REVERT: A 4839 MET cc_start: 0.8693 (tmm) cc_final: 0.8231 (tmm) REVERT: A 4989 MET cc_start: 0.9311 (ppp) cc_final: 0.9028 (ppp) REVERT: B 247 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: B 359 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.7472 (p90) REVERT: B 483 MET cc_start: 0.8377 (mmt) cc_final: 0.7686 (mmm) REVERT: B 649 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: B 2153 MET cc_start: 0.9228 (mmm) cc_final: 0.8930 (mmm) REVERT: B 2203 MET cc_start: 0.9263 (mpp) cc_final: 0.8962 (mpp) REVERT: B 2423 MET cc_start: 0.8197 (ppp) cc_final: 0.7407 (ppp) REVERT: B 4023 MET cc_start: 0.9144 (tpt) cc_final: 0.8802 (tpt) REVERT: B 4839 MET cc_start: 0.9049 (tmm) cc_final: 0.8655 (tmm) REVERT: B 4989 MET cc_start: 0.9310 (ppp) cc_final: 0.9061 (ppp) REVERT: D 322 LYS cc_start: 0.5331 (mmmt) cc_final: 0.5087 (mmtt) REVERT: D 359 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.7511 (p90) REVERT: D 403 MET cc_start: 0.9650 (mtm) cc_final: 0.9379 (mtp) REVERT: D 649 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8625 (m-80) REVERT: D 941 MET cc_start: 0.5469 (mmm) cc_final: 0.4524 (tpp) REVERT: D 1152 MET cc_start: 0.7225 (tpp) cc_final: 0.6872 (tpp) REVERT: D 1256 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6841 (pm20) REVERT: D 1636 MET cc_start: 0.8940 (ppp) cc_final: 0.8593 (ppp) REVERT: D 2211 MET cc_start: 0.9271 (tmm) cc_final: 0.8933 (tmm) REVERT: D 2423 MET cc_start: 0.8213 (ppp) cc_final: 0.7314 (ppp) REVERT: D 4839 MET cc_start: 0.9083 (tmm) cc_final: 0.8596 (tmm) REVERT: C 152 PRO cc_start: 0.8376 (OUTLIER) cc_final: 0.7998 (Cg_exo) REVERT: C 322 LYS cc_start: 0.5336 (mmmt) cc_final: 0.5028 (mmtt) REVERT: C 359 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.7555 (p90) REVERT: C 403 MET cc_start: 0.9382 (mmp) cc_final: 0.9182 (mmm) REVERT: C 959 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7404 (m-10) REVERT: C 1260 MET cc_start: 0.8275 (mmp) cc_final: 0.8058 (mmm) REVERT: C 1636 MET cc_start: 0.8872 (ppp) cc_final: 0.8574 (ppp) REVERT: C 2211 MET cc_start: 0.9214 (tmm) cc_final: 0.8943 (tmm) REVERT: C 2423 MET cc_start: 0.8235 (ppp) cc_final: 0.7373 (ppp) REVERT: C 4026 MET cc_start: 0.9477 (tmm) cc_final: 0.9107 (tmm) REVERT: C 4804 TYR cc_start: 0.9200 (OUTLIER) cc_final: 0.8883 (m-10) REVERT: C 4839 MET cc_start: 0.9030 (tmm) cc_final: 0.8597 (tmm) REVERT: C 4874 MET cc_start: 0.8190 (mmm) cc_final: 0.7966 (tpp) outliers start: 267 outliers final: 180 residues processed: 715 average time/residue: 0.8673 time to fit residues: 1141.2369 Evaluate side-chains 632 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 440 time to evaluate : 8.622 ------------------------------------------------------------------------------- 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: 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 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 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 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 ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN A2884 ASN ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3946 GLN ** A3994 HIS ** 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 ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5031 GLN ** 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 395 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 536 ASN ** 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** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B4805 ASN ** 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 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 579 GLN ** 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 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** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 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** ** D3700 GLN ** 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 ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4947 GLN ** 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 465 GLN ** 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 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 765 GLN C 909 ASN ** C1198 GLN ** 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** 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** ** 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** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.8299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.482 118058 Z= 2.326 Angle : 2.606 38.991 161014 Z= 1.303 Chirality : 0.102 0.586 18856 Planarity : 0.017 0.234 21167 Dihedral : 12.926 176.301 17467 Min Nonbonded Distance : 1.312 Molprobity Statistics. All-atom Clashscore : 104.84 Ramachandran Plot: Outliers : 1.50 % Allowed : 38.79 % Favored : 59.71 % Rotamer: Outliers : 2.01 % Allowed : 15.69 % Favored : 82.29 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.68 % Twisted General : 3.06 % 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: -7.21 (0.05), residues: 12684 helix: -4.63 (0.03), residues: 5916 sheet: -3.61 (0.16), residues: 788 loop : -5.19 (0.06), residues: 5980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.008 TRP C3661 HIS 0.049 0.007 HIS D3771 PHE 0.090 0.010 PHE D4093 TYR 0.097 0.009 TYR A 103 ARG 0.040 0.003 ARG C1110 *********************** 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 644 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 446 time to evaluate : 8.804 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: A 150 MET cc_start: 0.8632 (mpp) cc_final: 0.8347 (mpp) REVERT: A 196 MET cc_start: 0.8783 (mmp) cc_final: 0.8519 (mmm) REVERT: A 1100 MET cc_start: 0.6963 (mtt) cc_final: 0.6755 (mtt) REVERT: A 1260 MET cc_start: 0.8437 (mmp) cc_final: 0.8131 (mmm) REVERT: A 1636 MET cc_start: 0.8764 (ppp) cc_final: 0.8385 (ppp) REVERT: A 2178 MET cc_start: 0.9232 (ppp) cc_final: 0.8937 (ppp) REVERT: A 2203 MET cc_start: 0.9237 (mpp) cc_final: 0.9029 (mpp) REVERT: A 2423 MET cc_start: 0.8340 (ppp) cc_final: 0.7510 (ppp) REVERT: A 3723 MET cc_start: 0.9251 (mmt) cc_final: 0.9014 (tpp) REVERT: A 4804 TYR cc_start: 0.9303 (OUTLIER) cc_final: 0.8898 (m-10) REVERT: A 4839 MET cc_start: 0.8610 (tmm) cc_final: 0.8229 (tmm) REVERT: A 4916 PHE cc_start: 0.9569 (OUTLIER) cc_final: 0.9336 (t80) REVERT: A 4989 MET cc_start: 0.9316 (ppp) cc_final: 0.9019 (ppp) REVERT: B 1170 MET cc_start: 0.7595 (ppp) cc_final: 0.7331 (ppp) REVERT: B 1260 MET cc_start: 0.8488 (mmp) cc_final: 0.8220 (mmm) REVERT: B 1970 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8036 (pp30) REVERT: B 2153 MET cc_start: 0.9217 (mmm) cc_final: 0.8873 (mmm) REVERT: B 2423 MET cc_start: 0.8199 (ppp) cc_final: 0.7317 (ppp) REVERT: B 3673 MET cc_start: 0.8512 (mmp) cc_final: 0.8276 (mmp) REVERT: B 4093 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7374 (t80) REVERT: B 4839 MET cc_start: 0.9041 (tmm) cc_final: 0.8444 (tmm) REVERT: B 4989 MET cc_start: 0.9314 (ppp) cc_final: 0.9043 (ppp) REVERT: D 116 MET cc_start: 0.9172 (tmm) cc_final: 0.8595 (tmm) REVERT: D 322 LYS cc_start: 0.5212 (mmmt) cc_final: 0.4966 (mmtm) REVERT: D 483 MET cc_start: 0.8068 (mmt) cc_final: 0.7615 (mmm) REVERT: D 667 MET cc_start: 0.8616 (tpt) cc_final: 0.8341 (tpt) REVERT: D 1152 MET cc_start: 0.7124 (tpp) cc_final: 0.6740 (tpp) REVERT: D 1260 MET cc_start: 0.8468 (mmp) cc_final: 0.8204 (mmm) REVERT: D 2211 MET cc_start: 0.9303 (tmm) cc_final: 0.9053 (tmm) REVERT: D 2423 MET cc_start: 0.8309 (ppp) cc_final: 0.7453 (ppp) REVERT: D 3652 MET cc_start: 0.9052 (mpp) cc_final: 0.8768 (mpp) REVERT: D 3673 MET cc_start: 0.9001 (mmp) cc_final: 0.8729 (mmp) REVERT: D 4093 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7371 (t80) REVERT: D 4839 MET cc_start: 0.9063 (tmm) cc_final: 0.8614 (tmm) REVERT: C 403 MET cc_start: 0.9416 (mmp) cc_final: 0.9180 (mmm) REVERT: C 483 MET cc_start: 0.7736 (mmt) cc_final: 0.7003 (mmp) REVERT: C 1100 MET cc_start: 0.7122 (mtt) cc_final: 0.6747 (mtt) REVERT: C 1170 MET cc_start: 0.7464 (ppp) cc_final: 0.7262 (ppp) REVERT: C 1260 MET cc_start: 0.8474 (mmp) cc_final: 0.8215 (mmm) REVERT: C 2203 MET cc_start: 0.9491 (pmm) cc_final: 0.8941 (pmm) REVERT: C 2211 MET cc_start: 0.9239 (tmm) cc_final: 0.8867 (tmm) REVERT: C 2423 MET cc_start: 0.8259 (ppp) cc_final: 0.7465 (ppp) REVERT: C 4023 MET cc_start: 0.9175 (tpt) cc_final: 0.8910 (tpt) REVERT: C 4026 MET cc_start: 0.9470 (tmm) cc_final: 0.9150 (tmm) REVERT: C 4231 MET cc_start: 0.9060 (mmm) cc_final: 0.8854 (mmm) REVERT: C 4804 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.8982 (m-10) REVERT: C 4839 MET cc_start: 0.9048 (tmm) cc_final: 0.8494 (tmm) REVERT: C 4916 PHE cc_start: 0.9572 (OUTLIER) cc_final: 0.9267 (t80) outliers start: 198 outliers final: 133 residues processed: 643 average time/residue: 0.8752 time to fit residues: 1033.5615 Evaluate side-chains 575 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 435 time to evaluate : 8.718 ------------------------------------------------------------------------------- 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 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 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** ** 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** ** A4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** 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 383 HIS ** B 395 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 705 ASN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1696 HIS ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** 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** ** 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 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 536 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 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** ** D1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1775 HIS ** 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** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 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** D4806 ASN ** 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 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1678 ASN ** 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** ** 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** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.8592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.464 118058 Z= 2.328 Angle : 2.604 37.183 161014 Z= 1.304 Chirality : 0.103 0.625 18856 Planarity : 0.017 0.234 21167 Dihedral : 13.143 177.167 17467 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 106.21 Ramachandran Plot: Outliers : 1.63 % Allowed : 40.46 % Favored : 57.91 % Rotamer: Outliers : 1.13 % Allowed : 13.07 % Favored : 85.80 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.71 % Twisted General : 3.41 % 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: -7.31 (0.05), residues: 12684 helix: -4.69 (0.03), residues: 5916 sheet: -3.68 (0.16), residues: 792 loop : -5.26 (0.06), residues: 5976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.008 TRP C 891 HIS 0.049 0.008 HIS B3771 PHE 0.105 0.009 PHE A4921 TYR 0.121 0.009 TYR A3765 ARG 0.052 0.003 ARG B2359 *********************** 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 556 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 445 time to evaluate : 8.791 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: A 196 MET cc_start: 0.8799 (mmp) cc_final: 0.8488 (mmm) REVERT: A 1100 MET cc_start: 0.6922 (mtt) cc_final: 0.6601 (mtt) REVERT: A 1170 MET cc_start: 0.7443 (ppp) cc_final: 0.7174 (ppp) REVERT: A 1260 MET cc_start: 0.8536 (mmp) cc_final: 0.8216 (mmm) REVERT: A 1608 MET cc_start: 0.8021 (mtp) cc_final: 0.7788 (mtp) REVERT: A 2423 MET cc_start: 0.8363 (ppp) cc_final: 0.7489 (ppp) REVERT: A 3723 MET cc_start: 0.9199 (mmt) cc_final: 0.8873 (mmm) REVERT: A 4023 MET cc_start: 0.9216 (tpt) cc_final: 0.8890 (tpt) REVERT: A 4047 MET cc_start: 0.9459 (tmm) cc_final: 0.9187 (tmm) REVERT: A 4057 MET cc_start: 0.9195 (pmm) cc_final: 0.8716 (pmm) REVERT: A 4804 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8754 (m-10) REVERT: A 4839 MET cc_start: 0.8746 (tmm) cc_final: 0.8239 (tmm) REVERT: B 116 MET cc_start: 0.8733 (tpt) cc_final: 0.8323 (tpt) REVERT: B 121 LEU cc_start: 0.9383 (mt) cc_final: 0.9157 (mt) REVERT: B 941 MET cc_start: 0.6115 (tpt) cc_final: 0.0774 (mpp) REVERT: B 1170 MET cc_start: 0.7484 (ppp) cc_final: 0.7240 (ppp) REVERT: B 1260 MET cc_start: 0.8545 (mmp) cc_final: 0.8278 (mmm) REVERT: B 2153 MET cc_start: 0.9230 (mmm) cc_final: 0.8872 (mmm) REVERT: B 2211 MET cc_start: 0.9201 (tmm) cc_final: 0.8900 (tmm) REVERT: B 2423 MET cc_start: 0.8078 (ppp) cc_final: 0.7200 (ppp) REVERT: B 3793 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8542 (mmp) REVERT: B 3963 ASN cc_start: 0.9570 (OUTLIER) cc_final: 0.9310 (m-40) REVERT: B 4195 PHE cc_start: 0.9597 (OUTLIER) cc_final: 0.9311 (p90) REVERT: B 4839 MET cc_start: 0.9033 (tmm) cc_final: 0.8565 (tmm) REVERT: D 941 MET cc_start: 0.4968 (tpp) cc_final: 0.4560 (tpp) REVERT: D 1152 MET cc_start: 0.7283 (tpp) cc_final: 0.6970 (tpp) REVERT: D 1260 MET cc_start: 0.8457 (mmp) cc_final: 0.8203 (mmm) REVERT: D 1608 MET cc_start: 0.7956 (mtp) cc_final: 0.7724 (mtp) REVERT: D 1636 MET cc_start: 0.8863 (ppp) cc_final: 0.8424 (ppp) REVERT: D 2211 MET cc_start: 0.9280 (tmm) cc_final: 0.8870 (tmm) REVERT: D 2423 MET cc_start: 0.8364 (ppp) cc_final: 0.7441 (ppp) REVERT: D 3652 MET cc_start: 0.9057 (mpp) cc_final: 0.8815 (mpp) REVERT: D 4839 MET cc_start: 0.9022 (tmm) cc_final: 0.8614 (tmm) REVERT: C 196 MET cc_start: 0.8420 (mpp) cc_final: 0.8199 (mpp) REVERT: C 403 MET cc_start: 0.9438 (mmp) cc_final: 0.9191 (mmm) REVERT: C 483 MET cc_start: 0.7584 (mmt) cc_final: 0.6752 (mmp) REVERT: C 1100 MET cc_start: 0.7218 (mtt) cc_final: 0.7007 (mtt) REVERT: C 1260 MET cc_start: 0.8485 (mmp) cc_final: 0.8180 (mmm) REVERT: C 1608 MET cc_start: 0.8010 (mtp) cc_final: 0.7795 (mtp) REVERT: C 1636 MET cc_start: 0.8756 (ppp) cc_final: 0.8385 (ppp) REVERT: C 2153 MET cc_start: 0.9174 (mmm) cc_final: 0.8950 (mmm) REVERT: C 2211 MET cc_start: 0.9109 (tmm) cc_final: 0.8815 (tmm) REVERT: C 2423 MET cc_start: 0.8252 (ppp) cc_final: 0.7565 (ppp) REVERT: C 3673 MET cc_start: 0.8775 (mmp) cc_final: 0.8496 (mmp) REVERT: C 3793 MET cc_start: 0.8937 (mmp) cc_final: 0.8599 (mmp) REVERT: C 4231 MET cc_start: 0.9137 (mmm) cc_final: 0.8876 (mmm) REVERT: C 4804 TYR cc_start: 0.9269 (OUTLIER) cc_final: 0.8855 (m-10) REVERT: C 4839 MET cc_start: 0.9022 (tmm) cc_final: 0.8476 (tmm) outliers start: 111 outliers final: 76 residues processed: 554 average time/residue: 0.8589 time to fit residues: 874.8284 Evaluate side-chains 519 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 438 time to evaluate : 8.615 ------------------------------------------------------------------------------- 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: 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 921 ASN A1127 HIS ** 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** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4691 GLN ** 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 395 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 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS ** B 904 HIS ** 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** ** 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** B3896 ASN B3994 HIS ** 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 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 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 ASN D 797 HIS D 812 HIS ** 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** ** D1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1775 HIS ** 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** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2260 ASN ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2324 ASN ** 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** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4574 ASN ** 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 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 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** ** C1678 ASN ** 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** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3699 HIS ** 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** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.8804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.467 118058 Z= 2.334 Angle : 2.609 36.310 161014 Z= 1.308 Chirality : 0.104 0.683 18856 Planarity : 0.017 0.237 21167 Dihedral : 13.329 176.211 17467 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 106.89 Ramachandran Plot: Outliers : 1.57 % Allowed : 41.51 % Favored : 56.92 % Rotamer: Outliers : 0.42 % Allowed : 11.29 % Favored : 88.29 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.05 % Twisted General : 3.67 % 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: -4.72 (0.03), residues: 5936 sheet: -3.69 (0.16), residues: 804 loop : -5.35 (0.06), residues: 5944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.108 0.008 TRP C3661 HIS 0.060 0.008 HIS D 582 PHE 0.113 0.010 PHE A4921 TYR 0.107 0.010 TYR A 714 ARG 0.056 0.003 ARG B4892 *********************** 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 492 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 451 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 revert: symmetry clash REVERT: A 196 MET cc_start: 0.8800 (mmp) cc_final: 0.8502 (mmm) REVERT: A 1260 MET cc_start: 0.8607 (mmp) cc_final: 0.8289 (mmm) REVERT: A 1608 MET cc_start: 0.7928 (mtp) cc_final: 0.7673 (mtp) REVERT: A 1636 MET cc_start: 0.8508 (ppp) cc_final: 0.8149 (ppp) REVERT: A 2423 MET cc_start: 0.8440 (ppp) cc_final: 0.7567 (ppp) REVERT: A 3723 MET cc_start: 0.9176 (mmt) cc_final: 0.8716 (mmm) REVERT: A 3955 MET cc_start: 0.9096 (pmm) cc_final: 0.8876 (pmm) REVERT: A 4023 MET cc_start: 0.9217 (tpt) cc_final: 0.8732 (tpt) REVERT: A 4057 MET cc_start: 0.9200 (pmm) cc_final: 0.8733 (pmm) REVERT: A 4839 MET cc_start: 0.8674 (tmm) cc_final: 0.8322 (tmm) REVERT: B 483 MET cc_start: 0.8242 (mmt) cc_final: 0.7586 (mmp) REVERT: B 941 MET cc_start: 0.6051 (tpt) cc_final: 0.4447 (mmm) REVERT: B 1260 MET cc_start: 0.8516 (mmp) cc_final: 0.8238 (mmm) REVERT: B 2153 MET cc_start: 0.9265 (mmm) cc_final: 0.8911 (mmm) REVERT: B 2423 MET cc_start: 0.8238 (ppp) cc_final: 0.7427 (ppp) REVERT: B 4023 MET cc_start: 0.9217 (tpt) cc_final: 0.9008 (tpt) REVERT: B 4839 MET cc_start: 0.9083 (tmm) cc_final: 0.8563 (tmm) REVERT: D 941 MET cc_start: 0.4755 (tpp) cc_final: 0.4270 (tpp) REVERT: D 1152 MET cc_start: 0.7290 (tpp) cc_final: 0.6913 (tpp) REVERT: D 1170 MET cc_start: 0.7347 (mmp) cc_final: 0.7120 (mmp) REVERT: D 1260 MET cc_start: 0.8500 (mmp) cc_final: 0.8201 (mmm) REVERT: D 1636 MET cc_start: 0.8976 (ppp) cc_final: 0.8525 (ppp) REVERT: D 2203 MET cc_start: 0.9119 (mpp) cc_final: 0.8792 (mpp) REVERT: D 2211 MET cc_start: 0.9240 (tmm) cc_final: 0.8865 (tmm) REVERT: D 2423 MET cc_start: 0.8404 (ppp) cc_final: 0.7475 (ppp) REVERT: D 3673 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8215 (mmp) REVERT: D 4839 MET cc_start: 0.9060 (tmm) cc_final: 0.8752 (tmm) REVERT: C 196 MET cc_start: 0.8231 (mpp) cc_final: 0.8029 (mpp) REVERT: C 403 MET cc_start: 0.9466 (mmp) cc_final: 0.9204 (mmm) REVERT: C 483 MET cc_start: 0.8136 (mmp) cc_final: 0.7381 (mmp) REVERT: C 941 MET cc_start: 0.4065 (tpp) cc_final: 0.3777 (tpp) REVERT: C 1260 MET cc_start: 0.8473 (mmp) cc_final: 0.8174 (mmm) REVERT: C 1608 MET cc_start: 0.7856 (mtp) cc_final: 0.7619 (mtp) REVERT: C 1636 MET cc_start: 0.8895 (ppp) cc_final: 0.8483 (ppp) REVERT: C 2153 MET cc_start: 0.9191 (mmm) cc_final: 0.8932 (mmm) REVERT: C 2423 MET cc_start: 0.8261 (ppp) cc_final: 0.7523 (ppp) REVERT: C 3793 MET cc_start: 0.8938 (mmp) cc_final: 0.8674 (mmp) REVERT: C 4039 MET cc_start: 0.8234 (ppp) cc_final: 0.8028 (ppp) REVERT: C 4839 MET cc_start: 0.9058 (tmm) cc_final: 0.8661 (tmm) REVERT: C 4993 MET cc_start: 0.8956 (tmm) cc_final: 0.8640 (tmm) outliers start: 41 outliers final: 31 residues processed: 491 average time/residue: 0.8776 time to fit residues: 788.2396 Evaluate side-chains 466 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 434 time to evaluate : 8.801 ------------------------------------------------------------------------------- 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: 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 479 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** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** A4109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4574 ASN ** 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 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 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** ** 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** ** 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 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** 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 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 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** D1861 GLN ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2763 HIS ** D3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** 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 44 ASN C 349 GLN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** 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 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1952 GLN ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 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** C4574 ASN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4805 ASN ** 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: 0.8983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.461 118058 Z= 2.344 Angle : 2.616 35.832 161014 Z= 1.314 Chirality : 0.105 0.812 18856 Planarity : 0.017 0.272 21167 Dihedral : 13.478 176.426 17467 Min Nonbonded Distance : 1.268 Molprobity Statistics. All-atom Clashscore : 107.94 Ramachandran Plot: Outliers : 1.57 % Allowed : 42.31 % Favored : 56.12 % Rotamer: Outliers : 0.09 % Allowed : 7.77 % Favored : 92.14 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.39 % Twisted General : 3.82 % 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 (0.04), residues: 12684 helix: -4.72 (0.03), residues: 5916 sheet: -3.75 (0.16), residues: 764 loop : -5.40 (0.05), residues: 6004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.009 TRP C3661 HIS 0.051 0.007 HIS D 582 PHE 0.102 0.010 PHE A4921 TYR 0.099 0.010 TYR A 714 ARG 0.053 0.003 ARG B4892 *********************** 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 459 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 450 time to evaluate : 8.755 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: A 150 MET cc_start: 0.8506 (mpp) cc_final: 0.8275 (mpp) REVERT: A 196 MET cc_start: 0.8781 (mmp) cc_final: 0.8550 (mmm) REVERT: A 1260 MET cc_start: 0.8616 (mmp) cc_final: 0.8269 (mmm) REVERT: A 1608 MET cc_start: 0.7978 (mtp) cc_final: 0.7748 (mtp) REVERT: A 1636 MET cc_start: 0.8339 (ppp) cc_final: 0.8078 (ppp) REVERT: A 2423 MET cc_start: 0.8269 (ppp) cc_final: 0.7537 (ppp) REVERT: A 3652 MET cc_start: 0.8956 (mpp) cc_final: 0.8725 (mpp) REVERT: A 3955 MET cc_start: 0.9105 (pmm) cc_final: 0.8899 (pmm) REVERT: A 4023 MET cc_start: 0.9184 (tpt) cc_final: 0.8775 (tpt) REVERT: A 4057 MET cc_start: 0.9168 (pmm) cc_final: 0.8719 (pmm) REVERT: A 4839 MET cc_start: 0.8692 (tmm) cc_final: 0.8368 (tmm) REVERT: B 116 MET cc_start: 0.8555 (tpt) cc_final: 0.7954 (tpt) REVERT: B 768 PHE cc_start: 0.8735 (m-80) cc_final: 0.8498 (m-80) REVERT: B 941 MET cc_start: 0.5931 (tpt) cc_final: 0.3678 (mmt) REVERT: B 1170 MET cc_start: 0.7494 (ppp) cc_final: 0.7261 (ppp) REVERT: B 1260 MET cc_start: 0.8595 (mmp) cc_final: 0.8308 (mmm) REVERT: B 1608 MET cc_start: 0.7862 (mtp) cc_final: 0.7658 (mtp) REVERT: B 2153 MET cc_start: 0.9261 (mmm) cc_final: 0.8906 (mmm) REVERT: B 2423 MET cc_start: 0.8245 (ppp) cc_final: 0.7510 (ppp) REVERT: B 4839 MET cc_start: 0.9060 (tmm) cc_final: 0.8642 (tmm) REVERT: D 196 MET cc_start: 0.7843 (mpp) cc_final: 0.7564 (mpp) REVERT: D 1152 MET cc_start: 0.7120 (tpp) cc_final: 0.6715 (tpp) REVERT: D 1260 MET cc_start: 0.8594 (mmp) cc_final: 0.8274 (mmm) REVERT: D 1636 MET cc_start: 0.8751 (ppp) cc_final: 0.8499 (ppp) REVERT: D 1708 ARG cc_start: 0.8970 (mtm-85) cc_final: 0.8628 (mtm-85) REVERT: D 2423 MET cc_start: 0.8246 (ppp) cc_final: 0.7605 (ppp) REVERT: D 4839 MET cc_start: 0.9088 (tmm) cc_final: 0.8774 (tmm) REVERT: D 4993 MET cc_start: 0.9057 (tmm) cc_final: 0.8784 (tmm) REVERT: C 196 MET cc_start: 0.8065 (mpp) cc_final: 0.7801 (mpp) REVERT: C 403 MET cc_start: 0.9465 (mmp) cc_final: 0.9228 (mmm) REVERT: C 483 MET cc_start: 0.8134 (mmp) cc_final: 0.7385 (mmp) REVERT: C 1260 MET cc_start: 0.8592 (mmp) cc_final: 0.8251 (mmm) REVERT: C 1608 MET cc_start: 0.7865 (mtp) cc_final: 0.7636 (mtp) REVERT: C 2153 MET cc_start: 0.9160 (mmm) cc_final: 0.8901 (mmm) REVERT: C 2423 MET cc_start: 0.8259 (ppp) cc_final: 0.7479 (ppp) REVERT: C 4039 MET cc_start: 0.8197 (ppp) cc_final: 0.7995 (ppp) REVERT: C 4839 MET cc_start: 0.9062 (tmm) cc_final: 0.8622 (tmm) outliers start: 9 outliers final: 6 residues processed: 459 average time/residue: 0.8886 time to fit residues: 745.5666 Evaluate side-chains 439 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 433 time to evaluate : 8.610 ------------------------------------------------------------------------------- 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 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 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 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2193 GLN ** 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 ** 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 ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** 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** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2035 HIS ** 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 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 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 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 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** ** 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** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2324 ASN ** 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** ** D4043 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 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** 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 582 HIS ** 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** ** C1678 ASN ** 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** ** 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** C4574 ASN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.9114 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= 2.346 Angle : 2.623 36.097 161014 Z= 1.319 Chirality : 0.105 0.627 18856 Planarity : 0.017 0.204 21167 Dihedral : 13.588 179.134 17467 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 108.50 Ramachandran Plot: Outliers : 1.58 % Allowed : 42.47 % Favored : 55.94 % Rotamer: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.39 % Twisted General : 3.98 % 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: -7.44 (0.04), residues: 12684 helix: -4.74 (0.03), residues: 5868 sheet: -3.70 (0.16), residues: 768 loop : -5.41 (0.05), residues: 6048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.009 TRP C3661 HIS 0.051 0.007 HIS B4983 PHE 0.131 0.010 PHE A4921 TYR 0.117 0.010 TYR D1712 ARG 0.047 0.003 ARG B4892 *********************** 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 456 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 453 time to evaluate : 8.791 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: A 116 MET cc_start: 0.9195 (tmm) cc_final: 0.8508 (tmm) REVERT: A 150 MET cc_start: 0.8503 (mpp) cc_final: 0.8277 (mpp) REVERT: A 196 MET cc_start: 0.8741 (mmp) cc_final: 0.8541 (mmm) REVERT: A 403 MET cc_start: 0.9414 (mmp) cc_final: 0.9211 (mmm) REVERT: A 1260 MET cc_start: 0.8692 (mmp) cc_final: 0.8360 (mmm) REVERT: A 1636 MET cc_start: 0.8397 (ppp) cc_final: 0.8018 (ppp) REVERT: A 2178 MET cc_start: 0.9232 (ppp) cc_final: 0.8974 (ppp) REVERT: A 2423 MET cc_start: 0.8253 (ppp) cc_final: 0.7532 (ppp) REVERT: A 3652 MET cc_start: 0.8961 (mpp) cc_final: 0.8732 (mpp) REVERT: A 4057 MET cc_start: 0.9175 (pmm) cc_final: 0.8728 (pmm) REVERT: A 4839 MET cc_start: 0.8712 (tmm) cc_final: 0.8339 (tmm) REVERT: A 4989 MET cc_start: 0.9292 (ppp) cc_final: 0.8993 (ppp) REVERT: B 116 MET cc_start: 0.8743 (tpt) cc_final: 0.8411 (tpt) REVERT: B 768 PHE cc_start: 0.8833 (m-80) cc_final: 0.8355 (m-80) REVERT: B 941 MET cc_start: 0.6070 (tpt) cc_final: 0.4369 (mmt) REVERT: B 1170 MET cc_start: 0.7260 (ppp) cc_final: 0.7024 (ppp) REVERT: B 1260 MET cc_start: 0.8605 (mmp) cc_final: 0.8280 (mmm) REVERT: B 2153 MET cc_start: 0.9257 (mmm) cc_final: 0.8884 (mmm) REVERT: B 2423 MET cc_start: 0.8274 (ppp) cc_final: 0.7549 (ppp) REVERT: B 3652 MET cc_start: 0.9007 (mpp) cc_final: 0.8802 (mpp) REVERT: B 4839 MET cc_start: 0.8984 (tmm) cc_final: 0.8638 (tmm) REVERT: D 196 MET cc_start: 0.7766 (mpp) cc_final: 0.7509 (mpp) REVERT: D 941 MET cc_start: 0.4692 (tpp) cc_final: 0.4251 (tpp) REVERT: D 1152 MET cc_start: 0.7135 (tpp) cc_final: 0.6717 (tpp) REVERT: D 1260 MET cc_start: 0.8622 (mmp) cc_final: 0.8306 (mmm) REVERT: D 1636 MET cc_start: 0.8809 (ppp) cc_final: 0.8525 (ppp) REVERT: D 1708 ARG cc_start: 0.8876 (mtm-85) cc_final: 0.8473 (mtm-85) REVERT: D 2423 MET cc_start: 0.8176 (ppp) cc_final: 0.7456 (ppp) REVERT: D 3673 MET cc_start: 0.8640 (mmp) cc_final: 0.8179 (mmp) REVERT: D 4796 MET cc_start: 0.8913 (tpp) cc_final: 0.8555 (tpt) REVERT: D 4839 MET cc_start: 0.9073 (tmm) cc_final: 0.8696 (tmm) REVERT: C 196 MET cc_start: 0.8133 (mpp) cc_final: 0.7899 (mpp) REVERT: C 403 MET cc_start: 0.9468 (mmp) cc_final: 0.9254 (mmm) REVERT: C 483 MET cc_start: 0.8054 (mmp) cc_final: 0.7251 (mmp) REVERT: C 1260 MET cc_start: 0.8609 (mmp) cc_final: 0.8258 (mmm) REVERT: C 2423 MET cc_start: 0.8065 (ppp) cc_final: 0.7420 (ppp) REVERT: C 4039 MET cc_start: 0.8192 (ppp) cc_final: 0.7989 (ppp) REVERT: C 4839 MET cc_start: 0.9048 (tmm) cc_final: 0.8542 (tmm) REVERT: C 4993 MET cc_start: 0.8972 (tmm) cc_final: 0.8756 (tmm) outliers start: 3 outliers final: 3 residues processed: 456 average time/residue: 0.9090 time to fit residues: 756.2706 Evaluate side-chains 436 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 433 time to evaluate : 8.612 ------------------------------------------------------------------------------- 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 479 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** ** A1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 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** ** A4043 GLN ** 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** ** 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 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** ** 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 105 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 479 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 838 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** ** 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** ** D2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D2872 GLN ** 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** ** 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 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** 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 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** ** C1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** 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** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.9277 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= 2.349 Angle : 2.636 36.213 161014 Z= 1.326 Chirality : 0.106 0.791 18856 Planarity : 0.017 0.238 21167 Dihedral : 13.712 175.067 17467 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 109.39 Ramachandran Plot: Outliers : 1.55 % Allowed : 43.45 % Favored : 55.00 % Rotamer: Outliers : 0.01 % Allowed : 2.33 % Favored : 97.66 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.90 % Twisted General : 4.12 % 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: -7.45 (0.04), residues: 12684 helix: -4.74 (0.03), residues: 5844 sheet: -3.86 (0.16), residues: 764 loop : -5.41 (0.05), residues: 6076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.009 TRP C3661 HIS 0.049 0.007 HIS B4983 PHE 0.139 0.010 PHE A4921 TYR 0.112 0.010 TYR D 247 ARG 0.058 0.003 ARG B4892 ********************** 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 448 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 447 time to evaluate : 8.656 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: A 116 MET cc_start: 0.9164 (tmm) cc_final: 0.8486 (tmm) REVERT: A 196 MET cc_start: 0.8676 (mmp) cc_final: 0.8426 (mmm) REVERT: A 403 MET cc_start: 0.9409 (mmp) cc_final: 0.9205 (mmm) REVERT: A 1579 MET cc_start: 0.8298 (mmp) cc_final: 0.7983 (mmp) REVERT: A 1636 MET cc_start: 0.8466 (ppp) cc_final: 0.8130 (ppp) REVERT: A 2178 MET cc_start: 0.9231 (ppp) cc_final: 0.8997 (ppp) REVERT: A 2423 MET cc_start: 0.8249 (ppp) cc_final: 0.7557 (ppp) REVERT: A 3652 MET cc_start: 0.8970 (mpp) cc_final: 0.8713 (mpp) REVERT: A 4039 MET cc_start: 0.8551 (ppp) cc_final: 0.8284 (ppp) REVERT: A 4057 MET cc_start: 0.9174 (pmm) cc_final: 0.8756 (pmm) REVERT: A 4839 MET cc_start: 0.8695 (tmm) cc_final: 0.8339 (tmm) REVERT: A 4989 MET cc_start: 0.9278 (ppp) cc_final: 0.8982 (ppp) REVERT: B 768 PHE cc_start: 0.8799 (m-80) cc_final: 0.8308 (m-80) REVERT: B 941 MET cc_start: 0.6310 (tpt) cc_final: 0.5484 (mmt) REVERT: B 1170 MET cc_start: 0.7230 (ppp) cc_final: 0.6995 (ppp) REVERT: B 1260 MET cc_start: 0.8624 (mmp) cc_final: 0.8314 (mmm) REVERT: B 2153 MET cc_start: 0.9257 (mmm) cc_final: 0.8934 (mmm) REVERT: B 2423 MET cc_start: 0.8302 (ppp) cc_final: 0.7580 (ppp) REVERT: B 3652 MET cc_start: 0.9000 (mpp) cc_final: 0.8785 (mpp) REVERT: B 3875 MET cc_start: 0.8568 (mmm) cc_final: 0.8357 (mmm) REVERT: B 4839 MET cc_start: 0.9015 (tmm) cc_final: 0.8644 (tmm) REVERT: D 196 MET cc_start: 0.7652 (mpp) cc_final: 0.7442 (mpp) REVERT: D 941 MET cc_start: 0.4376 (tpp) cc_final: 0.3908 (tpp) REVERT: D 1152 MET cc_start: 0.7085 (tpp) cc_final: 0.6550 (tpp) REVERT: D 1260 MET cc_start: 0.8707 (mmp) cc_final: 0.8378 (mmm) REVERT: D 1636 MET cc_start: 0.8795 (ppp) cc_final: 0.8543 (ppp) REVERT: D 1708 ARG cc_start: 0.8946 (mtm-85) cc_final: 0.8600 (mtm-85) REVERT: D 2178 MET cc_start: 0.9321 (ppp) cc_final: 0.8685 (ppp) REVERT: D 2423 MET cc_start: 0.8103 (ppp) cc_final: 0.7439 (ppp) REVERT: D 4796 MET cc_start: 0.8927 (tpp) cc_final: 0.8566 (tpt) REVERT: D 4839 MET cc_start: 0.9076 (tmm) cc_final: 0.8680 (tmm) REVERT: C 196 MET cc_start: 0.8055 (mpp) cc_final: 0.7809 (mpp) REVERT: C 403 MET cc_start: 0.9476 (mmp) cc_final: 0.9244 (mmm) REVERT: C 483 MET cc_start: 0.8049 (mmp) cc_final: 0.7241 (mmp) REVERT: C 1100 MET cc_start: 0.7242 (mtt) cc_final: 0.6995 (mtt) REVERT: C 1260 MET cc_start: 0.8591 (mmp) cc_final: 0.8227 (mmm) REVERT: C 1608 MET cc_start: 0.7542 (mtp) cc_final: 0.7301 (mtp) REVERT: C 2423 MET cc_start: 0.8075 (ppp) cc_final: 0.7469 (ppp) REVERT: C 3793 MET cc_start: 0.9134 (mmp) cc_final: 0.8870 (mmp) REVERT: C 4839 MET cc_start: 0.9053 (tmm) cc_final: 0.8523 (tmm) outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.9048 time to fit residues: 740.2586 Evaluate side-chains 434 residues out of total 11136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 8.587 ------------------------------------------------------------------------------- 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 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** 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 ** A1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1678 ASN ** 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** ** 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 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2035 HIS ** 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 ** 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 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** 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 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 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** ** 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** D2773 ASN ** D2872 GLN ** 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** ** 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 ** 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 582 HIS ** 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** ** C1678 ASN ** 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** ** C4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.061720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.046201 restraints weight = 972142.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.045359 restraints weight = 800430.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.045257 restraints weight = 939839.387| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.9397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.036 0.474 118058 Z= 2.351 Angle : 2.640 36.191 161014 Z= 1.328 Chirality : 0.106 0.849 18856 Planarity : 0.017 0.185 21167 Dihedral : 13.752 175.208 17467 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 109.78 Ramachandran Plot: Outliers : 1.58 % Allowed : 43.42 % Favored : 54.99 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.08 % Twisted General : 4.20 % 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: -7.46 (0.04), residues: 12684 helix: -4.74 (0.03), residues: 5884 sheet: -3.99 (0.16), residues: 688 loop : -5.41 (0.05), residues: 6112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.009 TRP D1143 HIS 0.048 0.007 HIS B4983 PHE 0.134 0.010 PHE A4921 TYR 0.109 0.010 TYR B3765 ARG 0.058 0.003 ARG B4892 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37193.12 seconds wall clock time: 646 minutes 6.31 seconds (38766.31 seconds total)