Starting phenix.real_space_refine on Sat Dec 9 13:39:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/12_2023/7k0s_22615_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/12_2023/7k0s_22615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/12_2023/7k0s_22615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/12_2023/7k0s_22615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/12_2023/7k0s_22615_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/12_2023/7k0s_22615_neut_updated.pdb" } resolution = 4.5 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= 0.007 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 12 5.49 5 Mg 5 5.21 5 S 625 5.16 5 C 73415 2.51 5 N 20552 2.21 5 O 21322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 76": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A GLU 2115": "OE1" <-> "OE2" Residue "A GLU 3755": "OE1" <-> "OE2" Residue "A GLU 3928": "OE1" <-> "OE2" Residue "A GLU 4212": "OE1" <-> "OE2" Residue "A GLU 4239": "OE1" <-> "OE2" Residue "A GLU 5002": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 2115": "OE1" <-> "OE2" Residue "B GLU 2209": "OE1" <-> "OE2" Residue "B GLU 3754": "OE1" <-> "OE2" Residue "B GLU 4212": "OE1" <-> "OE2" Residue "B GLU 4948": "OE1" <-> "OE2" Residue "B GLU 4952": "OE1" <-> "OE2" Residue "B GLU 5007": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1181": "OE1" <-> "OE2" Residue "D GLU 2115": "OE1" <-> "OE2" Residue "D GLU 2209": "OE1" <-> "OE2" Residue "D GLU 3754": "OE1" <-> "OE2" Residue "D PHE 4093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4212": "OE1" <-> "OE2" Residue "D GLU 4867": "OE1" <-> "OE2" Residue "D GLU 4869": "OE1" <-> "OE2" Residue "D GLU 4871": "OE1" <-> "OE2" Residue "D GLU 4981": "OE1" <-> "OE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1181": "OE1" <-> "OE2" Residue "C GLU 2209": "OE1" <-> "OE2" Residue "C PHE 4093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4172": "OE1" <-> "OE2" Residue "C GLU 4182": "OE1" <-> "OE2" Residue "C GLU 4212": "OE1" <-> "OE2" Residue "C GLU 4244": "OE1" <-> "OE2" Residue "C ARG 4892": "NH1" <-> "NH2" Residue "C GLU 5002": "OE1" <-> "OE2" Time to flip residues: 0.36s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 115935 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 28941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4110, 28941 Classifications: {'peptide': 4110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1233} Link IDs: {'PTRANS': 147, 'TRANS': 3962} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3015 Unresolved non-hydrogen angles: 4205 Unresolved non-hydrogen dihedrals: 1879 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 886, 'ASP:plan': 45, 'TYR:plan': 2, 'ASN:plan1': 18, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 5, 'GLU:plan': 87, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1771 Chain: "B" Number of atoms: 28940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4110, 28940 Classifications: {'peptide': 4110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1233} Link IDs: {'PTRANS': 147, 'TRANS': 3962} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3017 Unresolved non-hydrogen angles: 4210 Unresolved non-hydrogen dihedrals: 1883 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 19, 'UNK:plan-1': 886, 'ASP:plan': 45, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 89, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1775 Chain: "D" Number of atoms: 28963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4110, 28963 Classifications: {'peptide': 4110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1227} Link IDs: {'PTRANS': 147, 'TRANS': 3962} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 2994 Unresolved non-hydrogen angles: 4181 Unresolved non-hydrogen dihedrals: 1864 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 886, 'ASP:plan': 45, 'TYR:plan': 3, 'ASN:plan1': 17, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 4, 'GLU:plan': 84, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1757 Chain: "C" Number of atoms: 28958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4110, 28958 Classifications: {'peptide': 4110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1230} Link IDs: {'PTRANS': 147, 'TRANS': 3962} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 2996 Unresolved non-hydrogen angles: 4179 Unresolved non-hydrogen dihedrals: 1862 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 886, 'ASP:plan': 46, 'TYR:plan': 1, 'ASN:plan1': 18, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 87, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1761 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28276 SG CYS A4958 180.882 178.034 121.709 1.00 20.03 S ATOM 28301 SG CYS A4961 180.776 176.002 118.403 1.00 20.49 S ATOM 57213 SG CYS B4958 205.130 179.256 121.759 1.00 26.15 S ATOM 57238 SG CYS B4961 205.762 181.597 118.738 1.00 26.27 S ATOM 86175 SG CYS D4958 178.051 204.221 121.706 1.00 24.98 S ATOM 86200 SG CYS D4961 175.842 202.810 118.184 1.00 32.62 S ATOM A0BOD SG CYS C4958 204.318 205.083 121.685 1.00 28.50 S ATOM A0BP2 SG CYS C4961 201.669 205.874 118.968 1.00 28.72 S Time building chain proxies: 43.50, per 1000 atoms: 0.38 Number of scatterers: 115935 At special positions: 0 Unit cell: (383.52, 384.88, 212.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 625 16.00 P 12 15.00 Mg 5 11.99 O 21322 8.00 N 20552 7.00 C 73415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 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: 31.64 Conformation dependent library (CDL) restraints added in 13.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " 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=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4983 " Number of angles added : 6 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31160 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: 468 helices and 56 sheets defined 55.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 27.73 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 5.046A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N CYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 84 removed outlier: 4.054A pdb=" N GLN A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 5.440A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 256' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.995A pdb=" N LEU A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 423 removed outlier: 3.950A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 4.995A pdb=" N VAL A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.521A pdb=" N SER A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 4.139A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.864A pdb=" N GLU A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 506' Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.783A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 4.314A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 541' Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.787A pdb=" N VAL A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.749A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 3.731A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.844A pdb=" N LYS A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.961A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 3.970A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 890 removed outlier: 4.171A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 removed outlier: 4.287A pdb=" N TYR A 920 " --> pdb=" O PRO A 916 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 950 removed outlier: 6.093A pdb=" N ASP A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1002 removed outlier: 4.537A pdb=" N THR A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 985 " --> pdb=" O GLN A 981 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 986 " --> pdb=" O THR A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1050 removed outlier: 4.446A pdb=" N GLN A1041 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A1044 " --> pdb=" O CYS A1040 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A1048 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1580 removed outlier: 4.347A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1652 through 1657 removed outlier: 3.915A pdb=" N ARG A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1652 through 1657' Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 3.758A pdb=" N ALA A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 3.506A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1701 removed outlier: 4.940A pdb=" N LEU A1695 " --> pdb=" O GLN A1691 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1698 " --> pdb=" O LEU A1694 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA A1701 " --> pdb=" O ALA A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1707 through 1724 removed outlier: 3.953A pdb=" N TYR A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A1713 " --> pdb=" O ALA A1709 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU A1721 " --> pdb=" O SER A1717 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER A1722 " --> pdb=" O ILE A1718 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A1723 " --> pdb=" O HIS A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1731 removed outlier: 3.640A pdb=" N MET A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.828A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.633A pdb=" N ARG A1820 " --> pdb=" O GLY A1816 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 removed outlier: 4.122A pdb=" N VAL A1839 " --> pdb=" O GLU A1835 " (cutoff:3.500A) Proline residue: A1840 - end of helix removed outlier: 5.111A pdb=" N LYS A1843 " --> pdb=" O VAL A1839 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A1851 " --> pdb=" O THR A1847 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1855 through 1867 removed outlier: 3.907A pdb=" N MET A1865 " --> pdb=" O GLN A1861 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE A1866 " --> pdb=" O ILE A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1981 removed outlier: 4.629A pdb=" N LEU A1937 " --> pdb=" O GLU A1933 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A1971 " --> pdb=" O ASP A1967 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A1972 " --> pdb=" O LYS A1968 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A1979 " --> pdb=" O SER A1975 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1980 " --> pdb=" O ARG A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1999 removed outlier: 3.539A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2015 removed outlier: 4.151A pdb=" N GLU A2015 " --> pdb=" O HIS A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2024 through 2043 removed outlier: 5.996A pdb=" N ARG A2028 " --> pdb=" O PRO A2024 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN A2029 " --> pdb=" O GLU A2025 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP A2030 " --> pdb=" O ASP A2026 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A2031 " --> pdb=" O ILE A2027 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.589A pdb=" N LEU A2097 " --> pdb=" O SER A2093 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.600A pdb=" N VAL A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A2128 " --> pdb=" O LEU A2124 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2141 Proline residue: A2139 - end of helix Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 4.151A pdb=" N THR A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2188 removed outlier: 4.020A pdb=" N ASN A2176 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A2185 " --> pdb=" O SER A2181 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET A2186 " --> pdb=" O ILE A2182 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN A2187 " --> pdb=" O GLY A2183 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2194 Processing helix chain 'A' and resid 2195 through 2202 Processing helix chain 'A' and resid 2203 through 2216 removed outlier: 3.677A pdb=" N VAL A2207 " --> pdb=" O MET A2203 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET A2208 " --> pdb=" O HIS A2204 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU A2209 " --> pdb=" O GLU A2205 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL A2210 " --> pdb=" O THR A2206 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A2211 " --> pdb=" O VAL A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2243 removed outlier: 3.504A pdb=" N PHE A2235 " --> pdb=" O SER A2231 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A2242 " --> pdb=" O TYR A2238 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2252 removed outlier: 4.031A pdb=" N SER A2249 " --> pdb=" O GLN A2245 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A2250 " --> pdb=" O ASN A2246 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A2251 " --> pdb=" O GLN A2247 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2245 through 2252' Processing helix chain 'A' and resid 2253 through 2262 removed outlier: 4.157A pdb=" N GLU A2259 " --> pdb=" O SER A2255 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2282 removed outlier: 4.017A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A2281 " --> pdb=" O ALA A2277 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP A2282 " --> pdb=" O ALA A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2291 removed outlier: 4.130A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) removed outlier: 5.875A 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 2308 removed outlier: 3.846A pdb=" N VAL A2298 " --> pdb=" O ASP A2294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A2307 " --> pdb=" O ALA A2303 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2315 removed outlier: 4.372A pdb=" N ALA A2315 " --> pdb=" O PRO A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2341 removed outlier: 4.070A pdb=" N LEU A2332 " --> pdb=" O GLY A2328 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASP A2333 " --> pdb=" O GLU A2329 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A2335 " --> pdb=" O TYR A2331 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A2336 " --> pdb=" O LEU A2332 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A2339 " --> pdb=" O LEU A2335 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL A2341 " --> pdb=" O PHE A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.627A pdb=" N ALA A2350 " --> pdb=" O VAL A2346 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A2353 " --> pdb=" O ASN A2349 " (cutoff:3.500A) removed outlier: 3.921A 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: 3.750A pdb=" N GLY A2370 " --> pdb=" O PRO A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2375 through 2390 Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2437 removed outlier: 4.158A pdb=" N ALA A2421 " --> pdb=" O HIS A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2441 through 2447 removed outlier: 4.005A pdb=" N ALA A2445 " --> pdb=" O HIS A2441 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY A2446 " --> pdb=" O LEU A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2448 through 2462 Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2464 through 2472 removed outlier: 4.226A pdb=" N GLY A2468 " --> pdb=" O ASP A2464 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A2472 " --> pdb=" O GLY A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2741 through 2746 removed outlier: 4.918A pdb=" N ILE A2746 " --> pdb=" O THR A2742 " (cutoff:3.500A) Processing helix chain 'A' and resid 2750 through 2774 removed outlier: 4.653A pdb=" N PHE A2754 " --> pdb=" O LYS A2750 " (cutoff:3.500A) Processing helix chain 'A' and resid 2793 through 2798 removed outlier: 4.091A pdb=" N PHE A2797 " --> pdb=" O PRO A2793 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER A2798 " --> pdb=" O TYR A2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2793 through 2798' Processing helix chain 'A' and resid 2799 through 2806 removed outlier: 5.166A pdb=" N GLU A2803 " --> pdb=" O GLU A2799 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) Processing helix chain 'A' and resid 2809 through 2820 removed outlier: 4.623A pdb=" N ALA A2815 " --> pdb=" O GLU A2811 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET A2816 " --> pdb=" O SER A2812 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A2817 " --> pdb=" O LEU A2813 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A2818 " --> pdb=" O LYS A2814 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A2819 " --> pdb=" O ALA A2815 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2898 removed outlier: 3.618A pdb=" N MET A2874 " --> pdb=" O GLU A2870 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A2896 " --> pdb=" O GLN A2892 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A2897 " --> pdb=" O GLU A2893 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A2898 " --> pdb=" O LEU A2894 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2934 removed outlier: 3.838A pdb=" N LYS A2916 " --> pdb=" O THR A2912 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A2917 " --> pdb=" O ALA A2913 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ARG A2920 " --> pdb=" O LYS A2916 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A2921 " --> pdb=" O ALA A2917 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN A2933 " --> pdb=" O PHE A2929 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY A2934 " --> pdb=" O LEU A2930 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3658 removed outlier: 4.716A pdb=" N LYS A3658 " --> pdb=" O LEU A3654 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3683 removed outlier: 4.494A pdb=" N ILE A3674 " --> pdb=" O GLU A3670 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A3675 " --> pdb=" O ASP A3671 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A3677 " --> pdb=" O MET A3673 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A3678 " --> pdb=" O ILE A3674 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A3681 " --> pdb=" O LEU A3677 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 removed outlier: 3.595A pdb=" N THR A3711 " --> pdb=" O ARG A3707 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3739 removed outlier: 3.639A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A3736 " --> pdb=" O SER A3732 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3771 removed outlier: 4.038A pdb=" N LYS A3756 " --> pdb=" O SER A3752 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU A3757 " --> pdb=" O PHE A3753 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A3758 " --> pdb=" O GLU A3754 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N HIS A3771 " --> pdb=" O GLN A3767 " (cutoff:3.500A) Processing helix chain 'A' and resid 3775 through 3786 removed outlier: 4.786A pdb=" N VAL A3779 " --> pdb=" O ALA A3775 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A3785 " --> pdb=" O GLN A3781 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS A3786 " --> pdb=" O MET A3782 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 4.180A pdb=" N LYS A3799 " --> pdb=" O SER A3795 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A3800 " --> pdb=" O SER A3796 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A3801 " --> pdb=" O THR A3797 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3824 removed outlier: 4.078A pdb=" N GLN A3813 " --> pdb=" O ASN A3809 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A3814 " --> pdb=" O ALA A3810 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A3815 " --> pdb=" O GLU A3811 " (cutoff:3.500A) Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 7.174A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3858 removed outlier: 3.831A pdb=" N GLY A3855 " --> pdb=" O ASN A3851 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A3857 " --> pdb=" O ALA A3853 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N MET A3858 " --> pdb=" O GLU A3854 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3893 removed outlier: 4.629A pdb=" N ASP A3883 " --> pdb=" O GLU A3879 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A3884 " --> pdb=" O PHE A3880 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE A3885 " --> pdb=" O THR A3881 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 6.604A pdb=" N GLN A3900 " --> pdb=" O ASN A3896 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN A3901 " --> pdb=" O ASN A3897 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.821A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 4.351A pdb=" N GLU A3967 " --> pdb=" O ASN A3963 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A3968 " --> pdb=" O SER A3964 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 3.830A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A3983 " --> pdb=" O SER A3979 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4003 removed outlier: 3.542A pdb=" N GLY A3991 " --> pdb=" O ASP A3987 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N MET A3999 " --> pdb=" O VAL A3995 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET A4000 " --> pdb=" O PHE A3996 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.729A pdb=" N LEU A4013 " --> pdb=" O GLN A4009 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4052 Processing helix chain 'A' and resid 4053 through 4072 removed outlier: 5.278A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A4058 " --> pdb=" O ASN A4054 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A4069 " --> pdb=" O PHE A4065 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A4072 " --> pdb=" O LEU A4068 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4082 removed outlier: 4.041A pdb=" N GLN A4078 " --> pdb=" O SER A4074 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A4080 " --> pdb=" O ALA A4076 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A4081 " --> pdb=" O PHE A4077 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N THR A4082 " --> pdb=" O GLN A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 4.014A pdb=" N PHE A4093 " --> pdb=" O SER A4089 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 5.016A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4154 removed outlier: 3.670A pdb=" N ASN A4130 " --> pdb=" O GLU A4126 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A4131 " --> pdb=" O GLU A4127 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Proline residue: A4135 - end of helix removed outlier: 4.307A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 3.767A pdb=" N ARG A4161 " --> pdb=" O ASP A4157 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN A4162 " --> pdb=" O PRO A4158 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 Processing helix chain 'A' and resid 4198 through 4207 removed outlier: 5.004A pdb=" N ARG A4202 " --> pdb=" O SER A4198 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A4206 " --> pdb=" O ARG A4202 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4224 removed outlier: 3.704A pdb=" N ASN A4223 " --> pdb=" O PHE A4219 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A4224 " --> pdb=" O ASP A4220 " (cutoff:3.500A) Processing helix chain 'A' and resid 4229 through 4252 removed outlier: 4.529A pdb=" N LEU A4233 " --> pdb=" O GLU A4229 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE A4234 " --> pdb=" O LYS A4230 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A4235 " --> pdb=" O MET A4231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A4236 " --> pdb=" O GLU A4232 " (cutoff:3.500A) Processing helix chain 'A' and resid 4540 through 4559 removed outlier: 3.877A pdb=" N GLU A4545 " --> pdb=" O TRP A4541 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A4546 " --> pdb=" O GLY A4542 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN A4558 " --> pdb=" O TYR A4554 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE A4559 " --> pdb=" O LEU A4555 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4579 removed outlier: 4.992A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4642 through 4684 removed outlier: 4.413A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix removed outlier: 4.005A pdb=" N ILE A4670 " --> pdb=" O VAL A4666 " (cutoff:3.500A) Processing helix chain 'A' and resid 4696 through 4701 removed outlier: 3.743A pdb=" N GLN A4700 " --> pdb=" O ASP A4696 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4729 removed outlier: 4.238A pdb=" N LYS A4723 " --> pdb=" O PHE A4719 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A4724 " --> pdb=" O VAL A4720 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4749 through 4755 removed outlier: 3.535A pdb=" N ASN A4754 " --> pdb=" O ILE A4750 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A4755 " --> pdb=" O THR A4751 " (cutoff:3.500A) Processing helix chain 'A' and resid 4766 through 4771 removed outlier: 3.621A pdb=" N SER A4770 " --> pdb=" O THR A4766 " (cutoff:3.500A) Processing helix chain 'A' and resid 4772 through 4786 removed outlier: 3.544A pdb=" N VAL A4782 " --> pdb=" O TRP A4778 " (cutoff:3.500A) Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 5.023A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4820 removed outlier: 3.842A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY A4819 " --> pdb=" O ASP A4815 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A4820 " --> pdb=" O ILE A4816 " (cutoff:3.500A) Processing helix chain 'A' and resid 4822 through 4859 removed outlier: 4.283A pdb=" N ILE A4826 " --> pdb=" O THR A4822 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY A4834 " --> pdb=" O VAL A4830 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS A4835 " --> pdb=" O THR A4831 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN A4836 " --> pdb=" O HIS A4832 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A4838 " --> pdb=" O GLY A4834 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET A4839 " --> pdb=" O LYS A4835 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4894 removed outlier: 5.078A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY A4894 " --> pdb=" O GLY A4890 " (cutoff:3.500A) Processing helix chain 'A' and resid 4897 through 4902 removed outlier: 5.276A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4957 removed outlier: 4.175A pdb=" N ARG A4913 " --> pdb=" O TYR A4909 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A4914 " --> pdb=" O GLU A4910 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A4916 " --> pdb=" O TYR A4912 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE A4927 " --> pdb=" O PHE A4923 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU A4928 " --> pdb=" O VAL A4924 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU A4929 " --> pdb=" O ILE A4925 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A4936 " --> pdb=" O ILE A4932 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A4951 " --> pdb=" O GLN A4947 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 4.671A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP A4969 " --> pdb=" O SER A4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4964 through 4969' Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4999 removed outlier: 6.595A pdb=" N TYR A4988 " --> pdb=" O ASN A4984 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A4996 " --> pdb=" O LEU A4992 " (cutoff:3.500A) removed outlier: 5.222A 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 5032 removed outlier: 6.454A pdb=" N GLN A5031 " --> pdb=" O CYS A5027 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR A5032 " --> pdb=" O PHE A5028 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5027 through 5032' Processing helix chain 'A' and resid 3861 through 3867 removed outlier: 5.145A pdb=" N THR A3864 " --> pdb=" O GLU A3861 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL A3865 " --> pdb=" O ASP A3862 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE A3866 " --> pdb=" O GLY A3863 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASN A3867 " --> pdb=" O THR A3864 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3861 through 3867' Processing helix chain 'A' and resid 54 through 59 Proline residue: A 59 - end of helix No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'B' and resid 61 through 66 removed outlier: 5.107A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N CYS B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 66' Processing helix chain 'B' and resid 74 through 84 removed outlier: 4.139A pdb=" N GLN B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 256 removed outlier: 5.847A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 256' Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.039A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 423 removed outlier: 3.938A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 5.045A pdb=" N VAL B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 482 removed outlier: 3.547A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.634A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.797A pdb=" N GLU B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 506' Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.734A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 520 " --> pdb=" O LYS B 516 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 4.411A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 541' Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.815A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.632A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 3.862A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.462A pdb=" N LYS B 584 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 585 " --> pdb=" O ASN B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.878A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 removed outlier: 3.960A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 890 removed outlier: 4.168A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 removed outlier: 4.300A pdb=" N TYR B 920 " --> pdb=" O PRO B 916 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 935 " --> pdb=" O THR B 931 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 950 removed outlier: 6.106A pdb=" N ASP B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1002 removed outlier: 4.522A pdb=" N THR B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL B 985 " --> pdb=" O GLN B 981 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1050 removed outlier: 4.443A pdb=" N GLN B1041 " --> pdb=" O ASP B1037 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA B1042 " --> pdb=" O SER B1038 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B1044 " --> pdb=" O CYS B1040 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B1048 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B1049 " --> pdb=" O THR B1045 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1574 through 1580 removed outlier: 4.337A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1652 through 1657 removed outlier: 3.774A pdb=" N ARG B1656 " --> pdb=" O GLU B1652 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1652 through 1657' Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 3.878A pdb=" N ALA B1675 " --> pdb=" O ARG B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1690 Processing helix chain 'B' and resid 1691 through 1701 removed outlier: 4.909A pdb=" N LEU B1695 " --> pdb=" O GLN B1691 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA B1701 " --> pdb=" O ALA B1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 1707 through 1724 removed outlier: 3.958A pdb=" N TYR B1711 " --> pdb=" O LEU B1707 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP B1713 " --> pdb=" O ALA B1709 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU B1721 " --> pdb=" O SER B1717 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER B1722 " --> pdb=" O ILE B1718 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA B1723 " --> pdb=" O HIS B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1725 through 1731 Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.845A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.689A pdb=" N ARG B1820 " --> pdb=" O GLY B1816 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 removed outlier: 4.122A pdb=" N VAL B1839 " --> pdb=" O GLU B1835 " (cutoff:3.500A) Proline residue: B1840 - end of helix removed outlier: 5.102A pdb=" N LYS B1843 " --> pdb=" O VAL B1839 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B1851 " --> pdb=" O THR B1847 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY B1852 " --> pdb=" O LEU B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1867 removed outlier: 3.926A pdb=" N MET B1865 " --> pdb=" O GLN B1861 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE B1866 " --> pdb=" O ILE B1862 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1981 removed outlier: 5.269A pdb=" N LEU B1937 " --> pdb=" O GLU B1933 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B1971 " --> pdb=" O ASP B1967 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN B1972 " --> pdb=" O LYS B1968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1987 through 1999 removed outlier: 3.566A pdb=" N ARG B1996 " --> pdb=" O ALA B1992 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2015 removed outlier: 4.204A pdb=" N GLU B2015 " --> pdb=" O HIS B2011 " (cutoff:3.500A) Processing helix chain 'B' and resid 2024 through 2043 removed outlier: 5.974A pdb=" N ARG B2028 " --> pdb=" O PRO B2024 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLN B2029 " --> pdb=" O GLU B2025 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP B2030 " --> pdb=" O ASP B2026 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B2031 " --> pdb=" O ILE B2027 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.502A pdb=" N LEU B2097 " --> pdb=" O SER B2093 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.668A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B2128 " --> pdb=" O LEU B2124 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2141 Proline residue: B2139 - end of helix Processing helix chain 'B' and resid 2148 through 2169 removed outlier: 4.227A pdb=" N THR B2152 " --> pdb=" O SER B2148 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2188 removed outlier: 3.799A pdb=" N ASN B2176 " --> pdb=" O PRO B2172 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B2186 " --> pdb=" O ILE B2182 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B2187 " --> pdb=" O GLY B2183 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2194 Processing helix chain 'B' and resid 2195 through 2202 Processing helix chain 'B' and resid 2203 through 2216 removed outlier: 4.436A pdb=" N MET B2208 " --> pdb=" O HIS B2204 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU B2209 " --> pdb=" O GLU B2205 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL B2210 " --> pdb=" O THR B2206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET B2211 " --> pdb=" O VAL B2207 " (cutoff:3.500A) Processing helix chain 'B' and resid 2227 through 2243 removed outlier: 4.351A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B2235 " --> pdb=" O SER B2231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.691A 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 SER B2249 " --> pdb=" O GLN B2245 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET B2250 " --> pdb=" O ASN B2246 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B2251 " --> pdb=" O GLN B2247 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2245 through 2252' Processing helix chain 'B' and resid 2253 through 2262 removed outlier: 4.154A pdb=" N GLU B2259 " --> pdb=" O SER B2255 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2282 removed outlier: 3.699A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B2281 " --> pdb=" O ALA B2277 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP B2282 " --> pdb=" O ALA B2278 " (cutoff:3.500A) Processing helix chain 'B' and resid 2286 through 2291 removed outlier: 4.024A pdb=" N LEU B2290 " --> pdb=" O LEU B2286 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN B2291 " --> pdb=" O ALA B2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2286 through 2291' Processing helix chain 'B' and resid 2294 through 2308 removed outlier: 4.083A pdb=" N VAL B2298 " --> pdb=" O ASP B2294 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B2306 " --> pdb=" O LEU B2302 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B2307 " --> pdb=" O ALA B2303 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 4.405A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2341 removed outlier: 4.115A pdb=" N LEU B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASP B2333 " --> pdb=" O GLU B2329 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B2335 " --> pdb=" O TYR B2331 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B2336 " --> pdb=" O LEU B2332 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B2339 " --> pdb=" O LEU B2335 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B2340 " --> pdb=" O ARG B2336 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL B2341 " --> pdb=" O PHE B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 3.603A pdb=" N ALA B2350 " --> pdb=" O VAL B2346 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL B2353 " --> pdb=" O ASN B2349 " (cutoff:3.500A) removed outlier: 3.938A 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 Processing helix chain 'B' and resid 2375 through 2390 Proline residue: B2390 - end of helix Processing helix chain 'B' and resid 2417 through 2437 removed outlier: 4.164A pdb=" N ALA B2421 " --> pdb=" O HIS B2417 " (cutoff:3.500A) Processing helix chain 'B' and resid 2441 through 2447 removed outlier: 4.345A pdb=" N ALA B2445 " --> pdb=" O HIS B2441 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLY B2446 " --> pdb=" O LEU B2442 " (cutoff:3.500A) Processing helix chain 'B' and resid 2448 through 2462 Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2464 through 2472 removed outlier: 4.066A pdb=" N GLY B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B2472 " --> pdb=" O GLY B2468 " (cutoff:3.500A) Processing helix chain 'B' and resid 2741 through 2746 removed outlier: 4.920A pdb=" N ILE B2746 " --> pdb=" O THR B2742 " (cutoff:3.500A) Processing helix chain 'B' and resid 2750 through 2774 removed outlier: 4.676A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2798 removed outlier: 4.074A pdb=" N PHE B2797 " --> pdb=" O PRO B2793 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER B2798 " --> pdb=" O TYR B2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2793 through 2798' Processing helix chain 'B' and resid 2799 through 2806 removed outlier: 5.163A pdb=" N GLU B2803 " --> pdb=" O GLU B2799 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) Processing helix chain 'B' and resid 2809 through 2820 removed outlier: 4.829A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET B2816 " --> pdb=" O SER B2812 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B2817 " --> pdb=" O LEU B2813 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B2818 " --> pdb=" O LYS B2814 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP B2819 " --> pdb=" O ALA B2815 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2898 removed outlier: 3.600A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B2896 " --> pdb=" O GLN B2892 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B2897 " --> pdb=" O GLU B2893 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B2898 " --> pdb=" O LEU B2894 " (cutoff:3.500A) Processing helix chain 'B' and resid 2912 through 2934 removed outlier: 3.841A pdb=" N LYS B2916 " --> pdb=" O THR B2912 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B2917 " --> pdb=" O ALA B2913 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ARG B2920 " --> pdb=" O LYS B2916 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU B2921 " --> pdb=" O ALA B2917 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN B2933 " --> pdb=" O PHE B2929 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY B2934 " --> pdb=" O LEU B2930 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3658 removed outlier: 4.640A pdb=" N LYS B3658 " --> pdb=" O LEU B3654 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3683 removed outlier: 4.783A pdb=" N ILE B3674 " --> pdb=" O GLU B3670 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B3678 " --> pdb=" O ILE B3674 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY B3681 " --> pdb=" O LEU B3677 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 removed outlier: 3.631A pdb=" N THR B3711 " --> pdb=" O ARG B3707 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3739 removed outlier: 3.649A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3771 removed outlier: 3.951A pdb=" N LYS B3756 " --> pdb=" O SER B3752 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU B3757 " --> pdb=" O PHE B3753 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B3771 " --> pdb=" O GLN B3767 " (cutoff:3.500A) Processing helix chain 'B' and resid 3775 through 3786 removed outlier: 4.944A pdb=" N VAL B3779 " --> pdb=" O ALA B3775 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B3785 " --> pdb=" O GLN B3781 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N CYS B3786 " --> pdb=" O MET B3782 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 removed outlier: 4.233A pdb=" N LYS B3799 " --> pdb=" O SER B3795 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B3800 " --> pdb=" O SER B3796 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B3801 " --> pdb=" O THR B3797 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 removed outlier: 4.169A pdb=" N GLN B3813 " --> pdb=" O ASN B3809 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN B3814 " --> pdb=" O ALA B3810 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B3815 " --> pdb=" O GLU B3811 " (cutoff:3.500A) Processing helix chain 'B' and resid 3826 through 3839 removed outlier: 7.262A pdb=" N GLN B3830 " --> pdb=" O VAL B3826 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N CYS B3839 " --> pdb=" O LEU B3835 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3858 removed outlier: 3.880A pdb=" N GLY B3855 " --> pdb=" O ASN B3851 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B3856 " --> pdb=" O LYS B3852 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY B3857 " --> pdb=" O ALA B3853 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N MET B3858 " --> pdb=" O GLU B3854 " (cutoff:3.500A) Processing helix chain 'B' and resid 3879 through 3893 removed outlier: 4.623A pdb=" N ASP B3883 " --> pdb=" O GLU B3879 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B3884 " --> pdb=" O PHE B3880 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B3885 " --> pdb=" O THR B3881 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 6.531A pdb=" N GLN B3900 " --> pdb=" O ASN B3896 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN B3901 " --> pdb=" O ASN B3897 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 3.700A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.721A pdb=" N ALA B3958 " --> pdb=" O ALA B3954 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR B3968 " --> pdb=" O SER B3964 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3984 removed outlier: 3.906A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER B3983 " --> pdb=" O SER B3979 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4003 removed outlier: 3.591A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET B3999 " --> pdb=" O VAL B3995 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.888A pdb=" N LEU B4013 " --> pdb=" O GLN B4009 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B4032 " --> pdb=" O LEU B4028 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4052 Processing helix chain 'B' and resid 4053 through 4072 removed outlier: 6.021A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE B4058 " --> pdb=" O ASN B4054 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B4069 " --> pdb=" O PHE B4065 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL B4072 " --> pdb=" O LEU B4068 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4082 removed outlier: 4.070A pdb=" N GLN B4078 " --> pdb=" O SER B4074 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR B4080 " --> pdb=" O ALA B4076 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B4081 " --> pdb=" O PHE B4077 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR B4082 " --> pdb=" O GLN B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 3.865A pdb=" N PHE B4093 " --> pdb=" O SER B4089 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B4097 " --> pdb=" O PHE B4093 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4116 removed outlier: 5.071A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4154 removed outlier: 3.695A pdb=" N ASN B4130 " --> pdb=" O GLU B4126 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B4131 " --> pdb=" O GLU B4127 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Proline residue: B4135 - end of helix removed outlier: 4.196A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 3.790A pdb=" N ARG B4161 " --> pdb=" O ASP B4157 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN B4162 " --> pdb=" O PRO B4158 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 Processing helix chain 'B' and resid 4198 through 4207 removed outlier: 4.909A pdb=" N ARG B4202 " --> pdb=" O SER B4198 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B4206 " --> pdb=" O ARG B4202 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET B4207 " --> pdb=" O ALA B4203 " (cutoff:3.500A) Processing helix chain 'B' and resid 4208 through 4224 removed outlier: 3.631A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B4223 " --> pdb=" O PHE B4219 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B4224 " --> pdb=" O ASP B4220 " (cutoff:3.500A) Processing helix chain 'B' and resid 4229 through 4252 removed outlier: 4.825A pdb=" N LEU B4233 " --> pdb=" O GLU B4229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B4234 " --> pdb=" O LYS B4230 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B4235 " --> pdb=" O MET B4231 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B4236 " --> pdb=" O GLU B4232 " (cutoff:3.500A) Processing helix chain 'B' and resid 4540 through 4559 removed outlier: 4.679A pdb=" N GLU B4545 " --> pdb=" O TRP B4541 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL B4546 " --> pdb=" O GLY B4542 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN B4547 " --> pdb=" O GLU B4543 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B4555 " --> pdb=" O PHE B4551 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B4559 " --> pdb=" O LEU B4555 " (cutoff:3.500A) Processing helix chain 'B' and resid 4560 through 4579 removed outlier: 5.150A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4642 through 4684 removed outlier: 4.178A pdb=" N LEU B4648 " --> pdb=" O TRP B4644 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS B4663 " --> pdb=" O ILE B4659 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B4665 " --> pdb=" O TYR B4661 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL B4666 " --> pdb=" O ASN B4662 " (cutoff:3.500A) Proline residue: B4667 - end of helix removed outlier: 5.073A pdb=" N ILE B4670 " --> pdb=" O VAL B4666 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4701 removed outlier: 3.769A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4729 removed outlier: 4.290A pdb=" N LYS B4723 " --> pdb=" O PHE B4719 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B4724 " --> pdb=" O VAL B4720 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4749 through 4755 removed outlier: 3.754A pdb=" N GLU B4755 " --> pdb=" O THR B4751 " (cutoff:3.500A) Processing helix chain 'B' and resid 4766 through 4771 removed outlier: 3.573A pdb=" N SER B4770 " --> pdb=" O THR B4766 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 3.512A pdb=" N VAL B4782 " --> pdb=" O TRP B4778 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B4783 " --> pdb=" O LYS B4779 " (cutoff:3.500A) Processing helix chain 'B' and resid 4787 through 4804 removed outlier: 3.555A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4808 through 4820 removed outlier: 4.514A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B4819 " --> pdb=" O ASP B4815 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL B4820 " --> pdb=" O ILE B4816 " (cutoff:3.500A) Processing helix chain 'B' and resid 4822 through 4859 removed outlier: 3.799A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B4834 " --> pdb=" O VAL B4830 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS B4835 " --> pdb=" O THR B4831 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN B4836 " --> pdb=" O HIS B4832 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B4838 " --> pdb=" O GLY B4834 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4894 removed outlier: 4.494A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY B4894 " --> pdb=" O GLY B4890 " (cutoff:3.500A) Processing helix chain 'B' and resid 4897 through 4902 removed outlier: 3.857A pdb=" N ILE B4901 " --> pdb=" O ILE B4897 " (cutoff:3.500A) removed outlier: 5.277A 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 4957 removed outlier: 4.467A pdb=" N ARG B4913 " --> pdb=" O TYR B4909 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B4925 " --> pdb=" O PHE B4921 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B4926 " --> pdb=" O PHE B4922 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B4927 " --> pdb=" O PHE B4923 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU B4928 " --> pdb=" O VAL B4924 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU B4929 " --> pdb=" O ILE B4925 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B4951 " --> pdb=" O GLN B4947 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 4.620A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP B4969 " --> pdb=" O SER B4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4964 through 4969' Processing helix chain 'B' and resid 4973 through 4981 removed outlier: 3.692A pdb=" N THR B4979 " --> pdb=" O PHE B4975 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B4981 " --> pdb=" O THR B4977 " (cutoff:3.500A) Processing helix chain 'B' and resid 4984 through 4999 removed outlier: 6.615A pdb=" N TYR B4988 " --> pdb=" O ASN B4984 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET B4989 " --> pdb=" O LEU B4985 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B4996 " --> pdb=" O LEU B4992 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASP B4999 " --> pdb=" O LEU B4995 " (cutoff:3.500A) Processing helix chain 'B' and resid 5004 through 5017 Processing helix chain 'B' and resid 5027 through 5032 removed outlier: 6.401A pdb=" N GLN B5031 " --> pdb=" O CYS B5027 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR B5032 " --> pdb=" O PHE B5028 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 5027 through 5032' Processing helix chain 'B' and resid 3861 through 3867 removed outlier: 5.141A pdb=" N THR B3864 " --> pdb=" O GLU B3861 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL B3865 " --> pdb=" O ASP B3862 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B3866 " --> pdb=" O GLY B3863 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN B3867 " --> pdb=" O THR B3864 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3861 through 3867' Processing helix chain 'B' and resid 54 through 59 Proline residue: B 59 - end of helix No H-bonds generated for 'chain 'B' and resid 54 through 59' Processing helix chain 'D' and resid 61 through 66 removed outlier: 5.125A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N CYS D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 66' Processing helix chain 'D' and resid 74 through 84 removed outlier: 4.646A pdb=" N GLN D 79 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 256 removed outlier: 5.721A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 256' Processing helix chain 'D' and resid 364 through 371 removed outlier: 4.115A pdb=" N LEU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 423 removed outlier: 3.932A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 removed outlier: 4.833A pdb=" N VAL D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 482 removed outlier: 3.556A pdb=" N SER D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 3.605A 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: 4.454A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 506 removed outlier: 4.855A pdb=" N GLU D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 501 through 506' Processing helix chain 'D' and resid 510 through 531 removed outlier: 3.537A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP D 515 " --> pdb=" O ALA D 511 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE D 518 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN D 520 " --> pdb=" O LYS D 516 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 529 " --> pdb=" O LEU D 525 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG D 531 " --> pdb=" O ALA D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 541 removed outlier: 4.416A pdb=" N CYS D 537 " --> pdb=" O ASN D 533 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 541' Processing helix chain 'D' and resid 543 through 550 removed outlier: 3.829A pdb=" N VAL D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.680A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 3.804A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 594 removed outlier: 5.036A pdb=" N LYS D 584 " --> pdb=" O GLU D 580 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D 585 " --> pdb=" O ASN D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.921A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 626 removed outlier: 3.975A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 890 removed outlier: 4.169A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 936 removed outlier: 4.307A pdb=" N TYR D 920 " --> pdb=" O PRO D 916 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 950 removed outlier: 6.109A pdb=" N ASP D 948 " --> pdb=" O GLU D 944 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN D 949 " --> pdb=" O LYS D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 1002 removed outlier: 4.474A pdb=" N THR D 983 " --> pdb=" O PRO D 979 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU D 984 " --> pdb=" O ALA D 980 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL D 985 " --> pdb=" O GLN D 981 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP D 986 " --> pdb=" O THR D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1050 removed outlier: 4.445A pdb=" N GLN D1041 " --> pdb=" O ASP D1037 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA D1042 " --> pdb=" O SER D1038 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL D1043 " --> pdb=" O LEU D1039 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG D1044 " --> pdb=" O CYS D1040 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR D1045 " --> pdb=" O GLN D1041 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D1048 " --> pdb=" O ARG D1044 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR D1049 " --> pdb=" O THR D1045 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY D1050 " --> pdb=" O LEU D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1574 through 1580 removed outlier: 4.370A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET D1579 " --> pdb=" O LEU D1575 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1574 through 1580' Processing helix chain 'D' and resid 1652 through 1657 removed outlier: 3.950A pdb=" N ARG D1656 " --> pdb=" O GLU D1652 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1652 through 1657' Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 3.827A pdb=" N ALA D1675 " --> pdb=" O ARG D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1690 Processing helix chain 'D' and resid 1691 through 1701 removed outlier: 4.923A pdb=" N LEU D1695 " --> pdb=" O GLN D1691 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D1698 " --> pdb=" O LEU D1694 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP D1700 " --> pdb=" O HIS D1696 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA D1701 " --> pdb=" O ALA D1697 " (cutoff:3.500A) Processing helix chain 'D' and resid 1707 through 1724 removed outlier: 3.960A pdb=" N TYR D1711 " --> pdb=" O LEU D1707 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP D1713 " --> pdb=" O ALA D1709 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU D1721 " --> pdb=" O SER D1717 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER D1722 " --> pdb=" O ILE D1718 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA D1723 " --> pdb=" O HIS D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1725 through 1731 Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.880A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.700A pdb=" N ARG D1820 " --> pdb=" O GLY D1816 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 removed outlier: 4.139A pdb=" N VAL D1839 " --> pdb=" O GLU D1835 " (cutoff:3.500A) Proline residue: D1840 - end of helix removed outlier: 5.145A pdb=" N LYS D1843 " --> pdb=" O VAL D1839 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET D1851 " --> pdb=" O THR D1847 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY D1852 " --> pdb=" O LEU D1848 " (cutoff:3.500A) Processing helix chain 'D' and resid 1855 through 1867 removed outlier: 3.949A pdb=" N MET D1865 " --> pdb=" O GLN D1861 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE D1866 " --> pdb=" O ILE D1862 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1981 removed outlier: 4.614A pdb=" N LEU D1937 " --> pdb=" O GLU D1933 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA D1971 " --> pdb=" O ASP D1967 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN D1972 " --> pdb=" O LYS D1968 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 1999 removed outlier: 3.641A pdb=" N ARG D1996 " --> pdb=" O ALA D1992 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2015 removed outlier: 4.225A pdb=" N GLU D2015 " --> pdb=" O HIS D2011 " (cutoff:3.500A) Processing helix chain 'D' and resid 2024 through 2043 removed outlier: 5.966A pdb=" N ARG D2028 " --> pdb=" O PRO D2024 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLN D2029 " --> pdb=" O GLU D2025 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP D2030 " --> pdb=" O ASP D2026 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU D2031 " --> pdb=" O ILE D2027 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY D2043 " --> pdb=" O LEU D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.574A pdb=" N LEU D2097 " --> pdb=" O SER D2093 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.641A pdb=" N VAL D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D2128 " --> pdb=" O LEU D2124 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2141 Proline residue: D2139 - end of helix Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 4.183A pdb=" N THR D2152 " --> pdb=" O SER D2148 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2172 through 2188 removed outlier: 4.055A pdb=" N ASN D2176 " --> pdb=" O PRO D2172 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D2185 " --> pdb=" O SER D2181 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET D2186 " --> pdb=" O ILE D2182 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN D2187 " --> pdb=" O GLY D2183 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2194 Processing helix chain 'D' and resid 2195 through 2202 Processing helix chain 'D' and resid 2203 through 2216 removed outlier: 4.573A pdb=" N MET D2208 " --> pdb=" O HIS D2204 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU D2209 " --> pdb=" O GLU D2205 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL D2210 " --> pdb=" O THR D2206 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET D2211 " --> pdb=" O VAL D2207 " (cutoff:3.500A) Processing helix chain 'D' and resid 2227 through 2243 removed outlier: 4.410A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D2235 " --> pdb=" O SER D2231 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2252 removed outlier: 3.913A pdb=" N SER D2249 " --> pdb=" O GLN D2245 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET D2250 " --> pdb=" O ASN D2246 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE D2251 " --> pdb=" O GLN D2247 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2245 through 2252' Processing helix chain 'D' and resid 2253 through 2262 removed outlier: 4.177A pdb=" N GLU D2259 " --> pdb=" O SER D2255 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2282 removed outlier: 3.992A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D2281 " --> pdb=" O ALA D2277 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP D2282 " --> pdb=" O ALA D2278 " (cutoff:3.500A) Processing helix chain 'D' and resid 2286 through 2291 removed outlier: 3.790A pdb=" N LEU D2290 " --> pdb=" O LEU D2286 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN D2291 " --> pdb=" O ALA D2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2286 through 2291' Processing helix chain 'D' and resid 2294 through 2308 removed outlier: 4.043A pdb=" N VAL D2298 " --> pdb=" O ASP D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2315 removed outlier: 4.391A pdb=" N ALA D2315 " --> pdb=" O PRO D2311 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2341 removed outlier: 4.109A pdb=" N LEU D2332 " --> pdb=" O GLY D2328 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP D2333 " --> pdb=" O GLU D2329 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU D2335 " --> pdb=" O TYR D2331 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D2336 " --> pdb=" O LEU D2332 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL D2339 " --> pdb=" O LEU D2335 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE D2340 " --> pdb=" O ARG D2336 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL D2341 " --> pdb=" O PHE D2337 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.655A pdb=" N ALA D2350 " --> pdb=" O VAL D2346 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL D2353 " --> pdb=" O ASN D2349 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D2359 " --> pdb=" O ARG D2355 " (cutoff:3.500A) removed outlier: 4.308A 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 Processing helix chain 'D' and resid 2375 through 2390 Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2437 removed outlier: 4.215A pdb=" N ALA D2421 " --> pdb=" O HIS D2417 " (cutoff:3.500A) Processing helix chain 'D' and resid 2441 through 2447 removed outlier: 4.226A pdb=" N ALA D2445 " --> pdb=" O HIS D2441 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY D2446 " --> pdb=" O LEU D2442 " (cutoff:3.500A) Processing helix chain 'D' and resid 2448 through 2462 Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2464 through 2472 removed outlier: 3.840A pdb=" N GLY D2468 " --> pdb=" O ASP D2464 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU D2472 " --> pdb=" O GLY D2468 " (cutoff:3.500A) Processing helix chain 'D' and resid 2741 through 2746 removed outlier: 4.899A pdb=" N ILE D2746 " --> pdb=" O THR D2742 " (cutoff:3.500A) Processing helix chain 'D' and resid 2750 through 2774 removed outlier: 4.638A pdb=" N PHE D2754 " --> pdb=" O LYS D2750 " (cutoff:3.500A) Processing helix chain 'D' and resid 2793 through 2798 removed outlier: 4.048A pdb=" N PHE D2797 " --> pdb=" O PRO D2793 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER D2798 " --> pdb=" O TYR D2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2793 through 2798' Processing helix chain 'D' and resid 2799 through 2806 removed outlier: 5.180A pdb=" N GLU D2803 " --> pdb=" O GLU D2799 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR D2805 " --> pdb=" O ASP D2801 " (cutoff:3.500A) Processing helix chain 'D' and resid 2809 through 2820 removed outlier: 4.860A pdb=" N ALA D2815 " --> pdb=" O GLU D2811 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET D2816 " --> pdb=" O SER D2812 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D2817 " --> pdb=" O LEU D2813 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA D2818 " --> pdb=" O LYS D2814 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP D2819 " --> pdb=" O ALA D2815 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2898 removed outlier: 3.610A pdb=" N MET D2874 " --> pdb=" O GLU D2870 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS D2897 " --> pdb=" O GLU D2893 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY D2898 " --> pdb=" O LEU D2894 " (cutoff:3.500A) Processing helix chain 'D' and resid 2912 through 2934 removed outlier: 3.849A pdb=" N LYS D2916 " --> pdb=" O THR D2912 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA D2917 " --> pdb=" O ALA D2913 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARG D2920 " --> pdb=" O LYS D2916 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU D2921 " --> pdb=" O ALA D2917 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN D2933 " --> pdb=" O PHE D2929 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY D2934 " --> pdb=" O LEU D2930 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3658 removed outlier: 4.586A pdb=" N LYS D3658 " --> pdb=" O LEU D3654 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3683 removed outlier: 4.248A pdb=" N ILE D3674 " --> pdb=" O GLU D3670 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D3677 " --> pdb=" O MET D3673 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER D3678 " --> pdb=" O ILE D3674 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY D3681 " --> pdb=" O LEU D3677 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 removed outlier: 3.643A pdb=" N THR D3711 " --> pdb=" O ARG D3707 " (cutoff:3.500A) Processing helix chain 'D' and resid 3719 through 3739 removed outlier: 3.673A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU D3736 " --> pdb=" O SER D3732 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3771 removed outlier: 3.601A pdb=" N LYS D3756 " --> pdb=" O SER D3752 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D3757 " --> pdb=" O PHE D3753 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS D3771 " --> pdb=" O GLN D3767 " (cutoff:3.500A) Processing helix chain 'D' and resid 3775 through 3786 removed outlier: 5.010A pdb=" N VAL D3779 " --> pdb=" O ALA D3775 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU D3780 " --> pdb=" O ALA D3776 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA D3785 " --> pdb=" O GLN D3781 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS D3786 " --> pdb=" O MET D3782 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 removed outlier: 3.973A pdb=" N LYS D3799 " --> pdb=" O SER D3795 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D3800 " --> pdb=" O SER D3796 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D3801 " --> pdb=" O THR D3797 " (cutoff:3.500A) Processing helix chain 'D' and resid 3809 through 3824 removed outlier: 3.898A pdb=" N GLN D3813 " --> pdb=" O ASN D3809 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN D3814 " --> pdb=" O ALA D3810 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS D3815 " --> pdb=" O GLU D3811 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D3820 " --> pdb=" O MET D3816 " (cutoff:3.500A) Processing helix chain 'D' and resid 3826 through 3839 removed outlier: 7.178A pdb=" N GLN D3830 " --> pdb=" O VAL D3826 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3858 removed outlier: 3.843A pdb=" N GLY D3855 " --> pdb=" O ASN D3851 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU D3856 " --> pdb=" O LYS D3852 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D3857 " --> pdb=" O ALA D3853 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N MET D3858 " --> pdb=" O GLU D3854 " (cutoff:3.500A) Processing helix chain 'D' and resid 3879 through 3893 removed outlier: 4.546A pdb=" N ASP D3883 " --> pdb=" O GLU D3879 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D3884 " --> pdb=" O PHE D3880 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE D3885 " --> pdb=" O THR D3881 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS D3892 " --> pdb=" O LEU D3888 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 6.571A pdb=" N GLN D3900 " --> pdb=" O ASN D3896 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASN D3901 " --> pdb=" O ASN D3897 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.757A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D3936 " --> pdb=" O ASP D3932 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR D3937 " --> pdb=" O PHE D3933 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.767A pdb=" N ALA D3958 " --> pdb=" O ALA D3954 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU D3967 " --> pdb=" O ASN D3963 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR D3968 " --> pdb=" O SER D3964 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 3.865A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER D3983 " --> pdb=" O SER D3979 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4003 removed outlier: 3.619A pdb=" N GLY D3991 " --> pdb=" O ASP D3987 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET D3999 " --> pdb=" O VAL D3995 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N MET D4000 " --> pdb=" O PHE D3996 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.867A pdb=" N LEU D4013 " --> pdb=" O GLN D4009 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4039 through 4052 Processing helix chain 'D' and resid 4053 through 4072 removed outlier: 5.304A pdb=" N MET D4057 " --> pdb=" O SER D4053 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE D4058 " --> pdb=" O ASN D4054 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS D4069 " --> pdb=" O PHE D4065 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D4072 " --> pdb=" O LEU D4068 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4082 removed outlier: 4.006A pdb=" N GLN D4078 " --> pdb=" O SER D4074 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR D4080 " --> pdb=" O ALA D4076 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL D4081 " --> pdb=" O PHE D4077 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 3.999A pdb=" N PHE D4093 " --> pdb=" O SER D4089 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 5.127A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4154 removed outlier: 3.683A pdb=" N ASN D4130 " --> pdb=" O GLU D4126 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D4131 " --> pdb=" O GLU D4127 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Proline residue: D4135 - end of helix removed outlier: 4.296A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 3.745A pdb=" N ARG D4161 " --> pdb=" O ASP D4157 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN D4162 " --> pdb=" O PRO D4158 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE D4163 " --> pdb=" O ARG D4159 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4175 Processing helix chain 'D' and resid 4198 through 4207 removed outlier: 4.918A pdb=" N ARG D4202 " --> pdb=" O SER D4198 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU D4206 " --> pdb=" O ARG D4202 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4224 removed outlier: 3.733A pdb=" N VAL D4222 " --> pdb=" O ILE D4218 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D4223 " --> pdb=" O PHE D4219 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU D4224 " --> pdb=" O ASP D4220 " (cutoff:3.500A) Processing helix chain 'D' and resid 4229 through 4252 removed outlier: 4.273A pdb=" N LEU D4233 " --> pdb=" O GLU D4229 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE D4234 " --> pdb=" O LYS D4230 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D4235 " --> pdb=" O MET D4231 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D4236 " --> pdb=" O GLU D4232 " (cutoff:3.500A) Processing helix chain 'D' and resid 4540 through 4559 removed outlier: 4.734A pdb=" N GLU D4545 " --> pdb=" O TRP D4541 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL D4546 " --> pdb=" O GLY D4542 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN D4547 " --> pdb=" O GLU D4543 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN D4558 " --> pdb=" O TYR D4554 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE D4559 " --> pdb=" O LEU D4555 " (cutoff:3.500A) Processing helix chain 'D' and resid 4560 through 4579 removed outlier: 4.970A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4642 through 4684 removed outlier: 3.601A pdb=" N ILE D4659 " --> pdb=" O PHE D4655 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix removed outlier: 4.237A pdb=" N ILE D4670 " --> pdb=" O VAL D4666 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE D4671 " --> pdb=" O PRO D4667 " (cutoff:3.500A) Processing helix chain 'D' and resid 4696 through 4701 removed outlier: 3.558A pdb=" N GLN D4700 " --> pdb=" O ASP D4696 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4729 removed outlier: 4.191A pdb=" N LYS D4723 " --> pdb=" O PHE D4719 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D4724 " --> pdb=" O VAL D4720 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4749 through 4755 removed outlier: 4.136A pdb=" N GLU D4755 " --> pdb=" O THR D4751 " (cutoff:3.500A) Processing helix chain 'D' and resid 4766 through 4771 removed outlier: 3.632A pdb=" N SER D4770 " --> pdb=" O THR D4766 " (cutoff:3.500A) Processing helix chain 'D' and resid 4772 through 4786 removed outlier: 3.561A pdb=" N VAL D4782 " --> pdb=" O TRP D4778 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D4783 " --> pdb=" O LYS D4779 " (cutoff:3.500A) Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 4.724A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4808 through 4820 removed outlier: 4.372A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) Processing helix chain 'D' and resid 4822 through 4859 removed outlier: 3.923A pdb=" N ILE D4826 " --> pdb=" O THR D4822 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY D4834 " --> pdb=" O VAL D4830 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS D4835 " --> pdb=" O THR D4831 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN D4836 " --> pdb=" O HIS D4832 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D4838 " --> pdb=" O GLY D4834 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET D4839 " --> pdb=" O LYS D4835 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4894 removed outlier: 4.932A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY D4894 " --> pdb=" O GLY D4890 " (cutoff:3.500A) Processing helix chain 'D' and resid 4897 through 4902 removed outlier: 3.942A pdb=" N ILE D4901 " --> pdb=" O ILE D4897 " (cutoff:3.500A) removed outlier: 4.943A 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 4957 removed outlier: 3.836A pdb=" N ARG D4913 " --> pdb=" O TYR D4909 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL D4914 " --> pdb=" O GLU D4910 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL D4915 " --> pdb=" O LEU D4911 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE D4925 " --> pdb=" O PHE D4921 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL D4926 " --> pdb=" O PHE D4922 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D4927 " --> pdb=" O PHE D4923 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU D4928 " --> pdb=" O VAL D4924 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU D4929 " --> pdb=" O ILE D4925 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D4950 " --> pdb=" O GLN D4946 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS D4951 " --> pdb=" O GLN D4947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D4956 " --> pdb=" O GLU D4952 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 4.739A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP D4969 " --> pdb=" O SER D4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4964 through 4969' Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4999 removed outlier: 6.748A pdb=" N TYR D4988 " --> pdb=" O ASN D4984 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N MET D4989 " --> pdb=" O LEU D4985 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D4996 " --> pdb=" O LEU D4992 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D4997 " --> pdb=" O MET D4993 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP D4999 " --> pdb=" O LEU D4995 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5027 through 5032 removed outlier: 6.434A pdb=" N GLN D5031 " --> pdb=" O CYS D5027 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D5032 " --> pdb=" O PHE D5028 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5027 through 5032' Processing helix chain 'D' and resid 3861 through 3867 removed outlier: 5.151A pdb=" N THR D3864 " --> pdb=" O GLU D3861 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL D3865 " --> pdb=" O ASP D3862 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE D3866 " --> pdb=" O GLY D3863 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN D3867 " --> pdb=" O THR D3864 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3861 through 3867' Processing helix chain 'D' and resid 54 through 59 Proline residue: D 59 - end of helix No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing helix chain 'C' and resid 61 through 66 removed outlier: 5.261A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 66' Processing helix chain 'C' and resid 74 through 84 removed outlier: 4.301A pdb=" N GLN C 79 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 256 removed outlier: 5.594A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 256' Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.020A pdb=" N LEU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 423 removed outlier: 3.864A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 4.833A pdb=" N VAL C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 482 removed outlier: 3.560A pdb=" N SER C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.536A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 506 removed outlier: 4.758A pdb=" N GLU C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 506' Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.631A pdb=" N SER C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 529 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG C 531 " --> pdb=" O ALA C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 4.405A pdb=" N CYS C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 541' Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.777A pdb=" N VAL C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 3.774A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER C 571 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 3.713A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 594 removed outlier: 4.340A pdb=" N LYS C 584 " --> pdb=" O GLU C 580 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 585 " --> pdb=" O ASN C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.932A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 removed outlier: 3.982A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 890 removed outlier: 4.170A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 removed outlier: 4.306A pdb=" N TYR C 920 " --> pdb=" O PRO C 916 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 935 " --> pdb=" O THR C 931 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 950 removed outlier: 6.066A pdb=" N ASP C 948 " --> pdb=" O GLU C 944 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1002 removed outlier: 4.489A pdb=" N THR C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU C 984 " --> pdb=" O ALA C 980 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL C 985 " --> pdb=" O GLN C 981 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 986 " --> pdb=" O THR C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1050 removed outlier: 4.434A pdb=" N GLN C1041 " --> pdb=" O ASP C1037 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA C1042 " --> pdb=" O SER C1038 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL C1043 " --> pdb=" O LEU C1039 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG C1044 " --> pdb=" O CYS C1040 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR C1045 " --> pdb=" O GLN C1041 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY C1048 " --> pdb=" O ARG C1044 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR C1049 " --> pdb=" O THR C1045 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY C1050 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1574 through 1580 removed outlier: 4.441A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET C1579 " --> pdb=" O LEU C1575 " (cutoff:3.500A) Processing helix chain 'C' and resid 1652 through 1657 removed outlier: 4.011A pdb=" N ARG C1656 " --> pdb=" O GLU C1652 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C1657 " --> pdb=" O LEU C1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1652 through 1657' Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 3.807A pdb=" N ALA C1675 " --> pdb=" O ARG C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1690 Processing helix chain 'C' and resid 1691 through 1701 removed outlier: 4.844A pdb=" N LEU C1695 " --> pdb=" O GLN C1691 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C1698 " --> pdb=" O LEU C1694 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP C1700 " --> pdb=" O HIS C1696 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA C1701 " --> pdb=" O ALA C1697 " (cutoff:3.500A) Processing helix chain 'C' and resid 1707 through 1724 removed outlier: 3.923A pdb=" N TYR C1711 " --> pdb=" O LEU C1707 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP C1713 " --> pdb=" O ALA C1709 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU C1721 " --> pdb=" O SER C1717 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER C1722 " --> pdb=" O ILE C1718 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA C1723 " --> pdb=" O HIS C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1725 through 1731 removed outlier: 3.781A pdb=" N MET C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 3.786A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.517A pdb=" N ARG C1820 " --> pdb=" O GLY C1816 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 removed outlier: 4.212A pdb=" N VAL C1839 " --> pdb=" O GLU C1835 " (cutoff:3.500A) Proline residue: C1840 - end of helix removed outlier: 5.141A pdb=" N LYS C1843 " --> pdb=" O VAL C1839 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET C1851 " --> pdb=" O THR C1847 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY C1852 " --> pdb=" O LEU C1848 " (cutoff:3.500A) Processing helix chain 'C' and resid 1855 through 1867 removed outlier: 4.102A pdb=" N MET C1865 " --> pdb=" O GLN C1861 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE C1866 " --> pdb=" O ILE C1862 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1981 removed outlier: 4.502A pdb=" N LEU C1937 " --> pdb=" O GLU C1933 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C1971 " --> pdb=" O ASP C1967 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN C1972 " --> pdb=" O LYS C1968 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C1979 " --> pdb=" O SER C1975 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C1980 " --> pdb=" O ARG C1976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1987 through 1999 removed outlier: 3.581A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2015 removed outlier: 4.193A pdb=" N GLU C2015 " --> pdb=" O HIS C2011 " (cutoff:3.500A) Processing helix chain 'C' and resid 2024 through 2043 removed outlier: 5.967A pdb=" N ARG C2028 " --> pdb=" O PRO C2024 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN C2029 " --> pdb=" O GLU C2025 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP C2030 " --> pdb=" O ASP C2026 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU C2031 " --> pdb=" O ILE C2027 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 5.035A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.625A pdb=" N VAL C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR C2128 " --> pdb=" O LEU C2124 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2141 Proline residue: C2139 - end of helix Processing helix chain 'C' and resid 2148 through 2169 removed outlier: 4.151A pdb=" N THR C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2172 through 2188 removed outlier: 3.930A pdb=" N ASN C2176 " --> pdb=" O PRO C2172 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU C2177 " --> pdb=" O GLN C2173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C2185 " --> pdb=" O SER C2181 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET C2186 " --> pdb=" O ILE C2182 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN C2187 " --> pdb=" O GLY C2183 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2194 Processing helix chain 'C' and resid 2195 through 2202 Processing helix chain 'C' and resid 2203 through 2216 removed outlier: 3.596A pdb=" N VAL C2207 " --> pdb=" O MET C2203 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET C2208 " --> pdb=" O HIS C2204 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU C2209 " --> pdb=" O GLU C2205 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL C2210 " --> pdb=" O THR C2206 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET C2211 " --> pdb=" O VAL C2207 " (cutoff:3.500A) Processing helix chain 'C' and resid 2227 through 2243 removed outlier: 4.444A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C2235 " --> pdb=" O SER C2231 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C2242 " --> pdb=" O TYR C2238 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2252 removed outlier: 3.971A pdb=" N SER C2249 " --> pdb=" O GLN C2245 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET C2250 " --> pdb=" O ASN C2246 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C2251 " --> pdb=" O GLN C2247 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2245 through 2252' Processing helix chain 'C' and resid 2253 through 2262 removed outlier: 4.222A pdb=" N GLU C2259 " --> pdb=" O SER C2255 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2282 removed outlier: 3.693A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C2281 " --> pdb=" O ALA C2277 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP C2282 " --> pdb=" O ALA C2278 " (cutoff:3.500A) Processing helix chain 'C' and resid 2286 through 2291 removed outlier: 3.889A pdb=" N LEU C2290 " --> pdb=" O LEU C2286 " (cutoff:3.500A) removed outlier: 6.223A 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 2308 removed outlier: 4.045A pdb=" N VAL C2298 " --> pdb=" O ASP C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2315 removed outlier: 4.398A pdb=" N ALA C2315 " --> pdb=" O PRO C2311 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2341 removed outlier: 4.101A pdb=" N LEU C2332 " --> pdb=" O GLY C2328 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP C2333 " --> pdb=" O GLU C2329 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU C2335 " --> pdb=" O TYR C2331 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C2336 " --> pdb=" O LEU C2332 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL C2339 " --> pdb=" O LEU C2335 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C2340 " --> pdb=" O ARG C2336 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 3.727A pdb=" N ALA C2350 " --> pdb=" O VAL C2346 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL C2353 " --> pdb=" O ASN C2349 " (cutoff:3.500A) removed outlier: 4.039A 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: 3.750A pdb=" N GLY C2370 " --> pdb=" O PRO C2366 " (cutoff:3.500A) Processing helix chain 'C' and resid 2375 through 2390 Proline residue: C2390 - end of helix Processing helix chain 'C' and resid 2417 through 2437 removed outlier: 4.172A pdb=" N ALA C2421 " --> pdb=" O HIS C2417 " (cutoff:3.500A) Processing helix chain 'C' and resid 2441 through 2447 removed outlier: 4.293A pdb=" N ALA C2445 " --> pdb=" O HIS C2441 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY C2446 " --> pdb=" O LEU C2442 " (cutoff:3.500A) Processing helix chain 'C' and resid 2448 through 2462 Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2464 through 2472 removed outlier: 4.056A pdb=" N GLY C2468 " --> pdb=" O ASP C2464 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C2472 " --> pdb=" O GLY C2468 " (cutoff:3.500A) Processing helix chain 'C' and resid 2741 through 2746 removed outlier: 4.939A pdb=" N ILE C2746 " --> pdb=" O THR C2742 " (cutoff:3.500A) Processing helix chain 'C' and resid 2750 through 2774 removed outlier: 4.693A pdb=" N PHE C2754 " --> pdb=" O LYS C2750 " (cutoff:3.500A) Processing helix chain 'C' and resid 2793 through 2798 removed outlier: 4.024A pdb=" N PHE C2797 " --> pdb=" O PRO C2793 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER C2798 " --> pdb=" O TYR C2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2793 through 2798' Processing helix chain 'C' and resid 2799 through 2806 removed outlier: 5.222A pdb=" N GLU C2803 " --> pdb=" O GLU C2799 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR C2805 " --> pdb=" O ASP C2801 " (cutoff:3.500A) Processing helix chain 'C' and resid 2809 through 2820 removed outlier: 4.597A pdb=" N ALA C2815 " --> pdb=" O GLU C2811 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET C2816 " --> pdb=" O SER C2812 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2898 removed outlier: 3.594A pdb=" N MET C2874 " --> pdb=" O GLU C2870 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C2896 " --> pdb=" O GLN C2892 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS C2897 " --> pdb=" O GLU C2893 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C2898 " --> pdb=" O LEU C2894 " (cutoff:3.500A) Processing helix chain 'C' and resid 2912 through 2934 removed outlier: 3.834A pdb=" N LYS C2916 " --> pdb=" O THR C2912 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C2917 " --> pdb=" O ALA C2913 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG C2920 " --> pdb=" O LYS C2916 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU C2921 " --> pdb=" O ALA C2917 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C2933 " --> pdb=" O PHE C2929 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY C2934 " --> pdb=" O LEU C2930 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3658 removed outlier: 4.453A pdb=" N LYS C3658 " --> pdb=" O LEU C3654 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3683 removed outlier: 4.934A pdb=" N ILE C3674 " --> pdb=" O GLU C3670 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C3678 " --> pdb=" O ILE C3674 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY C3681 " --> pdb=" O LEU C3677 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 removed outlier: 3.659A pdb=" N THR C3711 " --> pdb=" O ARG C3707 " (cutoff:3.500A) Processing helix chain 'C' and resid 3719 through 3739 removed outlier: 3.798A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU C3736 " --> pdb=" O SER C3732 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3771 removed outlier: 4.057A pdb=" N GLN C3767 " --> pdb=" O LEU C3763 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C3768 " --> pdb=" O LEU C3764 " (cutoff:3.500A) Processing helix chain 'C' and resid 3775 through 3786 removed outlier: 5.292A pdb=" N VAL C3779 " --> pdb=" O ALA C3775 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C3780 " --> pdb=" O ALA C3776 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA C3785 " --> pdb=" O GLN C3781 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N CYS C3786 " --> pdb=" O MET C3782 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 3.815A pdb=" N LYS C3799 " --> pdb=" O SER C3795 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C3800 " --> pdb=" O SER C3796 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C3801 " --> pdb=" O THR C3797 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3824 removed outlier: 3.879A pdb=" N GLN C3813 " --> pdb=" O ASN C3809 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN C3814 " --> pdb=" O ALA C3810 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C3815 " --> pdb=" O GLU C3811 " (cutoff:3.500A) Processing helix chain 'C' and resid 3826 through 3839 removed outlier: 7.198A pdb=" N GLN C3830 " --> pdb=" O VAL C3826 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS C3839 " --> pdb=" O LEU C3835 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3858 removed outlier: 3.836A pdb=" N GLY C3855 " --> pdb=" O ASN C3851 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU C3856 " --> pdb=" O LYS C3852 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY C3857 " --> pdb=" O ALA C3853 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N MET C3858 " --> pdb=" O GLU C3854 " (cutoff:3.500A) Processing helix chain 'C' and resid 3879 through 3893 removed outlier: 4.809A pdb=" N ASP C3883 " --> pdb=" O GLU C3879 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C3884 " --> pdb=" O PHE C3880 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE C3885 " --> pdb=" O THR C3881 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3905 removed outlier: 6.544A pdb=" N GLN C3900 " --> pdb=" O ASN C3896 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN C3901 " --> pdb=" O ASN C3897 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 3.790A pdb=" N CYS C3918 " --> pdb=" O ASN C3914 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.695A pdb=" N ALA C3958 " --> pdb=" O ALA C3954 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C3967 " --> pdb=" O ASN C3963 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR C3968 " --> pdb=" O SER C3964 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3984 removed outlier: 3.902A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C3983 " --> pdb=" O SER C3979 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG C3984 " --> pdb=" O LEU C3980 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4003 removed outlier: 3.566A pdb=" N GLY C3991 " --> pdb=" O ASP C3987 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET C3999 " --> pdb=" O VAL C3995 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET C4000 " --> pdb=" O PHE C3996 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 3.862A pdb=" N LEU C4013 " --> pdb=" O GLN C4009 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4039 through 4052 Processing helix chain 'C' and resid 4053 through 4072 removed outlier: 5.132A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C4058 " --> pdb=" O ASN C4054 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C4069 " --> pdb=" O PHE C4065 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C4072 " --> pdb=" O LEU C4068 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4082 removed outlier: 4.097A pdb=" N GLN C4078 " --> pdb=" O SER C4074 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR C4080 " --> pdb=" O ALA C4076 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C4081 " --> pdb=" O PHE C4077 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR C4082 " --> pdb=" O GLN C4078 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 3.991A pdb=" N PHE C4093 " --> pdb=" O SER C4089 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 5.112A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4154 removed outlier: 3.685A pdb=" N ASN C4130 " --> pdb=" O GLU C4126 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C4131 " --> pdb=" O GLU C4127 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Proline residue: C4135 - end of helix removed outlier: 4.124A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 3.693A pdb=" N ARG C4161 " --> pdb=" O ASP C4157 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN C4162 " --> pdb=" O PRO C4158 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4175 Processing helix chain 'C' and resid 4198 through 4207 removed outlier: 4.975A pdb=" N ARG C4202 " --> pdb=" O SER C4198 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU C4206 " --> pdb=" O ARG C4202 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N MET C4207 " --> pdb=" O ALA C4203 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4224 removed outlier: 3.584A pdb=" N VAL C4222 " --> pdb=" O ILE C4218 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C4223 " --> pdb=" O PHE C4219 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU C4224 " --> pdb=" O ASP C4220 " (cutoff:3.500A) Processing helix chain 'C' and resid 4229 through 4252 removed outlier: 4.807A pdb=" N LEU C4233 " --> pdb=" O GLU C4229 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C4234 " --> pdb=" O LYS C4230 " (cutoff:3.500A) Processing helix chain 'C' and resid 4540 through 4559 removed outlier: 4.682A pdb=" N GLU C4545 " --> pdb=" O TRP C4541 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL C4546 " --> pdb=" O GLY C4542 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN C4547 " --> pdb=" O GLU C4543 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN C4558 " --> pdb=" O TYR C4554 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE C4559 " --> pdb=" O LEU C4555 " (cutoff:3.500A) Processing helix chain 'C' and resid 4560 through 4579 removed outlier: 4.930A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4642 through 4684 removed outlier: 3.585A pdb=" N ILE C4659 " --> pdb=" O PHE C4655 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL C4666 " --> pdb=" O ASN C4662 " (cutoff:3.500A) Proline residue: C4667 - end of helix removed outlier: 4.251A pdb=" N ILE C4670 " --> pdb=" O VAL C4666 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C4671 " --> pdb=" O PRO C4667 " (cutoff:3.500A) Processing helix chain 'C' and resid 4696 through 4701 removed outlier: 3.550A pdb=" N GLN C4700 " --> pdb=" O ASP C4696 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4729 removed outlier: 4.188A pdb=" N LYS C4723 " --> pdb=" O PHE C4719 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C4724 " --> pdb=" O VAL C4720 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4749 through 4755 removed outlier: 4.020A pdb=" N GLU C4755 " --> pdb=" O THR C4751 " (cutoff:3.500A) Processing helix chain 'C' and resid 4766 through 4771 removed outlier: 3.616A pdb=" N SER C4770 " --> pdb=" O THR C4766 " (cutoff:3.500A) Processing helix chain 'C' and resid 4772 through 4786 removed outlier: 3.588A pdb=" N VAL C4782 " --> pdb=" O TRP C4778 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C4783 " --> pdb=" O LYS C4779 " (cutoff:3.500A) Processing helix chain 'C' and resid 4787 through 4804 removed outlier: 3.504A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4808 through 4820 removed outlier: 3.845A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY C4819 " --> pdb=" O ASP C4815 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL C4820 " --> pdb=" O ILE C4816 " (cutoff:3.500A) Processing helix chain 'C' and resid 4822 through 4859 removed outlier: 3.816A pdb=" N ILE C4826 " --> pdb=" O THR C4822 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C4834 " --> pdb=" O VAL C4830 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LYS C4835 " --> pdb=" O THR C4831 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN C4836 " --> pdb=" O HIS C4832 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C4838 " --> pdb=" O GLY C4834 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET C4839 " --> pdb=" O LYS C4835 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4894 removed outlier: 4.630A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY C4894 " --> pdb=" O GLY C4890 " (cutoff:3.500A) Processing helix chain 'C' and resid 4897 through 4902 removed outlier: 4.275A pdb=" N ILE C4901 " --> pdb=" O ILE C4897 " (cutoff:3.500A) removed outlier: 5.486A 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 4957 removed outlier: 4.465A pdb=" N ARG C4913 " --> pdb=" O TYR C4909 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C4914 " --> pdb=" O GLU C4910 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE C4925 " --> pdb=" O PHE C4921 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL C4926 " --> pdb=" O PHE C4922 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE C4927 " --> pdb=" O PHE C4923 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C4928 " --> pdb=" O VAL C4924 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C4929 " --> pdb=" O ILE C4925 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C4936 " --> pdb=" O ILE C4932 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C4951 " --> pdb=" O GLN C4947 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 4.638A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP C4969 " --> pdb=" O SER C4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4964 through 4969' Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4999 removed outlier: 6.422A pdb=" N TYR C4988 " --> pdb=" O ASN C4984 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C4996 " --> pdb=" O LEU C4992 " (cutoff:3.500A) removed outlier: 5.266A 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 5032 removed outlier: 6.456A pdb=" N GLN C5031 " --> pdb=" O CYS C5027 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR C5032 " --> pdb=" O PHE C5028 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5027 through 5032' Processing helix chain 'C' and resid 3861 through 3867 removed outlier: 5.158A pdb=" N THR C3864 " --> pdb=" O GLU C3861 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL C3865 " --> pdb=" O ASP C3862 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE C3866 " --> pdb=" O GLY C3863 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN C3867 " --> pdb=" O THR C3864 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3861 through 3867' Processing helix chain 'C' and resid 54 through 59 Proline residue: C 59 - end of helix No H-bonds generated for 'chain 'C' and resid 54 through 59' Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.531A pdb=" N CYS A 36 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 52 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.109A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 14.372A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.924A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS A 105 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 119 through 122 removed outlier: 4.040A pdb=" N ASP A 134 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 229 through 233 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'A' and resid 288 through 291 removed outlier: 4.755A pdb=" N ILE A 282 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL A 285 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N LEU A 259 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 218 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 313 through 318 removed outlier: 7.888A pdb=" N SER A 313 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 348 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 714 through 717 removed outlier: 3.564A pdb=" N TRP A 686 " --> pdb=" O TYR A 714 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 684 " --> pdb=" O PHE A 716 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 754 through 759 removed outlier: 5.826A pdb=" N SER A 754 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY A 660 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU A 665 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 829 through 832 removed outlier: 5.451A pdb=" N TYR A 829 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP A1088 " --> pdb=" O ILE A1153 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A1153 " --> pdb=" O TRP A1088 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A1090 " --> pdb=" O CYS A1151 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A1147 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 891 through 894 removed outlier: 3.710A pdb=" N GLY A 894 " --> pdb=" O HIS A 904 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1134 through 1138 removed outlier: 3.591A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A1126 " --> pdb=" O MET A1100 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N VAL A1072 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N SER A1241 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A1237 " --> pdb=" O ARG A1076 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 2775 through 2778 removed outlier: 4.831A pdb=" N GLY A2778 " --> pdb=" O HIS A2788 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 4178 through 4184 removed outlier: 4.028A pdb=" N PHE A4195 " --> pdb=" O GLY A4179 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 4580 through 4584 Processing sheet with id= 15, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.636A pdb=" N PHE B 48 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 38 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS B 36 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 52 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 14.403A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.505A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS B 105 " --> pdb=" O MET B 150 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 119 through 122 removed outlier: 4.026A pdb=" N ASP B 134 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 229 through 233 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain 'B' and resid 288 through 291 removed outlier: 4.759A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 285 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N LEU B 259 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 218 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 313 through 318 removed outlier: 7.876A pdb=" N SER B 313 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 348 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 714 through 717 removed outlier: 3.524A pdb=" N TRP B 686 " --> pdb=" O TYR B 714 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 684 " --> pdb=" O PHE B 716 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 754 through 759 removed outlier: 4.033A pdb=" N SER B 754 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 748 " --> pdb=" O TRP B 662 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP B 662 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 750 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY B 660 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU B 665 " --> pdb=" O LEU B 792 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 829 through 832 removed outlier: 5.264A pdb=" N TYR B 829 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP B1088 " --> pdb=" O ILE B1153 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B1153 " --> pdb=" O TRP B1088 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B1090 " --> pdb=" O CYS B1151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B1151 " --> pdb=" O PHE B1090 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B1147 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 891 through 894 removed outlier: 3.567A pdb=" N GLY B 894 " --> pdb=" O HIS B 904 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 1134 through 1138 removed outlier: 3.599A pdb=" N VAL B1123 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY B1126 " --> pdb=" O MET B1100 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N MET B1100 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 10.468A pdb=" N VAL B1072 " --> pdb=" O SER B1241 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N SER B1241 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B1239 " --> pdb=" O ILE B1074 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP B1237 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 2775 through 2778 removed outlier: 4.821A pdb=" N GLY B2778 " --> pdb=" O HIS B2788 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 4178 through 4184 removed outlier: 3.658A pdb=" N PHE B4195 " --> pdb=" O GLY B4179 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 4580 through 4584 Processing sheet with id= 29, first strand: chain 'D' and resid 47 through 52 removed outlier: 3.585A pdb=" N PHE D 48 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 38 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 52 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 14.382A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.638A pdb=" N LEU D 108 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS D 105 " --> pdb=" O MET D 150 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 119 through 122 removed outlier: 4.296A pdb=" N ASP D 134 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 229 through 233 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'D' and resid 288 through 291 removed outlier: 4.758A pdb=" N ILE D 282 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL D 285 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N LEU D 259 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS D 218 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 313 through 318 removed outlier: 7.874A pdb=" N SER D 313 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL D 348 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 714 through 717 removed outlier: 3.658A pdb=" N PHE D 716 " --> pdb=" O VAL D 684 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 684 " --> pdb=" O PHE D 716 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 754 through 759 removed outlier: 4.089A pdb=" N SER D 754 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS D 746 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP D 662 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY D 660 " --> pdb=" O LEU D 750 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU D 665 " --> pdb=" O LEU D 792 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 829 through 832 removed outlier: 5.300A pdb=" N TYR D 829 " --> pdb=" O VAL D 840 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP D1088 " --> pdb=" O ILE D1153 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE D1153 " --> pdb=" O TRP D1088 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D1090 " --> pdb=" O CYS D1151 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D1094 " --> pdb=" O ASP D1147 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP D1147 " --> pdb=" O ALA D1094 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 891 through 894 removed outlier: 3.628A pdb=" N GLY D 894 " --> pdb=" O HIS D 904 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 1134 through 1138 removed outlier: 3.615A pdb=" N VAL D1123 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 10.534A pdb=" N VAL D1072 " --> pdb=" O SER D1241 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N SER D1241 " --> pdb=" O VAL D1072 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP D1237 " --> pdb=" O ARG D1076 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 2775 through 2778 removed outlier: 4.835A pdb=" N GLY D2778 " --> pdb=" O HIS D2788 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 4178 through 4184 removed outlier: 3.591A pdb=" N PHE D4195 " --> pdb=" O GLY D4179 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 4580 through 4584 Processing sheet with id= 43, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.604A pdb=" N PHE C 48 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 52 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.865A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.648A pdb=" N LEU C 108 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N HIS C 105 " --> pdb=" O MET C 150 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 119 through 122 removed outlier: 4.008A pdb=" N ASP C 134 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 229 through 233 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'C' and resid 288 through 291 removed outlier: 4.771A pdb=" N ILE C 282 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL C 285 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N LEU C 259 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS C 218 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 313 through 318 removed outlier: 7.916A pdb=" N SER C 313 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 348 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 714 through 717 removed outlier: 3.784A pdb=" N TRP C 686 " --> pdb=" O TYR C 714 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE C 716 " --> pdb=" O VAL C 684 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 684 " --> pdb=" O PHE C 716 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 754 through 759 removed outlier: 4.704A pdb=" N SER C 754 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP C 749 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C 746 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 748 " --> pdb=" O TRP C 662 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLY C 660 " --> pdb=" O LEU C 750 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU C 665 " --> pdb=" O LEU C 792 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 829 through 832 removed outlier: 5.222A pdb=" N TYR C 829 " --> pdb=" O VAL C 840 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP C1088 " --> pdb=" O ILE C1153 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C1153 " --> pdb=" O TRP C1088 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE C1090 " --> pdb=" O CYS C1151 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP C1147 " --> pdb=" O ALA C1094 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 891 through 894 removed outlier: 3.638A pdb=" N GLY C 894 " --> pdb=" O HIS C 904 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 1134 through 1138 removed outlier: 3.644A pdb=" N VAL C1123 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C1126 " --> pdb=" O MET C1100 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET C1100 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA C1077 " --> pdb=" O PRO C1190 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL C1072 " --> pdb=" O SER C1241 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N SER C1241 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C1237 " --> pdb=" O ARG C1076 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 2775 through 2778 removed outlier: 4.823A pdb=" N GLY C2778 " --> pdb=" O HIS C2788 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 4178 through 4184 removed outlier: 3.605A pdb=" N PHE C4195 " --> pdb=" O GLY C4179 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 4580 through 4584 4305 hydrogen bonds defined for protein. 12879 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: 55.42 Time building geometry restraints manager: 35.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 19773 1.32 - 1.44: 30094 1.44 - 1.57: 67200 1.57 - 1.69: 21 1.69 - 1.82: 998 Bond restraints: 118086 Sorted by residual: bond pdb=" C UNK A3492 " pdb=" N UNK A3493 " ideal model delta sigma weight residual 1.329 1.471 -0.142 1.40e-02 5.10e+03 1.02e+02 bond pdb=" C UNK A3491 " pdb=" N UNK A3492 " ideal model delta sigma weight residual 1.329 1.469 -0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" C ARG C4892 " pdb=" N ALA C4893 " ideal model delta sigma weight residual 1.335 1.250 0.084 1.36e-02 5.41e+03 3.85e+01 bond pdb=" O3A ACP B5101 " pdb=" PB ACP B5101 " ideal model delta sigma weight residual 1.698 1.591 0.107 2.00e-02 2.50e+03 2.87e+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 2.64e+01 ... (remaining 118081 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.87: 1893 104.87 - 112.67: 63387 112.67 - 120.48: 45627 120.48 - 128.28: 49362 128.28 - 136.09: 788 Bond angle restraints: 161057 Sorted by residual: angle pdb=" C GLU C4869 " pdb=" CA GLU C4869 " pdb=" CB GLU C4869 " ideal model delta sigma weight residual 116.54 105.04 11.50 1.15e+00 7.56e-01 1.00e+02 angle pdb=" O VAL C4891 " pdb=" C VAL C4891 " pdb=" N ARG C4892 " ideal model delta sigma weight residual 121.87 131.18 -9.31 9.70e-01 1.06e+00 9.21e+01 angle pdb=" C VAL D3751 " pdb=" N SER D3752 " pdb=" CA SER D3752 " ideal model delta sigma weight residual 120.82 107.66 13.16 1.47e+00 4.63e-01 8.01e+01 angle pdb=" C SER B3668 " pdb=" N PHE B3669 " pdb=" CA PHE B3669 " ideal model delta sigma weight residual 122.26 109.58 12.68 1.59e+00 3.96e-01 6.36e+01 angle pdb=" C UNK A3492 " pdb=" N UNK A3493 " pdb=" CA UNK A3493 " ideal model delta sigma weight residual 121.70 107.89 13.81 1.80e+00 3.09e-01 5.89e+01 ... (remaining 161052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.47: 67488 27.47 - 54.95: 2766 54.95 - 82.42: 214 82.42 - 109.89: 15 109.89 - 137.36: 1 Dihedral angle restraints: 70484 sinusoidal: 22584 harmonic: 47900 Sorted by residual: dihedral pdb=" C ASP B4868 " pdb=" N ASP B4868 " pdb=" CA ASP B4868 " pdb=" CB ASP B4868 " ideal model delta harmonic sigma weight residual -122.60 -142.33 19.73 0 2.50e+00 1.60e-01 6.23e+01 dihedral pdb=" N ASP B4868 " pdb=" C ASP B4868 " pdb=" CA ASP B4868 " pdb=" CB ASP B4868 " ideal model delta harmonic sigma weight residual 122.80 140.10 -17.30 0 2.50e+00 1.60e-01 4.79e+01 dihedral pdb=" CD ARG C4892 " pdb=" NE ARG C4892 " pdb=" CZ ARG C4892 " pdb=" NH1 ARG C4892 " ideal model delta sinusoidal sigma weight residual 0.00 49.50 -49.50 1 1.00e+01 1.00e-02 3.36e+01 ... (remaining 70481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 18755 0.139 - 0.278: 97 0.278 - 0.416: 11 0.416 - 0.555: 0 0.555 - 0.694: 1 Chirality restraints: 18864 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 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA LYS C4875 " pdb=" N LYS C4875 " pdb=" C LYS C4875 " pdb=" CB LYS C4875 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB VAL B3751 " pdb=" CA VAL B3751 " pdb=" CG1 VAL B3751 " pdb=" CG2 VAL B3751 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 18861 not shown) Planarity restraints: 21173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C4892 " 0.829 9.50e-02 1.11e+02 3.71e-01 8.38e+01 pdb=" NE ARG C4892 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG C4892 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C4892 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C4892 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D4864 " -0.023 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C ASN D4864 " 0.081 2.00e-02 2.50e+03 pdb=" O ASN D4864 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS D4865 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B3667 " -0.020 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C HIS B3667 " 0.075 2.00e-02 2.50e+03 pdb=" O HIS B3667 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B3668 " -0.026 2.00e-02 2.50e+03 ... (remaining 21170 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1166 2.63 - 3.20: 104326 3.20 - 3.77: 176078 3.77 - 4.33: 211666 4.33 - 4.90: 342763 Nonbonded interactions: 835999 Sorted by model distance: nonbonded pdb=" O SER B4866 " pdb=" CG GLU B4867 " model vdw 2.069 3.440 nonbonded pdb=" O2B ACP C5101 " pdb=" O2G ACP C5101 " model vdw 2.069 3.040 nonbonded pdb=" O HIS B4812 " pdb=" ND1 HIS B4812 " model vdw 2.129 2.520 nonbonded pdb=" O GLU C4869 " pdb=" O ASP C4870 " model vdw 2.162 3.040 nonbonded pdb=" O1G ACP B5101 " pdb="MG MG B5103 " model vdw 2.166 2.170 ... (remaining 835994 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 75 or (resid 76 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 162 or (resid 163 and ( \ name N or name CA or name C or name O or name CB )) or resid 164 through 167 or \ (resid 168 through 169 and (name N or name CA or name C or name O or name CB )) \ or resid 170 through 754 or (resid 755 and (name N or name CA or name C or name \ O or name CB )) or resid 756 through 3654 or (resid 3655 and (name N or name CA \ or name C or name O or name CB )) or resid 3656 through 3660 or (resid 3661 and \ (name N or name CA or name C or name O or name CB )) or resid 3662 through 3664 \ or (resid 3665 and (name N or name CA or name C or name O or name CB )) or resid \ 3666 through 3760 or (resid 3761 and (name N or name CA or name C or name O or \ name CB )) or resid 3762 through 4025 or (resid 4026 and (name N or name CA or n \ ame C or name O or name CB )) or resid 4027 through 4629 or (resid 4630 through \ 4631 and (name N or name CA or name C or name O or name CB )) or resid 4632 thro \ ugh 4633 or (resid 4634 and (name N or name CA or name C or name O or name CB )) \ or resid 4635 through 4638 or (resid 4639 through 4640 and (name N or name CA o \ r name C or name O or name CB )) or resid 4641 through 4763 or (resid 4764 throu \ gh 4765 and (name N or name CA or name C or name O or name CB )) or resid 4766 t \ hrough 4811 or (resid 4812 and (name N or name CA or name C or name O or name CB \ )) or resid 4813 through 4815 or (resid 4816 through 4817 and (name N or name C \ A or name C or name O or name CB )) or resid 4818 through 4954 or (resid 4955 an \ d (name N or name CA or name C or name O or name CB )) or resid 4956 through 503 \ 7 or resid 5101 through 5103)) selection = (chain 'B' and (resid 12 through 75 or (resid 76 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 167 or (resid 168 throu \ gh 169 and (name N or name CA or name C or name O or name CB )) or resid 170 thr \ ough 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) \ or resid 749 through 754 or (resid 755 and (name N or name CA or name C or name \ O or name CB )) or resid 756 through 3772 or (resid 3773 and (name N or name CA \ or name C or name O or name CB )) or resid 3774 through 4025 or (resid 4026 and \ (name N or name CA or name C or name O or name CB )) or resid 4027 through 4180 \ or (resid 4181 and (name N or name CA or name C or name O or name CB )) or resid \ 4182 through 4580 or (resid 4581 and (name N or name CA or name C or name O or \ name CB )) or resid 4582 through 4629 or (resid 4630 through 4631 and (name N or \ name CA or name C or name O or name CB )) or resid 4632 through 4748 or (resid \ 4749 and (name N or name CA or name C or name O or name CB )) or resid 4750 thro \ ugh 4754 or (resid 4755 through 4757 and (name N or name CA or name C or name O \ or name CB )) or resid 4758 through 4811 or (resid 4812 and (name N or name CA o \ r name C or name O or name CB )) or resid 4813 through 4815 or (resid 4816 throu \ gh 4817 and (name N or name CA or name C or name O or name CB )) or resid 4818 t \ hrough 4863 or (resid 4864 and (name N or name CA or name C or name O or name CB \ )) or resid 4865 through 4900 or (resid 4901 and (name N or name CA or name C o \ r name O or name CB )) or resid 4902 through 4907 or (resid 4908 and (name N or \ name CA or name C or name O or name CB )) or resid 4909 through 4983 or (resid 4 \ 984 and (name N or name CA or name C or name O or name CB )) or resid 4985 throu \ gh 5037 or resid 5101 through 5103)) selection = (chain 'C' and (resid 12 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB )) or resid 164 through 168 or (resid 169 and (name N o \ r name CA or name C or name O or name CB )) or resid 170 through 747 or (resid 7 \ 48 and (name N or name CA or name C or name O or name CB )) or resid 749 or (res \ id 750 and (name N or name CA or name C or name O or name CB )) or resid 751 thr \ ough 754 or (resid 755 and (name N or name CA or name C or name O or name CB )) \ or resid 756 through 3654 or (resid 3655 and (name N or name CA or name C or nam \ e O or name CB )) or resid 3656 through 3660 or (resid 3661 and (name N or name \ CA or name C or name O or name CB )) or resid 3662 through 3664 or (resid 3665 a \ nd (name N or name CA or name C or name O or name CB )) or resid 3666 through 37 \ 60 or (resid 3761 and (name N or name CA or name C or name O or name CB )) or re \ sid 3762 through 3772 or (resid 3773 and (name N or name CA or name C or name O \ or name CB )) or resid 3774 through 4180 or (resid 4181 and (name N or name CA o \ r name C or name O or name CB )) or resid 4182 through 4580 or (resid 4581 and ( \ name N or name CA or name C or name O or name CB )) or resid 4582 through 4629 o \ r (resid 4630 through 4631 and (name N or name CA or name C or name O or name CB \ )) or resid 4632 through 4633 or (resid 4634 and (name N or name CA or name C o \ r name O or name CB )) or resid 4635 through 4637 or (resid 4638 through 4640 an \ d (name N or name CA or name C or name O or name CB )) or resid 4641 through 481 \ 1 or (resid 4812 and (name N or name CA or name C or name O or name CB )) or res \ id 4813 through 4815 or (resid 4816 through 4817 and (name N or name CA or name \ C or name O or name CB )) or resid 4818 through 4900 or (resid 4901 and (name N \ or name CA or name C or name O or name CB )) or resid 4902 through 4907 or (resi \ d 4908 and (name N or name CA or name C or name O or name CB )) or resid 4909 th \ rough 4980 or (resid 4981 and (name N or name CA or name C or name O or name CB \ )) or resid 4982 through 5037 or resid 5101 through 5103)) selection = (chain 'D' and (resid 12 through 75 or (resid 76 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 162 or (resid 163 and ( \ name N or name CA or name C or name O or name CB )) or resid 164 through 167 or \ (resid 168 through 169 and (name N or name CA or name C or name O or name CB )) \ or resid 170 through 747 or (resid 748 and (name N or name CA or name C or name \ O or name CB )) or resid 749 or (resid 750 and (name N or name CA or name C or n \ ame O or name CB )) or resid 751 through 3654 or (resid 3655 and (name N or name \ CA or name C or name O or name CB )) or resid 3656 through 3660 or (resid 3661 \ and (name N or name CA or name C or name O or name CB )) or resid 3662 through 3 \ 664 or (resid 3665 and (name N or name CA or name C or name O or name CB )) or r \ esid 3666 through 3760 or (resid 3761 and (name N or name CA or name C or name O \ or name CB )) or resid 3762 through 3772 or (resid 3773 and (name N or name CA \ or name C or name O or name CB )) or resid 3774 through 4025 or (resid 4026 and \ (name N or name CA or name C or name O or name CB )) or resid 4027 through 4180 \ or (resid 4181 and (name N or name CA or name C or name O or name CB )) or resid \ 4182 through 4580 or (resid 4581 and (name N or name CA or name C or name O or \ name CB )) or resid 4582 through 4630 or (resid 4631 and (name N or name CA or n \ ame C or name O or name CB )) or resid 4632 through 4633 or (resid 4634 and (nam \ e N or name CA or name C or name O or name CB )) or resid 4635 through 4638 or ( \ resid 4639 through 4640 and (name N or name CA or name C or name O or name CB )) \ or resid 4641 through 4754 or (resid 4755 through 4757 and (name N or name CA o \ r name C or name O or name CB )) or resid 4758 through 4863 or (resid 4864 and ( \ name N or name CA or name C or name O or name CB )) or resid 4865 through 4900 o \ r (resid 4901 and (name N or name CA or name C or name O or name CB )) or resid \ 4902 through 4907 or (resid 4908 and (name N or name CA or name C or name O or n \ ame CB )) or resid 4909 through 4954 or (resid 4955 and (name N or name CA or na \ me C or name O or name CB )) or resid 4956 through 4980 or (resid 4981 and (name \ N or name CA or name C or name O or name CB )) or resid 4982 through 5037 or re \ sid 5101 through 5103)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.110 Extract box with map and model: 12.980 Check model and map are aligned: 1.210 Set scattering table: 0.740 Process input model: 259.530 Find NCS groups from input model: 7.680 Set up NCS constraints: 0.390 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: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 286.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 0.142 118086 Z= 0.204 Angle : 0.641 14.274 161057 Z= 0.362 Chirality : 0.039 0.694 18864 Planarity : 0.005 0.371 21173 Dihedral : 14.043 137.363 39312 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.78 % Favored : 91.99 % Rotamer: Outliers : 0.95 % Allowed : 0.89 % Favored : 98.17 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.12 (0.08), residues: 12760 helix: 1.78 (0.07), residues: 5672 sheet: -0.83 (0.19), residues: 824 loop : -1.84 (0.08), residues: 6264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B1143 HIS 0.005 0.000 HIS D 405 PHE 0.027 0.001 PHE A3753 TYR 0.028 0.001 TYR A 920 ARG 0.008 0.000 ARG C4860 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1335 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1242 time to evaluate : 8.798 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 outliers start: 93 outliers final: 36 residues processed: 1321 average time/residue: 0.8759 time to fit residues: 2119.7002 Evaluate side-chains 974 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 938 time to evaluate : 7.684 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.8443 time to fit residues: 65.5027 ------------------------------------------------------------------------------- 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: 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 GLN A1775 HIS A1928 GLN A1953 HIS A2041 HIS ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3809 ASN A3850 GLN ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3994 HIS ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4714 ASN ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS A4886 HIS ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN B1691 GLN B1693 GLN ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1953 HIS ** B2029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2041 HIS ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2161 GLN ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B3647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3845 ASN ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3895 HIS ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4714 ASN ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D1158 ASN ** 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** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 GLN D1928 GLN D1953 HIS ** D2029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2041 HIS ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS D2161 GLN ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3845 ASN ** D3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3994 HIS ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4714 ASN ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4973 HIS ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1691 GLN ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1928 GLN C1953 HIS ** C2029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2041 HIS ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3781 GLN C3845 ASN ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4714 ASN ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 0.452 118086 Z= 2.791 Angle : 3.089 41.425 161057 Z= 1.600 Chirality : 0.123 0.696 18864 Planarity : 0.021 0.209 21173 Dihedral : 13.160 113.338 17494 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 119.58 Ramachandran Plot: Outliers : 4.38 % Allowed : 24.21 % Favored : 71.41 % Rotamer: Outliers : 14.54 % Allowed : 20.87 % Favored : 64.59 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 2.89 % 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: -6.09 (0.05), residues: 12760 helix: -4.08 (0.04), residues: 5532 sheet: -2.17 (0.21), residues: 620 loop : -4.31 (0.06), residues: 6608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.011 TRP B4794 HIS 0.058 0.010 HIS C4978 PHE 0.127 0.013 PHE C1782 TYR 0.093 0.013 TYR D3765 ARG 0.037 0.004 ARG B3886 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2080 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1427 poor density : 653 time to evaluate : 8.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1427 outliers final: 796 residues processed: 2049 average time/residue: 0.8797 time to fit residues: 3317.6160 Evaluate side-chains 1403 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 796 poor density : 607 time to evaluate : 7.768 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 796 outliers final: 24 residues processed: 796 average time/residue: 0.8082 time to fit residues: 1236.4460 ------------------------------------------------------------------------------- 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: 8.9990 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4005 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4973 HIS ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 ASN ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2029 GLN ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3960 GLN ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4803 HIS ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1035 ASN ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2029 GLN ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4728 HIS D4803 HIS ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1035 ASN ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2029 GLN ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3889 GLN ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4803 HIS C4886 HIS ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.443 118086 Z= 2.698 Angle : 3.008 36.577 161057 Z= 1.555 Chirality : 0.120 0.717 18864 Planarity : 0.021 0.226 21173 Dihedral : 14.570 117.396 17494 Min Nonbonded Distance : 1.261 Molprobity Statistics. All-atom Clashscore : 128.55 Ramachandran Plot: Outliers : 3.61 % Allowed : 35.14 % Favored : 61.25 % Rotamer: Outliers : 11.33 % Allowed : 19.87 % Favored : 68.80 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 4.94 % 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: -6.96 (0.05), residues: 12760 helix: -4.62 (0.03), residues: 5604 sheet: -3.29 (0.17), residues: 768 loop : -4.91 (0.06), residues: 6388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.010 TRP A4767 HIS 0.053 0.010 HIS A4728 PHE 0.118 0.012 PHE D1946 TYR 0.100 0.012 TYR A2110 ARG 0.025 0.003 ARG A3886 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1714 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1112 poor density : 602 time to evaluate : 8.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1112 outliers final: 775 residues processed: 1678 average time/residue: 0.8598 time to fit residues: 2672.6816 Evaluate side-chains 1345 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 775 poor density : 570 time to evaluate : 7.784 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 775 outliers final: 34 residues processed: 775 average time/residue: 0.7963 time to fit residues: 1191.9058 ------------------------------------------------------------------------------- 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: 8.9990 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 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 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 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 GLN ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3850 GLN ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1693 GLN ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2253 HIS ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3667 HIS ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4691 GLN ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 797 HIS ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 GLN ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3850 GLN ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4005 GLN ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.8686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 0.441 118086 Z= 2.733 Angle : 3.034 37.050 161057 Z= 1.563 Chirality : 0.121 0.914 18864 Planarity : 0.021 0.231 21173 Dihedral : 15.056 125.876 17494 Min Nonbonded Distance : 1.426 Molprobity Statistics. All-atom Clashscore : 132.30 Ramachandran Plot: Outliers : 3.08 % Allowed : 39.33 % Favored : 57.59 % Rotamer: Outliers : 8.85 % Allowed : 20.70 % Favored : 70.45 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.67 % Twisted General : 5.65 % 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: -7.18 (0.05), residues: 12760 helix: -4.69 (0.03), residues: 5632 sheet: -3.64 (0.16), residues: 748 loop : -5.11 (0.06), residues: 6380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.010 TRP B3986 HIS 0.050 0.009 HIS C 308 PHE 0.121 0.012 PHE D4065 TYR 0.099 0.012 TYR C 640 ARG 0.040 0.003 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 869 poor density : 568 time to evaluate : 8.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 869 outliers final: 668 residues processed: 1420 average time/residue: 0.8815 time to fit residues: 2326.8318 Evaluate side-chains 1206 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 668 poor density : 538 time to evaluate : 10.061 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 668 outliers final: 22 residues processed: 668 average time/residue: 0.8444 time to fit residues: 1092.1882 ------------------------------------------------------------------------------- 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: 7.9990 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 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN A 576 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2245 GLN ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4973 HIS ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1949 GLN ** D2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3667 HIS ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4005 GLN ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.9086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.445 118086 Z= 2.728 Angle : 3.030 36.398 161057 Z= 1.564 Chirality : 0.122 0.905 18864 Planarity : 0.021 0.250 21173 Dihedral : 15.464 111.095 17494 Min Nonbonded Distance : 1.315 Molprobity Statistics. All-atom Clashscore : 134.32 Ramachandran Plot: Outliers : 3.13 % Allowed : 41.12 % Favored : 55.74 % Rotamer: Outliers : 6.72 % Allowed : 18.63 % Favored : 74.65 % Cbeta Deviations : 1.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.86 % Twisted General : 6.56 % 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: -7.30 (0.05), residues: 12760 helix: -4.74 (0.03), residues: 5664 sheet: -3.53 (0.18), residues: 704 loop : -5.24 (0.06), residues: 6392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.010 TRP D4767 HIS 0.052 0.009 HIS B 308 PHE 0.124 0.012 PHE B3992 TYR 0.115 0.013 TYR B2110 ARG 0.044 0.003 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 660 poor density : 553 time to evaluate : 8.623 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 outliers start: 660 outliers final: 537 residues processed: 1199 average time/residue: 0.8694 time to fit residues: 1931.6152 Evaluate side-chains 1054 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 537 poor density : 517 time to evaluate : 8.518 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 537 outliers final: 26 residues processed: 537 average time/residue: 0.7922 time to fit residues: 825.5783 ------------------------------------------------------------------------------- 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: 8.9990 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 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 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 HIS ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 ASN ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3761 GLN ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3978 GLN ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4005 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS A4947 GLN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2007 ASN ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2245 GLN ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3889 GLN ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2007 ASN ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 797 HIS ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2007 ASN ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4043 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.9368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 0.448 118086 Z= 2.736 Angle : 3.046 36.402 161057 Z= 1.571 Chirality : 0.123 0.917 18864 Planarity : 0.021 0.263 21173 Dihedral : 15.684 108.557 17494 Min Nonbonded Distance : 1.326 Molprobity Statistics. All-atom Clashscore : 133.94 Ramachandran Plot: Outliers : 3.17 % Allowed : 42.36 % Favored : 54.47 % Rotamer: Outliers : 4.77 % Allowed : 15.96 % Favored : 79.27 % Cbeta Deviations : 1.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.18 % Twisted General : 6.89 % 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: -7.37 (0.05), residues: 12760 helix: -4.74 (0.03), residues: 5576 sheet: -3.76 (0.16), residues: 772 loop : -5.33 (0.06), residues: 6412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.011 TRP B4794 HIS 0.075 0.009 HIS D4983 PHE 0.123 0.012 PHE D4065 TYR 0.117 0.013 TYR D4177 ARG 0.032 0.003 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 468 poor density : 564 time to evaluate : 8.745 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 outliers start: 468 outliers final: 376 residues processed: 1027 average time/residue: 0.8922 time to fit residues: 1689.9242 Evaluate side-chains 899 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 523 time to evaluate : 8.560 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 376 outliers final: 8 residues processed: 376 average time/residue: 0.8105 time to fit residues: 595.7687 ------------------------------------------------------------------------------- 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: 7.9990 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 12 GLN ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 HIS ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2933 ASN ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3889 GLN ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4728 HIS ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3978 GLN ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4005 GLN ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4805 ASN ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.9555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 0.454 118086 Z= 2.742 Angle : 3.060 36.612 161057 Z= 1.579 Chirality : 0.126 1.297 18864 Planarity : 0.021 0.267 21173 Dihedral : 15.853 109.028 17494 Min Nonbonded Distance : 1.323 Molprobity Statistics. All-atom Clashscore : 134.09 Ramachandran Plot: Outliers : 3.13 % Allowed : 43.10 % Favored : 53.77 % Rotamer: Outliers : 2.54 % Allowed : 13.77 % Favored : 83.69 % Cbeta Deviations : 1.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.69 % Twisted General : 7.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.43 (0.05), residues: 12760 helix: -4.75 (0.03), residues: 5560 sheet: -3.69 (0.18), residues: 656 loop : -5.42 (0.05), residues: 6544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.011 TRP B4701 HIS 0.065 0.009 HIS D 308 PHE 0.145 0.013 PHE C1946 TYR 0.130 0.013 TYR B4177 ARG 0.041 0.003 ARG C3886 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 555 time to evaluate : 8.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 249 outliers final: 184 residues processed: 801 average time/residue: 0.9024 time to fit residues: 1331.8344 Evaluate side-chains 701 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 517 time to evaluate : 8.553 Switching outliers to nearest non-outliers outliers start: 184 outliers final: 8 residues processed: 184 average time/residue: 0.8208 time to fit residues: 300.5905 ------------------------------------------------------------------------------- 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: 8.9990 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 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 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 HIS ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 911 HIS ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2253 HIS ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4886 HIS ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 HIS ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1158 ASN ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3978 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4805 ASN ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.9719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 0.456 118086 Z= 2.751 Angle : 3.084 35.927 161057 Z= 1.594 Chirality : 0.128 2.183 18864 Planarity : 0.021 0.234 21173 Dihedral : 16.052 109.638 17494 Min Nonbonded Distance : 1.412 Molprobity Statistics. All-atom Clashscore : 134.84 Ramachandran Plot: Outliers : 3.29 % Allowed : 43.83 % Favored : 52.88 % Rotamer: Outliers : 0.81 % Allowed : 10.34 % Favored : 88.85 % Cbeta Deviations : 1.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.37 % Twisted General : 7.46 % 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 (0.05), residues: 12760 helix: -4.76 (0.03), residues: 5640 sheet: -3.88 (0.16), residues: 756 loop : -5.43 (0.06), residues: 6364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.126 0.011 TRP A4767 HIS 0.082 0.010 HIS D4983 PHE 0.123 0.013 PHE C1946 TYR 0.127 0.013 TYR B2110 ARG 0.040 0.003 ARG C3886 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 555 time to evaluate : 8.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 57 residues processed: 632 average time/residue: 0.9143 time to fit residues: 1062.0114 Evaluate side-chains 571 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 514 time to evaluate : 8.592 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 57 outliers final: 9 residues processed: 57 average time/residue: 0.8634 time to fit residues: 103.7397 ------------------------------------------------------------------------------- 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: 8.9990 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 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 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 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3699 HIS ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4728 HIS ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4946 GLN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3699 HIS B3766 GLN ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3699 HIS ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4054 ASN ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3699 HIS ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4078 GLN ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4728 HIS C4805 ASN ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.9845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 0.462 118086 Z= 2.760 Angle : 3.094 36.223 161057 Z= 1.600 Chirality : 0.130 1.770 18864 Planarity : 0.021 0.253 21173 Dihedral : 16.191 110.519 17494 Min Nonbonded Distance : 1.403 Molprobity Statistics. All-atom Clashscore : 134.68 Ramachandran Plot: Outliers : 3.36 % Allowed : 44.09 % Favored : 52.55 % Rotamer: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.77 % Cbeta Deviations : 1.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.05 % Twisted General : 7.75 % 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: -7.51 (0.05), residues: 12760 helix: -4.75 (0.03), residues: 5648 sheet: -3.96 (0.16), residues: 788 loop : -5.50 (0.05), residues: 6324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.120 0.012 TRP A4767 HIS 0.075 0.010 HIS D4983 PHE 0.138 0.013 PHE C1946 TYR 0.133 0.014 TYR A2110 ARG 0.042 0.003 ARG C3886 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 563 time to evaluate : 8.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 565 average time/residue: 0.9287 time to fit residues: 961.6621 Evaluate side-chains 518 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 516 time to evaluate : 8.534 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7759 time to fit residues: 14.5416 ------------------------------------------------------------------------------- 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: 7.9990 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 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 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2933 ASN ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 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 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2032 GLN ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.9943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 0.468 118086 Z= 2.768 Angle : 3.111 35.518 161057 Z= 1.609 Chirality : 0.134 3.238 18864 Planarity : 0.021 0.334 21173 Dihedral : 16.287 111.373 17494 Min Nonbonded Distance : 1.414 Molprobity Statistics. All-atom Clashscore : 135.21 Ramachandran Plot: Outliers : 3.30 % Allowed : 44.26 % Favored : 52.44 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 1.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.73 % Twisted General : 7.73 % 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: -7.53 (0.05), residues: 12760 helix: -4.74 (0.03), residues: 5576 sheet: -4.05 (0.16), residues: 736 loop : -5.53 (0.05), residues: 6448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.130 0.012 TRP D4767 HIS 0.079 0.010 HIS D4983 PHE 0.145 0.013 PHE C1946 TYR 0.137 0.014 TYR D1711 ARG 0.040 0.003 ARG C3886 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25520 Ramachandran restraints generated. 12760 Oldfield, 0 Emsley, 12760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 8.540 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 outliers start: 0 outliers final: 0 residues processed: 550 average time/residue: 0.9316 time to fit residues: 940.2272 Evaluate side-chains 514 residues out of total 11196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 8.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.5353 ------------------------------------------------------------------------------- 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: 7.9990 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 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 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 GLN ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 579 GLN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 HIS ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4805 ASN ** C4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.063499 restraints weight = 666644.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.063640 restraints weight = 1102281.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.064077 restraints weight = 727748.490| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 1.0065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 0.461 118086 Z= 2.766 Angle : 3.115 35.768 161057 Z= 1.611 Chirality : 0.132 2.425 18864 Planarity : 0.022 0.257 21173 Dihedral : 16.371 112.520 17494 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 136.00 Ramachandran Plot: Outliers : 3.41 % Allowed : 44.49 % Favored : 52.10 % Rotamer: Outliers : 0.01 % Allowed : 3.10 % Favored : 96.89 % Cbeta Deviations : 1.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.07 % Twisted General : 7.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.53 (0.04), residues: 12760 helix: -4.74 (0.03), residues: 5528 sheet: -3.91 (0.17), residues: 684 loop : -5.56 (0.05), residues: 6548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.135 0.012 TRP A4701 HIS 0.073 0.010 HIS D4983 PHE 0.146 0.013 PHE C1946 TYR 0.136 0.014 TYR D1711 ARG 0.040 0.003 ARG C3886 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54160.53 seconds wall clock time: 933 minutes 52.00 seconds (56032.00 seconds total)