Starting phenix.real_space_refine on Mon Mar 25 00:11:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua4_26414/03_2024/7ua4_26414_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua4_26414/03_2024/7ua4_26414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua4_26414/03_2024/7ua4_26414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua4_26414/03_2024/7ua4_26414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua4_26414/03_2024/7ua4_26414_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua4_26414/03_2024/7ua4_26414_updated.pdb" } resolution = 2.93 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= 0.012 sd= 0.033 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 Ca 4 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 976 5.16 5 C 93900 2.51 5 N 25184 2.21 5 O 27764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3190": "NH1" <-> "NH2" Residue "A PHE 3319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3381": "NH1" <-> "NH2" Residue "A PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "I PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1074": "NH1" <-> "NH2" Residue "B TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3190": "NH1" <-> "NH2" Residue "B PHE 3319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3381": "NH1" <-> "NH2" Residue "B PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1074": "NH1" <-> "NH2" Residue "C TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3190": "NH1" <-> "NH2" Residue "C PHE 3319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3381": "NH1" <-> "NH2" Residue "C PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1074": "NH1" <-> "NH2" Residue "D TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3190": "NH1" <-> "NH2" Residue "D PHE 3319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3381": "NH1" <-> "NH2" Residue "D PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.43s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147856 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 34959 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4369, 34951 Classifications: {'peptide': 4369} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4204} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4369, 34951 Classifications: {'peptide': 4369} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4204} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 35694 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "I" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 34959 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4369, 34951 Classifications: {'peptide': 4369} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4204} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4369, 34951 Classifications: {'peptide': 4369} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4204} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 35694 Chain: "C" Number of atoms: 34959 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4369, 34951 Classifications: {'peptide': 4369} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4204} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4369, 34951 Classifications: {'peptide': 4369} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4204} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 35694 Chain: "D" Number of atoms: 34959 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4369, 34951 Classifications: {'peptide': 4369} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4204} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4369, 34951 Classifications: {'peptide': 4369} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4204} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 35694 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34280 SG CYS A4888 169.269 199.241 122.766 1.00208.27 S ATOM 34305 SG CYS A4891 170.598 197.062 119.896 1.00191.61 S ATOM 76959 SG CYS B4888 199.388 201.830 122.701 1.00208.27 S ATOM 76984 SG CYS B4891 197.208 200.499 119.833 1.00191.61 S ATOM A0972 SG CYS C4888 201.629 171.827 122.789 1.00208.27 S ATOM A097R SG CYS C4891 200.291 174.012 119.927 1.00191.61 S ATOM A1065 SG CYS D4888 171.875 169.151 122.703 1.00208.27 S ATOM A106U SG CYS D4891 174.058 170.485 119.838 1.00191.61 S Time building chain proxies: 99.62, per 1000 atoms: 0.67 Number of scatterers: 147856 At special positions: 0 Unit cell: (371.072, 371.904, 208, 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 Ca 4 19.99 S 976 16.00 P 24 15.00 O 27764 8.00 N 25184 7.00 C 93900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 45.32 Conformation dependent library (CDL) restraints added in 36.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 34656 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: 752 helices and 84 sheets defined 60.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 42.59 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.792A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 219 through 224 removed outlier: 5.538A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.997A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 5.119A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 5.497A pdb=" N THR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 438 removed outlier: 4.220A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.623A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.723A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 4.707A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 4.161A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.834A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.680A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.538A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.444A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.129A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 3.506A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 removed outlier: 5.157A pdb=" N LYS A 962 " --> pdb=" O GLU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 4.929A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1041 through 1061 removed outlier: 4.126A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.836A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1225' Processing helix chain 'A' and resid 1226 through 1231 Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.950A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 Processing helix chain 'A' and resid 1565 through 1572 removed outlier: 3.765A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS A1572 " --> pdb=" O ALA A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.160A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1640 through 1648' Processing helix chain 'A' and resid 1649 through 1666 removed outlier: 3.644A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.739A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.897A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.646A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1805 removed outlier: 3.707A pdb=" N LEU A1804 " --> pdb=" O LYS A1800 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A1805 " --> pdb=" O GLU A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1835 through 1847 removed outlier: 4.250A pdb=" N LEU A1839 " --> pdb=" O HIS A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.933A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1899 through 1955 removed outlier: 3.982A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN A1952 " --> pdb=" O MET A1948 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N MET A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1966 removed outlier: 4.523A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 4.945A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 Processing helix chain 'A' and resid 2057 through 2073 Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.597A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.936A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.575A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 5.016A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 4.004A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.796A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 Processing helix chain 'A' and resid 2238 through 2248 Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.691A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.616A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2332 through 2337 removed outlier: 4.237A pdb=" N ARG A2336 " --> pdb=" O GLY A2332 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLY A2337 " --> pdb=" O PRO A2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2332 through 2337' Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 2403 Processing helix chain 'A' and resid 2405 through 2412 Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2438 Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.785A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A2467 " --> pdb=" O ASP A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2504 removed outlier: 3.738A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 4.454A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2511' Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 5.404A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 3.847A pdb=" N LEU A2549 " --> pdb=" O ILE A2545 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 4.059A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A2595 " --> pdb=" O ARG A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.156A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2715 through 2740 removed outlier: 4.803A pdb=" N TYR A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.653A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2767 through 2784 removed outlier: 4.325A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.444A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.813A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2947 Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.477A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 4.307A pdb=" N PHE A3022 " --> pdb=" O ARG A3018 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3018 through 3023' Processing helix chain 'A' and resid 3024 through 3040 removed outlier: 4.192A pdb=" N SER A3028 " --> pdb=" O ASN A3024 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3078 removed outlier: 3.536A pdb=" N LEU A3061 " --> pdb=" O LEU A3057 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLN A3077 " --> pdb=" O GLU A3073 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 3.606A pdb=" N THR A3098 " --> pdb=" O ILE A3094 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3124 through 3143 Processing helix chain 'A' and resid 3145 through 3152 removed outlier: 4.472A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN A3151 " --> pdb=" O TYR A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3166 Processing helix chain 'A' and resid 3172 through 3180 removed outlier: 4.205A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N HIS A3178 " --> pdb=" O HIS A3174 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3172 through 3180' Processing helix chain 'A' and resid 3182 through 3187 Processing helix chain 'A' and resid 3188 through 3196 removed outlier: 4.817A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3210 through 3225 removed outlier: 4.733A pdb=" N ALA A3222 " --> pdb=" O ILE A3218 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU A3223 " --> pdb=" O VAL A3219 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY A3225 " --> pdb=" O LEU A3221 " (cutoff:3.500A) Processing helix chain 'A' and resid 3232 through 3250 removed outlier: 4.764A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix Processing helix chain 'A' and resid 3253 through 3258 removed outlier: 3.721A pdb=" N ASN A3257 " --> pdb=" O GLY A3253 " (cutoff:3.500A) Proline residue: A3258 - end of helix No H-bonds generated for 'chain 'A' and resid 3253 through 3258' Processing helix chain 'A' and resid 3269 through 3288 Processing helix chain 'A' and resid 3293 through 3310 removed outlier: 4.407A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A3304 " --> pdb=" O ALA A3300 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 4.476A pdb=" N ASN A3308 " --> pdb=" O GLN A3304 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS A3309 " --> pdb=" O PRO A3305 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL A3310 " --> pdb=" O ILE A3306 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3341 removed outlier: 4.401A pdb=" N LYS A3316 " --> pdb=" O PRO A3312 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A3319 " --> pdb=" O LEU A3315 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix Processing helix chain 'A' and resid 3351 through 3381 removed outlier: 4.504A pdb=" N ILE A3355 " --> pdb=" O ALA A3351 " (cutoff:3.500A) Proline residue: A3371 - end of helix removed outlier: 3.945A pdb=" N TYR A3379 " --> pdb=" O ARG A3375 " (cutoff:3.500A) Processing helix chain 'A' and resid 3382 through 3388 Proline residue: A3388 - end of helix Processing helix chain 'A' and resid 3389 through 3410 removed outlier: 3.692A pdb=" N GLU A3394 " --> pdb=" O PRO A3390 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU A3395 " --> pdb=" O GLU A3391 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A3396 " --> pdb=" O ALA A3392 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A3397 " --> pdb=" O GLU A3393 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N HIS A3410 " --> pdb=" O TRP A3406 " (cutoff:3.500A) Processing helix chain 'A' and resid 3411 through 3423 Processing helix chain 'A' and resid 3427 through 3439 removed outlier: 4.173A pdb=" N THR A3433 " --> pdb=" O SER A3429 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A3434 " --> pdb=" O PHE A3430 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR A3435 " --> pdb=" O LEU A3431 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS A3436 " --> pdb=" O ILE A3432 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A3437 " --> pdb=" O THR A3433 " (cutoff:3.500A) Processing helix chain 'A' and resid 3454 through 3459 Processing helix chain 'A' and resid 3464 through 3482 Proline residue: A3475 - end of helix removed outlier: 4.767A pdb=" N ALA A3482 " --> pdb=" O LEU A3478 " (cutoff:3.500A) Processing helix chain 'A' and resid 3483 through 3499 removed outlier: 3.974A pdb=" N GLU A3487 " --> pdb=" O PRO A3483 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A3488 " --> pdb=" O GLY A3484 " (cutoff:3.500A) Processing helix chain 'A' and resid 3501 through 3514 removed outlier: 3.547A pdb=" N ARG A3506 " --> pdb=" O GLU A3502 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP A3507 " --> pdb=" O ASP A3503 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS A3514 " --> pdb=" O ARG A3510 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3533 removed outlier: 5.019A pdb=" N ASP A3533 " --> pdb=" O ALA A3529 " (cutoff:3.500A) Processing helix chain 'A' and resid 3538 through 3543 removed outlier: 5.061A pdb=" N ASP A3543 " --> pdb=" O ASP A3539 " (cutoff:3.500A) Processing helix chain 'A' and resid 3544 through 3562 Processing helix chain 'A' and resid 3594 through 3605 Processing helix chain 'A' and resid 3607 through 3612 Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 3.899A pdb=" N ILE A3629 " --> pdb=" O GLU A3625 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3647 Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 4.019A pdb=" N HIS A3700 " --> pdb=" O ALA A3696 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP A3701 " --> pdb=" O LYS A3697 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.694A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.870A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.119A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 removed outlier: 3.767A pdb=" N GLY A3818 " --> pdb=" O ALA A3814 " (cutoff:3.500A) Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 3.574A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.936A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.512A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3938 Processing helix chain 'A' and resid 3939 through 3962 removed outlier: 3.611A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 4.219A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A4029 " --> pdb=" O ASP A4025 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 removed outlier: 4.295A pdb=" N TYR A4035 " --> pdb=" O THR A4031 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP A4036 " --> pdb=" O PHE A4032 " (cutoff:3.500A) Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 removed outlier: 3.984A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4070 Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.121A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 4.231A pdb=" N ASP A4093 " --> pdb=" O GLU A4089 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLY A4095 " --> pdb=" O ALA A4091 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A4098 " --> pdb=" O ILE A4094 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 removed outlier: 3.633A pdb=" N PHE A4118 " --> pdb=" O ARG A4114 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4131 Proline residue: A4131 - end of helix Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4178 Processing helix chain 'A' and resid 4184 through 4207 Processing helix chain 'A' and resid 4480 through 4499 Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.330A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4569 through 4612 removed outlier: 4.565A pdb=" N TYR A4590 " --> pdb=" O CYS A4586 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU A4593 " --> pdb=" O GLY A4589 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 4.235A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4675 through 4683 removed outlier: 4.157A pdb=" N PHE A4679 " --> pdb=" O ALA A4675 " (cutoff:3.500A) Processing helix chain 'A' and resid 4695 through 4701 Processing helix chain 'A' and resid 4702 through 4717 removed outlier: 5.410A pdb=" N ASN A4717 " --> pdb=" O VAL A4713 " (cutoff:3.500A) Processing helix chain 'A' and resid 4718 through 4735 removed outlier: 3.777A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.755A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.554A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A4761 " --> pdb=" O LEU A4757 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 4.328A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 3.943A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.180A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4884 removed outlier: 3.690A pdb=" N ILE A4866 " --> pdb=" O ILE A4862 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET A4884 " --> pdb=" O VAL A4880 " (cutoff:3.500A) Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 4.063A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 5.677A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A1776 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1772 through 1778' 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 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.792A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 219 through 224 removed outlier: 5.538A pdb=" N ALA B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.997A pdb=" N ARG B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 5.118A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 5.496A pdb=" N THR B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 438 removed outlier: 4.220A pdb=" N LYS B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.623A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.723A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 removed outlier: 4.707A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 removed outlier: 4.160A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.833A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.680A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.538A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.443A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 862 " --> pdb=" O THR B 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 875 through 901 removed outlier: 4.130A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 3.506A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 962 removed outlier: 5.157A pdb=" N LYS B 962 " --> pdb=" O GLU B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 4.928A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1041 through 1061 removed outlier: 4.125A pdb=" N SER B1049 " --> pdb=" O SER B1045 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.836A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LYS B1225 " --> pdb=" O VAL B1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1225' Processing helix chain 'B' and resid 1226 through 1231 Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.950A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 Processing helix chain 'B' and resid 1565 through 1572 removed outlier: 3.766A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B1572 " --> pdb=" O ALA B1568 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.160A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1640 through 1648' Processing helix chain 'B' and resid 1649 through 1666 removed outlier: 3.644A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.739A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.896A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.646A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1805 removed outlier: 3.707A pdb=" N LEU B1804 " --> pdb=" O LYS B1800 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B1805 " --> pdb=" O GLU B1801 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1835 through 1847 removed outlier: 4.250A pdb=" N LEU B1839 " --> pdb=" O HIS B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.933A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1899 through 1955 removed outlier: 3.982A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN B1952 " --> pdb=" O MET B1948 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N MET B1953 " --> pdb=" O GLN B1949 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1966 removed outlier: 4.523A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 4.945A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 Processing helix chain 'B' and resid 2057 through 2073 Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.597A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.936A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.575A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 5.015A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 4.004A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.796A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2238 through 2248 Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.690A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.615A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2332 through 2337 removed outlier: 4.237A pdb=" N ARG B2336 " --> pdb=" O GLY B2332 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY B2337 " --> pdb=" O PRO B2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2332 through 2337' Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 2403 Processing helix chain 'B' and resid 2405 through 2412 Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2438 Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.784A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B2467 " --> pdb=" O ASP B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2504 removed outlier: 3.738A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 4.454A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2511' Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 5.404A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 3.847A pdb=" N LEU B2549 " --> pdb=" O ILE B2545 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 4.059A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B2595 " --> pdb=" O ARG B2591 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.156A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2715 through 2740 removed outlier: 4.803A pdb=" N TYR B2719 " --> pdb=" O GLU B2715 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.653A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2767 through 2784 removed outlier: 4.325A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.445A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.814A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2947 Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.477A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 4.307A pdb=" N PHE B3022 " --> pdb=" O ARG B3018 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3018 through 3023' Processing helix chain 'B' and resid 3024 through 3040 removed outlier: 4.192A pdb=" N SER B3028 " --> pdb=" O ASN B3024 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3078 removed outlier: 3.536A pdb=" N LEU B3061 " --> pdb=" O LEU B3057 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLN B3077 " --> pdb=" O GLU B3073 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B3078 " --> pdb=" O ASN B3074 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 3.606A pdb=" N THR B3098 " --> pdb=" O ILE B3094 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3124 through 3143 Processing helix chain 'B' and resid 3145 through 3152 removed outlier: 4.473A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN B3151 " --> pdb=" O TYR B3147 " (cutoff:3.500A) Processing helix chain 'B' and resid 3153 through 3166 Processing helix chain 'B' and resid 3172 through 3180 removed outlier: 4.205A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N HIS B3178 " --> pdb=" O HIS B3174 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3172 through 3180' Processing helix chain 'B' and resid 3182 through 3187 Processing helix chain 'B' and resid 3188 through 3196 removed outlier: 4.817A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3210 through 3225 removed outlier: 4.733A pdb=" N ALA B3222 " --> pdb=" O ILE B3218 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU B3223 " --> pdb=" O VAL B3219 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY B3225 " --> pdb=" O LEU B3221 " (cutoff:3.500A) Processing helix chain 'B' and resid 3232 through 3250 removed outlier: 4.765A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix Processing helix chain 'B' and resid 3253 through 3258 removed outlier: 3.721A pdb=" N ASN B3257 " --> pdb=" O GLY B3253 " (cutoff:3.500A) Proline residue: B3258 - end of helix No H-bonds generated for 'chain 'B' and resid 3253 through 3258' Processing helix chain 'B' and resid 3269 through 3288 Processing helix chain 'B' and resid 3293 through 3310 removed outlier: 4.406A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B3304 " --> pdb=" O ALA B3300 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 4.476A pdb=" N ASN B3308 " --> pdb=" O GLN B3304 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS B3309 " --> pdb=" O PRO B3305 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL B3310 " --> pdb=" O ILE B3306 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3341 removed outlier: 4.401A pdb=" N LYS B3316 " --> pdb=" O PRO B3312 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B3319 " --> pdb=" O LEU B3315 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix Processing helix chain 'B' and resid 3351 through 3381 removed outlier: 4.505A pdb=" N ILE B3355 " --> pdb=" O ALA B3351 " (cutoff:3.500A) Proline residue: B3371 - end of helix removed outlier: 3.945A pdb=" N TYR B3379 " --> pdb=" O ARG B3375 " (cutoff:3.500A) Processing helix chain 'B' and resid 3382 through 3388 Proline residue: B3388 - end of helix Processing helix chain 'B' and resid 3389 through 3410 removed outlier: 3.692A pdb=" N GLU B3394 " --> pdb=" O PRO B3390 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU B3395 " --> pdb=" O GLU B3391 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE B3396 " --> pdb=" O ALA B3392 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG B3397 " --> pdb=" O GLU B3393 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N HIS B3410 " --> pdb=" O TRP B3406 " (cutoff:3.500A) Processing helix chain 'B' and resid 3411 through 3423 Processing helix chain 'B' and resid 3427 through 3439 removed outlier: 4.173A pdb=" N THR B3433 " --> pdb=" O SER B3429 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B3434 " --> pdb=" O PHE B3430 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR B3435 " --> pdb=" O LEU B3431 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS B3436 " --> pdb=" O ILE B3432 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B3437 " --> pdb=" O THR B3433 " (cutoff:3.500A) Processing helix chain 'B' and resid 3454 through 3459 Processing helix chain 'B' and resid 3464 through 3482 Proline residue: B3475 - end of helix removed outlier: 4.768A pdb=" N ALA B3482 " --> pdb=" O LEU B3478 " (cutoff:3.500A) Processing helix chain 'B' and resid 3483 through 3499 removed outlier: 3.973A pdb=" N GLU B3487 " --> pdb=" O PRO B3483 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B3488 " --> pdb=" O GLY B3484 " (cutoff:3.500A) Processing helix chain 'B' and resid 3501 through 3514 removed outlier: 3.547A pdb=" N ARG B3506 " --> pdb=" O GLU B3502 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP B3507 " --> pdb=" O ASP B3503 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS B3514 " --> pdb=" O ARG B3510 " (cutoff:3.500A) Processing helix chain 'B' and resid 3521 through 3533 removed outlier: 5.019A pdb=" N ASP B3533 " --> pdb=" O ALA B3529 " (cutoff:3.500A) Processing helix chain 'B' and resid 3538 through 3543 removed outlier: 5.061A pdb=" N ASP B3543 " --> pdb=" O ASP B3539 " (cutoff:3.500A) Processing helix chain 'B' and resid 3544 through 3562 Processing helix chain 'B' and resid 3594 through 3605 Processing helix chain 'B' and resid 3607 through 3612 Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 3.900A pdb=" N ILE B3629 " --> pdb=" O GLU B3625 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3647 Proline residue: B3647 - end of helix Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 4.019A pdb=" N HIS B3700 " --> pdb=" O ALA B3696 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B3701 " --> pdb=" O LYS B3697 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.694A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.870A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.119A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 removed outlier: 3.767A pdb=" N GLY B3818 " --> pdb=" O ALA B3814 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 3.575A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.935A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.512A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3938 Processing helix chain 'B' and resid 3939 through 3962 removed outlier: 3.610A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 4.219A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B4029 " --> pdb=" O ASP B4025 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 removed outlier: 4.294A pdb=" N TYR B4035 " --> pdb=" O THR B4031 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B4036 " --> pdb=" O PHE B4032 " (cutoff:3.500A) Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 removed outlier: 3.984A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4070 Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.120A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 4.230A pdb=" N ASP B4093 " --> pdb=" O GLU B4089 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLY B4095 " --> pdb=" O ALA B4091 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B4098 " --> pdb=" O ILE B4094 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 removed outlier: 3.633A pdb=" N PHE B4118 " --> pdb=" O ARG B4114 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4131 Proline residue: B4131 - end of helix Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4178 Processing helix chain 'B' and resid 4184 through 4207 Processing helix chain 'B' and resid 4480 through 4499 Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.330A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4569 through 4612 removed outlier: 4.565A pdb=" N TYR B4590 " --> pdb=" O CYS B4586 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU B4593 " --> pdb=" O GLY B4589 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 4.235A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4657 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4675 through 4683 removed outlier: 4.157A pdb=" N PHE B4679 " --> pdb=" O ALA B4675 " (cutoff:3.500A) Processing helix chain 'B' and resid 4695 through 4701 Processing helix chain 'B' and resid 4702 through 4717 removed outlier: 5.410A pdb=" N ASN B4717 " --> pdb=" O VAL B4713 " (cutoff:3.500A) Processing helix chain 'B' and resid 4718 through 4735 removed outlier: 3.777A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.754A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.555A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B4761 " --> pdb=" O LEU B4757 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 4.328A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 3.943A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.179A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4884 removed outlier: 3.690A pdb=" N ILE B4866 " --> pdb=" O ILE B4862 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET B4884 " --> pdb=" O VAL B4880 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 4.063A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 5.677A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR B1776 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1772 through 1778' 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 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.792A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 219 through 224 removed outlier: 5.538A pdb=" N ALA C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.997A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 5.118A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 removed outlier: 5.496A pdb=" N THR C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 438 removed outlier: 4.220A pdb=" N LYS C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.624A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.723A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 553 removed outlier: 4.708A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 563 removed outlier: 4.161A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.834A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 605 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.679A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.538A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.443A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE C 862 " --> pdb=" O THR C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 875 through 901 removed outlier: 4.129A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 3.506A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 962 removed outlier: 5.157A pdb=" N LYS C 962 " --> pdb=" O GLU C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 4.929A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1041 through 1061 removed outlier: 4.126A pdb=" N SER C1049 " --> pdb=" O SER C1045 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.836A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS C1225 " --> pdb=" O VAL C1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1220 through 1225' Processing helix chain 'C' and resid 1226 through 1231 Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.950A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 Processing helix chain 'C' and resid 1565 through 1572 removed outlier: 3.765A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS C1572 " --> pdb=" O ALA C1568 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.160A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1640 through 1648' Processing helix chain 'C' and resid 1649 through 1666 removed outlier: 3.644A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.739A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.897A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.646A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1805 removed outlier: 3.707A pdb=" N LEU C1804 " --> pdb=" O LYS C1800 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS C1805 " --> pdb=" O GLU C1801 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1835 through 1847 removed outlier: 4.250A pdb=" N LEU C1839 " --> pdb=" O HIS C1835 " (cutoff:3.500A) Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 3.933A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1899 through 1955 removed outlier: 3.982A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN C1952 " --> pdb=" O MET C1948 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N MET C1953 " --> pdb=" O GLN C1949 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1966 removed outlier: 4.523A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 4.945A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 Processing helix chain 'C' and resid 2057 through 2073 Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.597A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.935A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.575A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 5.016A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 4.004A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.796A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 Processing helix chain 'C' and resid 2238 through 2248 Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.690A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.615A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2332 through 2337 removed outlier: 4.237A pdb=" N ARG C2336 " --> pdb=" O GLY C2332 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLY C2337 " --> pdb=" O PRO C2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2332 through 2337' Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 2403 Processing helix chain 'C' and resid 2405 through 2412 Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2438 Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.785A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C2467 " --> pdb=" O ASP C2463 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2504 removed outlier: 3.738A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 4.454A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2511' Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 5.404A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 3.848A pdb=" N LEU C2549 " --> pdb=" O ILE C2545 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 4.059A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C2595 " --> pdb=" O ARG C2591 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.156A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2715 through 2740 removed outlier: 4.803A pdb=" N TYR C2719 " --> pdb=" O GLU C2715 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.653A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2767 through 2784 removed outlier: 4.326A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.444A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.814A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2947 Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.477A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 4.307A pdb=" N PHE C3022 " --> pdb=" O ARG C3018 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3018 through 3023' Processing helix chain 'C' and resid 3024 through 3040 removed outlier: 4.193A pdb=" N SER C3028 " --> pdb=" O ASN C3024 " (cutoff:3.500A) Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3078 removed outlier: 3.536A pdb=" N LEU C3061 " --> pdb=" O LEU C3057 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN C3077 " --> pdb=" O GLU C3073 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY C3078 " --> pdb=" O ASN C3074 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 3.606A pdb=" N THR C3098 " --> pdb=" O ILE C3094 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3124 through 3143 Processing helix chain 'C' and resid 3145 through 3152 removed outlier: 4.472A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN C3151 " --> pdb=" O TYR C3147 " (cutoff:3.500A) Processing helix chain 'C' and resid 3153 through 3166 Processing helix chain 'C' and resid 3172 through 3180 removed outlier: 4.205A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N HIS C3178 " --> pdb=" O HIS C3174 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3172 through 3180' Processing helix chain 'C' and resid 3182 through 3187 Processing helix chain 'C' and resid 3188 through 3196 removed outlier: 4.817A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3210 through 3225 removed outlier: 4.733A pdb=" N ALA C3222 " --> pdb=" O ILE C3218 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU C3223 " --> pdb=" O VAL C3219 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLY C3225 " --> pdb=" O LEU C3221 " (cutoff:3.500A) Processing helix chain 'C' and resid 3232 through 3250 removed outlier: 4.764A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix Processing helix chain 'C' and resid 3253 through 3258 removed outlier: 3.721A pdb=" N ASN C3257 " --> pdb=" O GLY C3253 " (cutoff:3.500A) Proline residue: C3258 - end of helix No H-bonds generated for 'chain 'C' and resid 3253 through 3258' Processing helix chain 'C' and resid 3269 through 3288 Processing helix chain 'C' and resid 3293 through 3310 removed outlier: 4.406A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C3304 " --> pdb=" O ALA C3300 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 4.476A pdb=" N ASN C3308 " --> pdb=" O GLN C3304 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS C3309 " --> pdb=" O PRO C3305 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL C3310 " --> pdb=" O ILE C3306 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3341 removed outlier: 4.401A pdb=" N LYS C3316 " --> pdb=" O PRO C3312 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C3319 " --> pdb=" O LEU C3315 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix Processing helix chain 'C' and resid 3351 through 3381 removed outlier: 4.504A pdb=" N ILE C3355 " --> pdb=" O ALA C3351 " (cutoff:3.500A) Proline residue: C3371 - end of helix removed outlier: 3.944A pdb=" N TYR C3379 " --> pdb=" O ARG C3375 " (cutoff:3.500A) Processing helix chain 'C' and resid 3382 through 3388 Proline residue: C3388 - end of helix Processing helix chain 'C' and resid 3389 through 3410 removed outlier: 3.691A pdb=" N GLU C3394 " --> pdb=" O PRO C3390 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU C3395 " --> pdb=" O GLU C3391 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE C3396 " --> pdb=" O ALA C3392 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG C3397 " --> pdb=" O GLU C3393 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N HIS C3410 " --> pdb=" O TRP C3406 " (cutoff:3.500A) Processing helix chain 'C' and resid 3411 through 3423 Processing helix chain 'C' and resid 3427 through 3439 removed outlier: 4.174A pdb=" N THR C3433 " --> pdb=" O SER C3429 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP C3434 " --> pdb=" O PHE C3430 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR C3435 " --> pdb=" O LEU C3431 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS C3436 " --> pdb=" O ILE C3432 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C3437 " --> pdb=" O THR C3433 " (cutoff:3.500A) Processing helix chain 'C' and resid 3454 through 3459 Processing helix chain 'C' and resid 3464 through 3482 Proline residue: C3475 - end of helix removed outlier: 4.768A pdb=" N ALA C3482 " --> pdb=" O LEU C3478 " (cutoff:3.500A) Processing helix chain 'C' and resid 3483 through 3499 removed outlier: 3.973A pdb=" N GLU C3487 " --> pdb=" O PRO C3483 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C3488 " --> pdb=" O GLY C3484 " (cutoff:3.500A) Processing helix chain 'C' and resid 3501 through 3514 removed outlier: 3.547A pdb=" N ARG C3506 " --> pdb=" O GLU C3502 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP C3507 " --> pdb=" O ASP C3503 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS C3514 " --> pdb=" O ARG C3510 " (cutoff:3.500A) Processing helix chain 'C' and resid 3521 through 3533 removed outlier: 5.019A pdb=" N ASP C3533 " --> pdb=" O ALA C3529 " (cutoff:3.500A) Processing helix chain 'C' and resid 3538 through 3543 removed outlier: 5.061A pdb=" N ASP C3543 " --> pdb=" O ASP C3539 " (cutoff:3.500A) Processing helix chain 'C' and resid 3544 through 3562 Processing helix chain 'C' and resid 3594 through 3605 Processing helix chain 'C' and resid 3607 through 3612 Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 3.898A pdb=" N ILE C3629 " --> pdb=" O GLU C3625 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3647 Proline residue: C3647 - end of helix Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 4.019A pdb=" N HIS C3700 " --> pdb=" O ALA C3696 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP C3701 " --> pdb=" O LYS C3697 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.694A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.871A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.119A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 removed outlier: 3.767A pdb=" N GLY C3818 " --> pdb=" O ALA C3814 " (cutoff:3.500A) Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 3.574A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.936A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.512A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3938 Processing helix chain 'C' and resid 3939 through 3962 removed outlier: 3.610A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 4.219A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C4029 " --> pdb=" O ASP C4025 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 removed outlier: 4.295A pdb=" N TYR C4035 " --> pdb=" O THR C4031 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C4036 " --> pdb=" O PHE C4032 " (cutoff:3.500A) Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 removed outlier: 3.984A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4070 Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.121A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 4.231A pdb=" N ASP C4093 " --> pdb=" O GLU C4089 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLY C4095 " --> pdb=" O ALA C4091 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C4098 " --> pdb=" O ILE C4094 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 removed outlier: 3.632A pdb=" N PHE C4118 " --> pdb=" O ARG C4114 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4131 Proline residue: C4131 - end of helix Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4178 Processing helix chain 'C' and resid 4184 through 4207 Processing helix chain 'C' and resid 4480 through 4499 Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.330A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4569 through 4612 removed outlier: 4.566A pdb=" N TYR C4590 " --> pdb=" O CYS C4586 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU C4593 " --> pdb=" O GLY C4589 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 4.236A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4657 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4675 through 4683 removed outlier: 4.158A pdb=" N PHE C4679 " --> pdb=" O ALA C4675 " (cutoff:3.500A) Processing helix chain 'C' and resid 4695 through 4701 Processing helix chain 'C' and resid 4702 through 4717 removed outlier: 5.410A pdb=" N ASN C4717 " --> pdb=" O VAL C4713 " (cutoff:3.500A) Processing helix chain 'C' and resid 4718 through 4735 removed outlier: 3.777A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.755A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.555A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR C4761 " --> pdb=" O LEU C4757 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 4.329A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 3.942A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.181A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4884 removed outlier: 3.690A pdb=" N ILE C4866 " --> pdb=" O ILE C4862 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET C4884 " --> pdb=" O VAL C4880 " (cutoff:3.500A) Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 4.063A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 5.677A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR C1776 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1772 through 1778' 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 helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.792A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 219 through 224 removed outlier: 5.537A pdb=" N ALA D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.996A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 5.119A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 removed outlier: 5.496A pdb=" N THR D 327 " --> pdb=" O ASP D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 438 removed outlier: 4.220A pdb=" N LYS D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.623A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.723A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 553 removed outlier: 4.708A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 563 removed outlier: 4.160A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.834A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 605 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.679A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.538A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.444A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 875 through 901 removed outlier: 4.129A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 3.507A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 962 removed outlier: 5.157A pdb=" N LYS D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 4.929A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1041 through 1061 removed outlier: 4.126A pdb=" N SER D1049 " --> pdb=" O SER D1045 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.835A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS D1225 " --> pdb=" O VAL D1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1225' Processing helix chain 'D' and resid 1226 through 1231 Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.950A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 Processing helix chain 'D' and resid 1565 through 1572 removed outlier: 3.766A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS D1572 " --> pdb=" O ALA D1568 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.160A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1640 through 1648' Processing helix chain 'D' and resid 1649 through 1666 removed outlier: 3.645A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.740A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.897A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.646A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1805 removed outlier: 3.707A pdb=" N LEU D1804 " --> pdb=" O LYS D1800 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS D1805 " --> pdb=" O GLU D1801 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1835 through 1847 removed outlier: 4.251A pdb=" N LEU D1839 " --> pdb=" O HIS D1835 " (cutoff:3.500A) Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 3.933A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1899 through 1955 removed outlier: 3.982A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN D1952 " --> pdb=" O MET D1948 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N MET D1953 " --> pdb=" O GLN D1949 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1966 removed outlier: 4.523A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 4.946A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 Processing helix chain 'D' and resid 2057 through 2073 Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.597A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.936A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.575A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 5.016A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 4.004A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.796A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 Processing helix chain 'D' and resid 2238 through 2248 Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.690A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.617A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2332 through 2337 removed outlier: 4.237A pdb=" N ARG D2336 " --> pdb=" O GLY D2332 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY D2337 " --> pdb=" O PRO D2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2332 through 2337' Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 2403 Processing helix chain 'D' and resid 2405 through 2412 Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2438 Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.785A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D2467 " --> pdb=" O ASP D2463 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2504 removed outlier: 3.739A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 4.453A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2511' Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 5.404A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 3.847A pdb=" N LEU D2549 " --> pdb=" O ILE D2545 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 4.059A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP D2595 " --> pdb=" O ARG D2591 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.156A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2715 through 2740 removed outlier: 4.804A pdb=" N TYR D2719 " --> pdb=" O GLU D2715 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.654A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2767 through 2784 removed outlier: 4.325A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.444A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.814A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2947 Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.478A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 4.306A pdb=" N PHE D3022 " --> pdb=" O ARG D3018 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3018 through 3023' Processing helix chain 'D' and resid 3024 through 3040 removed outlier: 4.192A pdb=" N SER D3028 " --> pdb=" O ASN D3024 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3078 removed outlier: 3.537A pdb=" N LEU D3061 " --> pdb=" O LEU D3057 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN D3077 " --> pdb=" O GLU D3073 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY D3078 " --> pdb=" O ASN D3074 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 3.607A pdb=" N THR D3098 " --> pdb=" O ILE D3094 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3124 through 3143 Processing helix chain 'D' and resid 3145 through 3152 removed outlier: 4.472A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN D3151 " --> pdb=" O TYR D3147 " (cutoff:3.500A) Processing helix chain 'D' and resid 3153 through 3166 Processing helix chain 'D' and resid 3172 through 3180 removed outlier: 4.204A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N HIS D3178 " --> pdb=" O HIS D3174 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3172 through 3180' Processing helix chain 'D' and resid 3182 through 3187 Processing helix chain 'D' and resid 3188 through 3196 removed outlier: 4.816A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3210 through 3225 removed outlier: 4.734A pdb=" N ALA D3222 " --> pdb=" O ILE D3218 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU D3223 " --> pdb=" O VAL D3219 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLY D3225 " --> pdb=" O LEU D3221 " (cutoff:3.500A) Processing helix chain 'D' and resid 3232 through 3250 removed outlier: 4.764A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix Processing helix chain 'D' and resid 3253 through 3258 removed outlier: 3.721A pdb=" N ASN D3257 " --> pdb=" O GLY D3253 " (cutoff:3.500A) Proline residue: D3258 - end of helix No H-bonds generated for 'chain 'D' and resid 3253 through 3258' Processing helix chain 'D' and resid 3269 through 3288 Processing helix chain 'D' and resid 3293 through 3310 removed outlier: 4.406A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D3304 " --> pdb=" O ALA D3300 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 4.476A pdb=" N ASN D3308 " --> pdb=" O GLN D3304 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS D3309 " --> pdb=" O PRO D3305 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL D3310 " --> pdb=" O ILE D3306 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3341 removed outlier: 4.401A pdb=" N LYS D3316 " --> pdb=" O PRO D3312 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE D3319 " --> pdb=" O LEU D3315 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix Processing helix chain 'D' and resid 3351 through 3381 removed outlier: 4.505A pdb=" N ILE D3355 " --> pdb=" O ALA D3351 " (cutoff:3.500A) Proline residue: D3371 - end of helix removed outlier: 3.944A pdb=" N TYR D3379 " --> pdb=" O ARG D3375 " (cutoff:3.500A) Processing helix chain 'D' and resid 3382 through 3388 Proline residue: D3388 - end of helix Processing helix chain 'D' and resid 3389 through 3410 removed outlier: 3.692A pdb=" N GLU D3394 " --> pdb=" O PRO D3390 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU D3395 " --> pdb=" O GLU D3391 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE D3396 " --> pdb=" O ALA D3392 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG D3397 " --> pdb=" O GLU D3393 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N HIS D3410 " --> pdb=" O TRP D3406 " (cutoff:3.500A) Processing helix chain 'D' and resid 3411 through 3423 Processing helix chain 'D' and resid 3427 through 3439 removed outlier: 4.173A pdb=" N THR D3433 " --> pdb=" O SER D3429 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP D3434 " --> pdb=" O PHE D3430 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR D3435 " --> pdb=" O LEU D3431 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS D3436 " --> pdb=" O ILE D3432 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D3437 " --> pdb=" O THR D3433 " (cutoff:3.500A) Processing helix chain 'D' and resid 3454 through 3459 Processing helix chain 'D' and resid 3464 through 3482 Proline residue: D3475 - end of helix removed outlier: 4.768A pdb=" N ALA D3482 " --> pdb=" O LEU D3478 " (cutoff:3.500A) Processing helix chain 'D' and resid 3483 through 3499 removed outlier: 3.973A pdb=" N GLU D3487 " --> pdb=" O PRO D3483 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D3488 " --> pdb=" O GLY D3484 " (cutoff:3.500A) Processing helix chain 'D' and resid 3501 through 3514 removed outlier: 3.547A pdb=" N ARG D3506 " --> pdb=" O GLU D3502 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP D3507 " --> pdb=" O ASP D3503 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS D3514 " --> pdb=" O ARG D3510 " (cutoff:3.500A) Processing helix chain 'D' and resid 3521 through 3533 removed outlier: 5.019A pdb=" N ASP D3533 " --> pdb=" O ALA D3529 " (cutoff:3.500A) Processing helix chain 'D' and resid 3538 through 3543 removed outlier: 5.062A pdb=" N ASP D3543 " --> pdb=" O ASP D3539 " (cutoff:3.500A) Processing helix chain 'D' and resid 3544 through 3562 Processing helix chain 'D' and resid 3594 through 3605 Processing helix chain 'D' and resid 3607 through 3612 Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 3.898A pdb=" N ILE D3629 " --> pdb=" O GLU D3625 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3647 Proline residue: D3647 - end of helix Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 4.019A pdb=" N HIS D3700 " --> pdb=" O ALA D3696 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP D3701 " --> pdb=" O LYS D3697 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.694A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.870A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.119A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 removed outlier: 3.767A pdb=" N GLY D3818 " --> pdb=" O ALA D3814 " (cutoff:3.500A) Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 3.575A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.936A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.512A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3938 Processing helix chain 'D' and resid 3939 through 3962 removed outlier: 3.611A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 4.219A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER D4029 " --> pdb=" O ASP D4025 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 removed outlier: 4.294A pdb=" N TYR D4035 " --> pdb=" O THR D4031 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP D4036 " --> pdb=" O PHE D4032 " (cutoff:3.500A) Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 removed outlier: 3.985A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4070 Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.121A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 4.232A pdb=" N ASP D4093 " --> pdb=" O GLU D4089 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLY D4095 " --> pdb=" O ALA D4091 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D4098 " --> pdb=" O ILE D4094 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 removed outlier: 3.633A pdb=" N PHE D4118 " --> pdb=" O ARG D4114 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4131 Proline residue: D4131 - end of helix Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4178 Processing helix chain 'D' and resid 4184 through 4207 Processing helix chain 'D' and resid 4480 through 4499 Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.329A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4569 through 4612 removed outlier: 4.565A pdb=" N TYR D4590 " --> pdb=" O CYS D4586 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU D4593 " --> pdb=" O GLY D4589 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 4.235A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4675 through 4683 removed outlier: 4.158A pdb=" N PHE D4679 " --> pdb=" O ALA D4675 " (cutoff:3.500A) Processing helix chain 'D' and resid 4695 through 4701 Processing helix chain 'D' and resid 4702 through 4717 removed outlier: 5.410A pdb=" N ASN D4717 " --> pdb=" O VAL D4713 " (cutoff:3.500A) Processing helix chain 'D' and resid 4718 through 4735 removed outlier: 3.778A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.754A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.555A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR D4761 " --> pdb=" O LEU D4757 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 4.328A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 3.943A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.180A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4884 removed outlier: 3.690A pdb=" N ILE D4866 " --> pdb=" O ILE D4862 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET D4884 " --> pdb=" O VAL D4880 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 4.062A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 5.677A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR D1776 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1772 through 1778' 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 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.657A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.130A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.114A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.658A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.129A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.114A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.658A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.129A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 4.114A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.658A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.129A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.113A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 21 removed outlier: 4.875A pdb=" N PHE I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP I 21 " --> pdb=" O PHE I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 7.944A pdb=" N THR I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 23 through 29' Processing helix chain 'I' and resid 30 through 41 removed outlier: 4.190A pdb=" N GLY I 34 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 56 removed outlier: 4.618A pdb=" N MET I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 78 Processing helix chain 'I' and resid 81 through 94 removed outlier: 4.889A pdb=" N GLU I 85 " --> pdb=" O ASP I 81 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP I 94 " --> pdb=" O PHE I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 111 Processing helix chain 'I' and resid 119 through 129 Processing helix chain 'I' and resid 138 through 148 removed outlier: 4.814A pdb=" N ALA I 148 " --> pdb=" O GLN I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 21 removed outlier: 4.875A pdb=" N PHE J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP J 21 " --> pdb=" O PHE J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 29 removed outlier: 7.944A pdb=" N THR J 27 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 23 through 29' Processing helix chain 'J' and resid 30 through 41 removed outlier: 4.190A pdb=" N GLY J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR J 35 " --> pdb=" O LYS J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 56 removed outlier: 4.618A pdb=" N MET J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 78 Processing helix chain 'J' and resid 81 through 94 removed outlier: 4.890A pdb=" N GLU J 85 " --> pdb=" O ASP J 81 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP J 94 " --> pdb=" O PHE J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 111 Processing helix chain 'J' and resid 119 through 129 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.814A pdb=" N ALA J 148 " --> pdb=" O GLN J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 21 removed outlier: 4.875A pdb=" N PHE K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 29 removed outlier: 7.944A pdb=" N THR K 27 " --> pdb=" O ASP K 23 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 23 through 29' Processing helix chain 'K' and resid 30 through 41 removed outlier: 4.191A pdb=" N GLY K 34 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR K 35 " --> pdb=" O LYS K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 4.618A pdb=" N MET K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 78 Processing helix chain 'K' and resid 81 through 94 removed outlier: 4.889A pdb=" N GLU K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP K 94 " --> pdb=" O PHE K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 111 Processing helix chain 'K' and resid 119 through 129 Processing helix chain 'K' and resid 138 through 148 removed outlier: 4.814A pdb=" N ALA K 148 " --> pdb=" O GLN K 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 21 removed outlier: 4.875A pdb=" N PHE L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP L 21 " --> pdb=" O PHE L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 29 removed outlier: 7.944A pdb=" N THR L 27 " --> pdb=" O ASP L 23 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 23 through 29' Processing helix chain 'L' and resid 30 through 41 removed outlier: 4.190A pdb=" N GLY L 34 " --> pdb=" O THR L 30 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR L 35 " --> pdb=" O LYS L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 56 removed outlier: 4.617A pdb=" N MET L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 78 Processing helix chain 'L' and resid 81 through 94 removed outlier: 4.889A pdb=" N GLU L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP L 94 " --> pdb=" O PHE L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 111 Processing helix chain 'L' and resid 119 through 129 Processing helix chain 'L' and resid 138 through 148 removed outlier: 4.814A pdb=" N ALA L 148 " --> pdb=" O GLN L 144 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.457A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.517A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A 19 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.535A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 159 through 164 removed outlier: 7.890A pdb=" N TRP A 159 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 243 through 246 removed outlier: 7.040A pdb=" N GLY A 264 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE A 387 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 313 through 318 removed outlier: 3.592A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 14.187A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 7, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.781A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.752A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 10, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.396A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 948 through 952 Processing sheet with id= 12, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= 13, first strand: chain 'A' and resid 1142 through 1146 removed outlier: 7.353A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1257 through 1260 removed outlier: 4.876A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.593A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 2443 through 2446 removed outlier: 3.870A pdb=" N ASN A2450 " --> pdb=" O ALA A2446 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 2788 through 2791 removed outlier: 4.358A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.774A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 20, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.457A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.517A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B 19 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.535A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 159 through 164 removed outlier: 7.889A pdb=" N TRP B 159 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 243 through 246 removed outlier: 7.039A pdb=" N GLY B 264 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE B 387 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 313 through 318 removed outlier: 3.592A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 14.187A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 26, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.782A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.753A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 29, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.396A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 948 through 952 Processing sheet with id= 31, first strand: chain 'B' and resid 1016 through 1019 Processing sheet with id= 32, first strand: chain 'B' and resid 1142 through 1146 removed outlier: 7.352A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 1257 through 1260 removed outlier: 4.876A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.594A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 2443 through 2446 removed outlier: 3.871A pdb=" N ASN B2450 " --> pdb=" O ALA B2446 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 2788 through 2791 removed outlier: 4.357A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.774A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 39, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.456A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.518A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU C 19 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.536A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 159 through 164 removed outlier: 7.890A pdb=" N TRP C 159 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 243 through 246 removed outlier: 7.040A pdb=" N GLY C 264 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE C 387 " --> pdb=" O GLY C 264 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 313 through 318 removed outlier: 3.593A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 14.187A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 45, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.781A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.753A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 48, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.397A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 948 through 952 Processing sheet with id= 50, first strand: chain 'C' and resid 1016 through 1019 Processing sheet with id= 51, first strand: chain 'C' and resid 1142 through 1146 removed outlier: 7.352A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 1257 through 1260 removed outlier: 4.876A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.594A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 2443 through 2446 removed outlier: 3.871A pdb=" N ASN C2450 " --> pdb=" O ALA C2446 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 2788 through 2791 removed outlier: 4.358A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.774A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 58, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.456A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.517A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU D 19 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.534A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.890A pdb=" N TRP D 159 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 243 through 246 removed outlier: 7.041A pdb=" N GLY D 264 " --> pdb=" O ILE D 387 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE D 387 " --> pdb=" O GLY D 264 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 313 through 318 removed outlier: 3.592A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 14.187A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 64, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.781A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.752A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 67, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.396A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 948 through 952 Processing sheet with id= 69, first strand: chain 'D' and resid 1016 through 1019 Processing sheet with id= 70, first strand: chain 'D' and resid 1142 through 1146 removed outlier: 7.353A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 1257 through 1260 removed outlier: 4.876A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.593A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 2443 through 2446 removed outlier: 3.870A pdb=" N ASN D2450 " --> pdb=" O ALA D2446 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 2788 through 2791 removed outlier: 4.358A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.774A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 4521 through 4524 Processing sheet with id= 77, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.692A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'E' and resid 22 through 25 Processing sheet with id= 79, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.693A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'F' and resid 22 through 25 Processing sheet with id= 81, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.692A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'G' and resid 22 through 25 Processing sheet with id= 83, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.693A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'H' and resid 22 through 25 7860 hydrogen bonds defined for protein. 23464 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: 128.11 Time building geometry restraints manager: 50.07 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: 24954 1.32 - 1.45: 40059 1.45 - 1.58: 84351 1.58 - 1.71: 44 1.71 - 1.84: 1592 Bond restraints: 151000 Sorted by residual: bond pdb=" C PRO C3483 " pdb=" O PRO C3483 " ideal model delta sigma weight residual 1.237 1.188 0.050 1.26e-02 6.30e+03 1.55e+01 bond pdb=" C PRO B3483 " pdb=" O PRO B3483 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.26e-02 6.30e+03 1.53e+01 bond pdb=" C PRO A3483 " pdb=" O PRO A3483 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.26e-02 6.30e+03 1.53e+01 bond pdb=" C PRO D3483 " pdb=" O PRO D3483 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.26e-02 6.30e+03 1.52e+01 bond pdb=" N LYS D3518 " pdb=" CA LYS D3518 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.25e-02 6.40e+03 9.65e+00 ... (remaining 150995 not shown) Histogram of bond angle deviations from ideal: 88.05 - 98.42: 20 98.42 - 108.78: 7655 108.78 - 119.15: 117499 119.15 - 129.52: 77748 129.52 - 139.89: 1078 Bond angle restraints: 204000 Sorted by residual: angle pdb=" CB MET K 77 " pdb=" CG MET K 77 " pdb=" SD MET K 77 " ideal model delta sigma weight residual 112.70 137.71 -25.01 3.00e+00 1.11e-01 6.95e+01 angle pdb=" CB MET J 77 " pdb=" CG MET J 77 " pdb=" SD MET J 77 " ideal model delta sigma weight residual 112.70 137.71 -25.01 3.00e+00 1.11e-01 6.95e+01 angle pdb=" CB MET L 77 " pdb=" CG MET L 77 " pdb=" SD MET L 77 " ideal model delta sigma weight residual 112.70 137.69 -24.99 3.00e+00 1.11e-01 6.94e+01 angle pdb=" CB MET I 77 " pdb=" CG MET I 77 " pdb=" SD MET I 77 " ideal model delta sigma weight residual 112.70 137.68 -24.98 3.00e+00 1.11e-01 6.93e+01 angle pdb=" CB MET C1729 " pdb=" CG MET C1729 " pdb=" SD MET C1729 " ideal model delta sigma weight residual 112.70 88.05 24.65 3.00e+00 1.11e-01 6.75e+01 ... (remaining 203995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 82093 17.96 - 35.92: 7261 35.92 - 53.88: 1294 53.88 - 71.85: 440 71.85 - 89.81: 116 Dihedral angle restraints: 91204 sinusoidal: 37492 harmonic: 53712 Sorted by residual: dihedral pdb=" CD ARG C3381 " pdb=" NE ARG C3381 " pdb=" CZ ARG C3381 " pdb=" NH1 ARG C3381 " ideal model delta sinusoidal sigma weight residual 0.00 51.11 -51.11 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CD ARG D3381 " pdb=" NE ARG D3381 " pdb=" CZ ARG D3381 " pdb=" NH1 ARG D3381 " ideal model delta sinusoidal sigma weight residual 0.00 51.09 -51.09 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CD ARG A3381 " pdb=" NE ARG A3381 " pdb=" CZ ARG A3381 " pdb=" NH1 ARG A3381 " ideal model delta sinusoidal sigma weight residual 0.00 51.09 -51.09 1 1.00e+01 1.00e-02 3.57e+01 ... (remaining 91201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 17973 0.051 - 0.102: 3663 0.102 - 0.154: 590 0.154 - 0.205: 98 0.205 - 0.256: 36 Chirality restraints: 22360 Sorted by residual: chirality pdb=" CB VAL K 143 " pdb=" CA VAL K 143 " pdb=" CG1 VAL K 143 " pdb=" CG2 VAL K 143 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL L 143 " pdb=" CA VAL L 143 " pdb=" CG1 VAL L 143 " pdb=" CG2 VAL L 143 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB VAL I 143 " pdb=" CA VAL I 143 " pdb=" CG1 VAL I 143 " pdb=" CG2 VAL I 143 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 22357 not shown) Planarity restraints: 26308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D3381 " 0.833 9.50e-02 1.11e+02 3.73e-01 8.45e+01 pdb=" NE ARG D3381 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG D3381 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D3381 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D3381 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C3381 " -0.833 9.50e-02 1.11e+02 3.73e-01 8.45e+01 pdb=" NE ARG C3381 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG C3381 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C3381 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C3381 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A3381 " 0.833 9.50e-02 1.11e+02 3.73e-01 8.44e+01 pdb=" NE ARG A3381 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A3381 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A3381 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A3381 " 0.023 2.00e-02 2.50e+03 ... (remaining 26305 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 33 2.12 - 2.81: 41185 2.81 - 3.51: 216258 3.51 - 4.20: 354200 4.20 - 4.90: 626515 Nonbonded interactions: 1238191 Sorted by model distance: nonbonded pdb=" O ALA K 129 " pdb=" OD1 ASP K 132 " model vdw 1.425 3.040 nonbonded pdb=" O ALA J 129 " pdb=" OD1 ASP J 132 " model vdw 1.425 3.040 nonbonded pdb=" O ALA I 129 " pdb=" OD1 ASP I 132 " model vdw 1.425 3.040 nonbonded pdb=" O ALA L 129 " pdb=" OD1 ASP L 132 " model vdw 1.426 3.040 nonbonded pdb=" NH2 ARG D3375 " pdb=" OG SER D3437 " model vdw 1.560 2.520 ... (remaining 1238186 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 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 10.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.180 Extract box with map and model: 32.390 Check model and map are aligned: 1.590 Set scattering table: 1.020 Process input model: 490.900 Find NCS groups from input model: 8.990 Set up NCS constraints: 1.210 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: 0.040 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 558.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 0.076 151000 Z= 0.204 Angle : 0.710 25.015 204000 Z= 0.378 Chirality : 0.043 0.256 22360 Planarity : 0.007 0.373 26308 Dihedral : 14.561 89.807 56536 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 1.34 % Allowed : 0.93 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 1.05 (0.06), residues: 18336 helix: 1.69 (0.05), residues: 9672 sheet: 0.09 (0.13), residues: 1776 loop : -0.53 (0.07), residues: 6888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A3250 HIS 0.020 0.001 HIS L 108 PHE 0.042 0.001 PHE D4508 TYR 0.036 0.001 TYR D2760 ARG 0.017 0.001 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1040 time to evaluate : 12.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8114 (mm) cc_final: 0.7907 (mm) REVERT: A 211 LEU cc_start: 0.8881 (mm) cc_final: 0.8676 (mt) REVERT: A 241 MET cc_start: 0.5756 (mmp) cc_final: 0.5379 (mpm) REVERT: A 1036 THR cc_start: 0.9357 (p) cc_final: 0.9155 (p) REVERT: A 1037 LEU cc_start: 0.8627 (mt) cc_final: 0.8309 (mt) REVERT: A 1721 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7657 (mpp) REVERT: A 2782 MET cc_start: 0.8405 (ptp) cc_final: 0.8090 (ptm) REVERT: A 2840 MET cc_start: 0.8813 (mtm) cc_final: 0.8485 (mtm) REVERT: A 3366 LEU cc_start: 0.8958 (tt) cc_final: 0.8588 (pp) REVERT: A 3401 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8331 (tp30) REVERT: A 4817 MET cc_start: 0.8647 (mmt) cc_final: 0.8362 (mmt) REVERT: E 50 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7659 (ttm110) REVERT: F 50 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7780 (ttp80) REVERT: G 62 GLU cc_start: 0.8294 (pt0) cc_final: 0.8072 (pt0) REVERT: I 50 GLN cc_start: 0.9484 (mm110) cc_final: 0.9190 (mm110) REVERT: I 106 LEU cc_start: 0.8249 (mt) cc_final: 0.7972 (mt) REVERT: I 138 ASN cc_start: 0.7538 (p0) cc_final: 0.7281 (p0) REVERT: I 142 PHE cc_start: 0.8674 (t80) cc_final: 0.7885 (OUTLIER) REVERT: J 19 LEU cc_start: 0.9332 (mt) cc_final: 0.9077 (pp) REVERT: J 50 GLN cc_start: 0.9372 (mm110) cc_final: 0.9064 (mm110) REVERT: J 125 MET cc_start: 0.7036 (mpp) cc_final: 0.6644 (mmm) REVERT: J 146 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.5106 (ppp) REVERT: K 14 LYS cc_start: 0.9173 (tptt) cc_final: 0.8890 (tppt) REVERT: K 50 GLN cc_start: 0.9305 (mm110) cc_final: 0.8992 (mm110) REVERT: K 125 MET cc_start: 0.7615 (mpp) cc_final: 0.5517 (tpt) REVERT: L 50 GLN cc_start: 0.9430 (mm110) cc_final: 0.9108 (mm110) REVERT: L 75 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.9083 (tmm-80) REVERT: L 125 MET cc_start: 0.6942 (mpp) cc_final: 0.6018 (tpt) REVERT: L 146 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.5496 (ppp) REVERT: B 81 MET cc_start: 0.7708 (tpt) cc_final: 0.7481 (tpp) REVERT: B 114 LEU cc_start: 0.8301 (mm) cc_final: 0.8094 (mm) REVERT: B 241 MET cc_start: 0.5844 (mmp) cc_final: 0.5580 (mpm) REVERT: B 494 MET cc_start: 0.8823 (mmm) cc_final: 0.8615 (mmm) REVERT: B 1037 LEU cc_start: 0.8923 (mt) cc_final: 0.8651 (mt) REVERT: B 1721 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7628 (mmt) REVERT: B 1975 MET cc_start: 0.8068 (ppp) cc_final: 0.7865 (ptp) REVERT: B 2840 MET cc_start: 0.8865 (mtm) cc_final: 0.8585 (mtm) REVERT: B 3366 LEU cc_start: 0.9106 (tt) cc_final: 0.8777 (pp) REVERT: B 3381 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7945 (ttm-80) REVERT: B 3401 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8423 (tp30) REVERT: B 3428 MET cc_start: 0.6945 (ttt) cc_final: 0.6681 (mmt) REVERT: C 241 MET cc_start: 0.6071 (mmp) cc_final: 0.5685 (mpm) REVERT: C 1036 THR cc_start: 0.9433 (p) cc_final: 0.9203 (p) REVERT: C 1037 LEU cc_start: 0.8924 (mt) cc_final: 0.8596 (mm) REVERT: C 1494 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5858 (tmm) REVERT: C 2688 MET cc_start: 0.8064 (mmm) cc_final: 0.7762 (mmp) REVERT: C 3366 LEU cc_start: 0.9079 (tt) cc_final: 0.8759 (pp) REVERT: C 3381 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7976 (ttm-80) REVERT: C 3401 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8524 (tp30) REVERT: C 4707 MET cc_start: 0.7809 (ttt) cc_final: 0.7543 (ttm) REVERT: D 111 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6808 (tpp-160) REVERT: D 1036 THR cc_start: 0.9371 (p) cc_final: 0.9149 (p) REVERT: D 1037 LEU cc_start: 0.8826 (mt) cc_final: 0.8499 (mt) REVERT: D 3072 MET cc_start: 0.7971 (ttp) cc_final: 0.7754 (ttm) REVERT: D 3366 LEU cc_start: 0.9114 (tt) cc_final: 0.8835 (pp) REVERT: D 3401 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8632 (tp30) REVERT: D 3528 MET cc_start: 0.7582 (pmm) cc_final: 0.7321 (mmm) outliers start: 208 outliers final: 46 residues processed: 1114 average time/residue: 2.1771 time to fit residues: 3463.9930 Evaluate side-chains 967 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 911 time to evaluate : 12.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1721 MET Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2540 HIS Chi-restraints excluded: chain A residue 3215 MET Chi-restraints excluded: chain A residue 3461 MET Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 15 GLU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 77 MET Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain L residue 15 GLU Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain B residue 1721 MET Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 3215 MET Chi-restraints excluded: chain B residue 3221 LEU Chi-restraints excluded: chain B residue 3381 ARG Chi-restraints excluded: chain B residue 3422 GLN Chi-restraints excluded: chain B residue 3461 MET Chi-restraints excluded: chain C residue 1494 MET Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2830 ASN Chi-restraints excluded: chain C residue 3215 MET Chi-restraints excluded: chain C residue 3221 LEU Chi-restraints excluded: chain C residue 3381 ARG Chi-restraints excluded: chain C residue 3422 GLN Chi-restraints excluded: chain C residue 3461 MET Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 2830 ASN Chi-restraints excluded: chain D residue 3215 MET Chi-restraints excluded: chain D residue 3221 LEU Chi-restraints excluded: chain D residue 3461 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 1553 optimal weight: 10.0000 chunk 1394 optimal weight: 0.9990 chunk 773 optimal weight: 10.0000 chunk 476 optimal weight: 9.9990 chunk 940 optimal weight: 1.9990 chunk 745 optimal weight: 7.9990 chunk 1442 optimal weight: 5.9990 chunk 558 optimal weight: 9.9990 chunk 876 optimal weight: 10.0000 chunk 1073 optimal weight: 10.0000 chunk 1670 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 GLN A 932 ASN A1503 ASN ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2838 HIS A A2838 HIS B ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A4961 GLN F 44 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS J 108 HIS ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 108 HIS L 61 ASN B 746 GLN B1503 ASN ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2838 HIS A B2838 HIS B ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B4961 GLN C 746 GLN C 932 ASN ** C2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2838 HIS A C2838 HIS B ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3230 GLN C3426 ASN ** C3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C4961 GLN D 746 GLN D 932 ASN D1503 ASN ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2838 HIS A D2838 HIS B ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN ** D4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 151000 Z= 0.398 Angle : 0.656 13.849 204000 Z= 0.336 Chirality : 0.044 0.239 22360 Planarity : 0.005 0.081 26308 Dihedral : 6.135 130.236 20410 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 0.96 % Allowed : 5.53 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 1.02 (0.06), residues: 18336 helix: 1.68 (0.05), residues: 9672 sheet: 0.10 (0.13), residues: 1656 loop : -0.56 (0.07), residues: 7008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D1156 HIS 0.011 0.001 HIS B3700 PHE 0.035 0.002 PHE A3906 TYR 0.034 0.002 TYR C2760 ARG 0.013 0.001 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 989 time to evaluate : 12.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 CYS cc_start: 0.8307 (m) cc_final: 0.7710 (t) REVERT: A 995 MET cc_start: 0.7309 (tmm) cc_final: 0.7066 (ttp) REVERT: A 1036 THR cc_start: 0.9374 (p) cc_final: 0.9122 (p) REVERT: A 1037 LEU cc_start: 0.8719 (mt) cc_final: 0.8418 (mt) REVERT: A 2734 MET cc_start: 0.8946 (mpt) cc_final: 0.8735 (mpt) REVERT: A 2785 TRP cc_start: 0.8401 (m-10) cc_final: 0.8164 (m-10) REVERT: A 3336 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: A 3366 LEU cc_start: 0.8901 (tt) cc_final: 0.8553 (pp) REVERT: A 3401 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8417 (tm-30) REVERT: A 3819 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6016 (ptp) REVERT: A 3854 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: A 4817 MET cc_start: 0.8969 (mmt) cc_final: 0.8425 (mmt) REVERT: E 4 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6942 (tm-30) REVERT: G 4 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6521 (tm-30) REVERT: G 18 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8941 (mptt) REVERT: G 58 LYS cc_start: 0.8647 (ptmm) cc_final: 0.8293 (ptmm) REVERT: G 61 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8221 (tp30) REVERT: G 62 GLU cc_start: 0.8245 (pt0) cc_final: 0.7994 (pt0) REVERT: G 74 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8636 (ttmt) REVERT: H 4 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6894 (tm-30) REVERT: H 61 GLU cc_start: 0.8312 (tp30) cc_final: 0.8101 (mm-30) REVERT: I 50 GLN cc_start: 0.9500 (mm110) cc_final: 0.9156 (mm110) REVERT: I 106 LEU cc_start: 0.8210 (mt) cc_final: 0.7985 (mp) REVERT: I 110 MET cc_start: 0.8029 (mmt) cc_final: 0.7811 (mmm) REVERT: J 9 GLN cc_start: 0.8545 (pm20) cc_final: 0.8311 (pm20) REVERT: J 50 GLN cc_start: 0.9373 (mm110) cc_final: 0.9001 (mm110) REVERT: J 75 ARG cc_start: 0.9006 (tmm-80) cc_final: 0.8341 (ttp80) REVERT: J 125 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6780 (tpt) REVERT: J 146 MET cc_start: 0.7227 (ppp) cc_final: 0.6829 (ppp) REVERT: K 50 GLN cc_start: 0.9344 (mm110) cc_final: 0.8933 (mm110) REVERT: K 75 ARG cc_start: 0.9339 (tmm-80) cc_final: 0.8774 (ttp80) REVERT: K 110 MET cc_start: 0.7438 (mmt) cc_final: 0.7212 (mmm) REVERT: L 50 GLN cc_start: 0.9431 (mm110) cc_final: 0.8999 (mm110) REVERT: L 75 ARG cc_start: 0.9276 (tmm-80) cc_final: 0.8625 (ttp80) REVERT: L 76 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.8972 (ttpp) REVERT: L 110 MET cc_start: 0.6747 (mmm) cc_final: 0.5881 (mpp) REVERT: L 125 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6209 (tpt) REVERT: L 142 PHE cc_start: 0.8624 (t80) cc_final: 0.8358 (t80) REVERT: L 146 MET cc_start: 0.7063 (ppp) cc_final: 0.6831 (ppp) REVERT: B 81 MET cc_start: 0.7753 (tpt) cc_final: 0.7499 (tpt) REVERT: B 317 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7498 (ptp) REVERT: B 995 MET cc_start: 0.7537 (tmm) cc_final: 0.6880 (ttp) REVERT: B 2192 MET cc_start: 0.8696 (tpt) cc_final: 0.8464 (tpt) REVERT: B 2734 MET cc_start: 0.9055 (mpt) cc_final: 0.8840 (mpt) REVERT: B 2828 MET cc_start: 0.8571 (mmt) cc_final: 0.8292 (mmt) REVERT: B 2840 MET cc_start: 0.9033 (mtm) cc_final: 0.8706 (mtm) REVERT: B 2895 PHE cc_start: 0.8872 (t80) cc_final: 0.8406 (t80) REVERT: B 3366 LEU cc_start: 0.9102 (tt) cc_final: 0.8781 (pp) REVERT: B 4048 PHE cc_start: 0.8922 (t80) cc_final: 0.8566 (t80) REVERT: B 4052 MET cc_start: 0.8206 (mtp) cc_final: 0.7969 (mtp) REVERT: B 4502 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7360 (mtm) REVERT: C 241 MET cc_start: 0.6072 (mmp) cc_final: 0.5726 (mpm) REVERT: C 995 MET cc_start: 0.7515 (tmm) cc_final: 0.7293 (tmm) REVERT: C 1036 THR cc_start: 0.9478 (p) cc_final: 0.9262 (p) REVERT: C 1037 LEU cc_start: 0.8893 (mt) cc_final: 0.8527 (mp) REVERT: C 1494 MET cc_start: 0.6164 (tmm) cc_final: 0.5795 (tmm) REVERT: C 3426 ASN cc_start: 0.6787 (OUTLIER) cc_final: 0.6572 (p0) REVERT: C 3689 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7346 (mtp) REVERT: D 995 MET cc_start: 0.7481 (tmm) cc_final: 0.7145 (ttp) REVERT: D 1036 THR cc_start: 0.9399 (p) cc_final: 0.9195 (p) REVERT: D 1037 LEU cc_start: 0.8818 (mt) cc_final: 0.8415 (mp) REVERT: D 2605 MET cc_start: 0.8409 (tmm) cc_final: 0.8196 (tmm) REVERT: D 3528 MET cc_start: 0.7574 (pmm) cc_final: 0.7333 (mmm) REVERT: D 3689 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7656 (mtp) outliers start: 148 outliers final: 44 residues processed: 1041 average time/residue: 2.2380 time to fit residues: 3339.5420 Evaluate side-chains 984 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 928 time to evaluate : 12.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2760 TYR Chi-restraints excluded: chain A residue 2843 MET Chi-restraints excluded: chain A residue 3241 MET Chi-restraints excluded: chain A residue 3336 GLU Chi-restraints excluded: chain A residue 3379 TYR Chi-restraints excluded: chain A residue 3819 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 ASN Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 3221 LEU Chi-restraints excluded: chain B residue 3336 GLU Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 3221 LEU Chi-restraints excluded: chain C residue 3336 GLU Chi-restraints excluded: chain C residue 3426 ASN Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3336 GLU Chi-restraints excluded: chain D residue 3379 TYR Chi-restraints excluded: chain D residue 3689 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 928 optimal weight: 8.9990 chunk 518 optimal weight: 20.0000 chunk 1390 optimal weight: 5.9990 chunk 1137 optimal weight: 4.9990 chunk 460 optimal weight: 3.9990 chunk 1673 optimal weight: 9.9990 chunk 1808 optimal weight: 1.9990 chunk 1490 optimal weight: 30.0000 chunk 1659 optimal weight: 2.9990 chunk 570 optimal weight: 1.9990 chunk 1342 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A1995 GLN A2700 ASN ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3256 ASN ** A3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1995 GLN ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3256 ASN ** B3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1995 GLN ** C2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3426 ASN ** C3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1498 GLN D2729 HIS ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 151000 Z= 0.257 Angle : 0.590 15.148 204000 Z= 0.299 Chirality : 0.041 0.238 22360 Planarity : 0.004 0.071 26308 Dihedral : 5.390 87.052 20270 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 0.99 % Allowed : 7.05 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 1.11 (0.06), residues: 18336 helix: 1.77 (0.05), residues: 9692 sheet: 0.07 (0.13), residues: 1704 loop : -0.54 (0.07), residues: 6940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D2732 HIS 0.009 0.001 HIS D3732 PHE 0.025 0.002 PHE D3906 TYR 0.029 0.001 TYR B3405 ARG 0.013 0.000 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 949 time to evaluate : 12.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 CYS cc_start: 0.8297 (m) cc_final: 0.7706 (t) REVERT: A 81 MET cc_start: 0.7548 (tpp) cc_final: 0.7310 (tpt) REVERT: A 241 MET cc_start: 0.5925 (mmp) cc_final: 0.5453 (mpm) REVERT: A 309 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5663 (pmm) REVERT: A 995 MET cc_start: 0.7290 (tmm) cc_final: 0.6861 (ttt) REVERT: A 1036 THR cc_start: 0.9365 (p) cc_final: 0.9115 (p) REVERT: A 1037 LEU cc_start: 0.8731 (mt) cc_final: 0.8446 (mt) REVERT: A 3104 MET cc_start: 0.7905 (mtp) cc_final: 0.7677 (mtm) REVERT: A 3366 LEU cc_start: 0.8904 (tt) cc_final: 0.8559 (pp) REVERT: A 3401 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8400 (tm-30) REVERT: A 3461 MET cc_start: 0.2739 (tpp) cc_final: 0.2353 (tmm) REVERT: A 3689 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7942 (mpp) REVERT: A 3854 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: A 4817 MET cc_start: 0.8934 (mmt) cc_final: 0.8369 (mmt) REVERT: E 4 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6884 (tm-30) REVERT: G 58 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8231 (ptmm) REVERT: G 62 GLU cc_start: 0.8181 (pt0) cc_final: 0.7939 (pt0) REVERT: H 61 GLU cc_start: 0.8326 (tp30) cc_final: 0.8123 (mm-30) REVERT: I 50 GLN cc_start: 0.9451 (mm110) cc_final: 0.9146 (mm110) REVERT: I 76 LYS cc_start: 0.9407 (ttpp) cc_final: 0.9195 (tmmm) REVERT: I 106 LEU cc_start: 0.8132 (mt) cc_final: 0.7903 (mp) REVERT: J 50 GLN cc_start: 0.9340 (mm110) cc_final: 0.8958 (mm110) REVERT: J 75 ARG cc_start: 0.9002 (tmm-80) cc_final: 0.8378 (ttp80) REVERT: J 76 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9044 (pptt) REVERT: J 125 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6627 (mmm) REVERT: J 146 MET cc_start: 0.7169 (ppp) cc_final: 0.6753 (ppp) REVERT: K 50 GLN cc_start: 0.9309 (mm110) cc_final: 0.8871 (mm110) REVERT: K 75 ARG cc_start: 0.9291 (tmm-80) cc_final: 0.8874 (ttp80) REVERT: K 77 MET cc_start: 0.8706 (ppp) cc_final: 0.8244 (ppp) REVERT: K 125 MET cc_start: 0.7231 (mtt) cc_final: 0.5320 (tpt) REVERT: L 50 GLN cc_start: 0.9381 (mm110) cc_final: 0.8944 (mm110) REVERT: L 75 ARG cc_start: 0.9257 (tmm-80) cc_final: 0.8583 (ttp80) REVERT: L 125 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6064 (tpt) REVERT: B 81 MET cc_start: 0.7744 (tpt) cc_final: 0.7485 (tpt) REVERT: B 241 MET cc_start: 0.6182 (mmp) cc_final: 0.5760 (mpm) REVERT: B 995 MET cc_start: 0.7518 (tmm) cc_final: 0.7004 (ttp) REVERT: B 2192 MET cc_start: 0.8724 (tpt) cc_final: 0.8518 (tpt) REVERT: B 2828 MET cc_start: 0.8517 (mmt) cc_final: 0.8118 (mmt) REVERT: B 2840 MET cc_start: 0.9172 (mtm) cc_final: 0.8936 (mtm) REVERT: B 2895 PHE cc_start: 0.8811 (t80) cc_final: 0.8238 (t80) REVERT: B 3366 LEU cc_start: 0.9119 (tt) cc_final: 0.8782 (pp) REVERT: B 3689 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7649 (mpp) REVERT: B 4048 PHE cc_start: 0.8916 (t80) cc_final: 0.8558 (t80) REVERT: B 4052 MET cc_start: 0.8189 (mtp) cc_final: 0.7971 (mtp) REVERT: B 4502 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7347 (mtm) REVERT: C 81 MET cc_start: 0.7222 (tpp) cc_final: 0.6984 (tpt) REVERT: C 241 MET cc_start: 0.5993 (mmp) cc_final: 0.5536 (mpm) REVERT: C 995 MET cc_start: 0.7476 (tmm) cc_final: 0.7276 (tmm) REVERT: C 1037 LEU cc_start: 0.8931 (mt) cc_final: 0.8565 (mp) REVERT: C 1494 MET cc_start: 0.6274 (tmm) cc_final: 0.5891 (tmm) REVERT: C 3366 LEU cc_start: 0.9171 (tp) cc_final: 0.8789 (tm) REVERT: C 3739 MET cc_start: 0.8934 (ttp) cc_final: 0.8680 (ttp) REVERT: D 81 MET cc_start: 0.7363 (tpp) cc_final: 0.7136 (tpt) REVERT: D 241 MET cc_start: 0.6045 (mmp) cc_final: 0.5452 (mpt) REVERT: D 982 ASP cc_start: 0.8716 (t0) cc_final: 0.8256 (p0) REVERT: D 1037 LEU cc_start: 0.8854 (mt) cc_final: 0.8554 (mt) REVERT: D 2584 MET cc_start: 0.7900 (ptm) cc_final: 0.7678 (ptp) REVERT: D 2605 MET cc_start: 0.8402 (tmm) cc_final: 0.8172 (tmm) REVERT: D 2782 MET cc_start: 0.8152 (ppp) cc_final: 0.7912 (ppp) REVERT: D 3461 MET cc_start: 0.2661 (tpp) cc_final: 0.2383 (tmm) REVERT: D 3528 MET cc_start: 0.7580 (pmm) cc_final: 0.7372 (mmm) REVERT: D 3689 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7606 (mtp) REVERT: D 3739 MET cc_start: 0.9009 (ttp) cc_final: 0.8802 (ttm) outliers start: 152 outliers final: 48 residues processed: 1006 average time/residue: 2.2405 time to fit residues: 3239.4568 Evaluate side-chains 980 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 923 time to evaluate : 12.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 3241 MET Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 142 PHE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 2757 MET Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3336 GLU Chi-restraints excluded: chain B residue 3369 PHE Chi-restraints excluded: chain B residue 3373 LEU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2757 MET Chi-restraints excluded: chain C residue 2830 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 2954 PHE Chi-restraints excluded: chain C residue 3336 GLU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3336 GLU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 4511 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 1653 optimal weight: 9.9990 chunk 1258 optimal weight: 9.9990 chunk 868 optimal weight: 0.3980 chunk 185 optimal weight: 0.9980 chunk 798 optimal weight: 0.0970 chunk 1124 optimal weight: 8.9990 chunk 1679 optimal weight: 20.0000 chunk 1778 optimal weight: 0.0670 chunk 877 optimal weight: 7.9990 chunk 1592 optimal weight: 0.0370 chunk 479 optimal weight: 5.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN A1498 GLN A2700 ASN A2729 HIS ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3256 ASN ** A3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 144 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3256 ASN ** B3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3256 ASN C3423 ASN ** C3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2729 HIS ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 151000 Z= 0.145 Angle : 0.569 16.944 204000 Z= 0.283 Chirality : 0.039 0.229 22360 Planarity : 0.004 0.069 26308 Dihedral : 5.047 79.598 20264 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 0.86 % Allowed : 8.03 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 1.26 (0.06), residues: 18336 helix: 1.92 (0.05), residues: 9668 sheet: 0.11 (0.13), residues: 1720 loop : -0.50 (0.07), residues: 6948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A2732 HIS 0.008 0.001 HIS B3732 PHE 0.058 0.001 PHE B3369 TYR 0.021 0.001 TYR J 139 ARG 0.014 0.000 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 957 time to evaluate : 12.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 CYS cc_start: 0.8282 (m) cc_final: 0.7671 (t) REVERT: A 81 MET cc_start: 0.7493 (tpp) cc_final: 0.7218 (tpt) REVERT: A 241 MET cc_start: 0.5911 (mmp) cc_final: 0.5475 (mpm) REVERT: A 309 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5646 (pmm) REVERT: A 1036 THR cc_start: 0.9365 (p) cc_final: 0.9115 (p) REVERT: A 1037 LEU cc_start: 0.8724 (mt) cc_final: 0.8450 (mt) REVERT: A 2734 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8569 (mpt) REVERT: A 3366 LEU cc_start: 0.8897 (tt) cc_final: 0.8542 (pp) REVERT: A 3401 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8385 (tm-30) REVERT: A 3461 MET cc_start: 0.2391 (tpp) cc_final: 0.2184 (tmm) REVERT: A 3689 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7800 (mpp) REVERT: E 4 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6776 (tm-30) REVERT: G 58 LYS cc_start: 0.8505 (ptmm) cc_final: 0.8167 (ptmm) REVERT: G 62 GLU cc_start: 0.8150 (pt0) cc_final: 0.7916 (pt0) REVERT: H 61 GLU cc_start: 0.8313 (tp30) cc_final: 0.8105 (mm-30) REVERT: H 62 GLU cc_start: 0.8059 (pt0) cc_final: 0.7846 (pt0) REVERT: H 108 GLU cc_start: 0.8155 (pt0) cc_final: 0.7930 (pt0) REVERT: I 19 LEU cc_start: 0.9410 (mt) cc_final: 0.9196 (pp) REVERT: I 50 GLN cc_start: 0.9425 (mm110) cc_final: 0.9123 (mm110) REVERT: J 14 LYS cc_start: 0.9527 (tptt) cc_final: 0.9102 (tppt) REVERT: J 19 LEU cc_start: 0.9479 (mt) cc_final: 0.9191 (pp) REVERT: J 50 GLN cc_start: 0.9328 (mm110) cc_final: 0.8931 (mm110) REVERT: J 73 MET cc_start: 0.8641 (mmm) cc_final: 0.8435 (tpt) REVERT: J 75 ARG cc_start: 0.8959 (tmm-80) cc_final: 0.8300 (ttp80) REVERT: J 125 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6643 (mmm) REVERT: J 142 PHE cc_start: 0.8521 (t80) cc_final: 0.8308 (t80) REVERT: K 14 LYS cc_start: 0.9381 (tptt) cc_final: 0.8923 (tppt) REVERT: K 50 GLN cc_start: 0.9312 (mm110) cc_final: 0.8931 (mm110) REVERT: K 75 ARG cc_start: 0.9254 (tmm-80) cc_final: 0.8869 (ttp80) REVERT: K 77 MET cc_start: 0.8777 (ppp) cc_final: 0.8458 (ppp) REVERT: L 50 GLN cc_start: 0.9403 (mm110) cc_final: 0.8920 (mm110) REVERT: L 75 ARG cc_start: 0.9223 (tmm-80) cc_final: 0.8589 (ttp80) REVERT: L 76 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9146 (ptmt) REVERT: L 125 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6057 (tpt) REVERT: L 145 MET cc_start: 0.8035 (pp-130) cc_final: 0.7728 (mmp) REVERT: B 81 MET cc_start: 0.7719 (tpt) cc_final: 0.7455 (tpt) REVERT: B 241 MET cc_start: 0.6102 (mmp) cc_final: 0.5691 (mpm) REVERT: B 995 MET cc_start: 0.7493 (tmm) cc_final: 0.7027 (ttp) REVERT: B 2192 MET cc_start: 0.8709 (tpt) cc_final: 0.8447 (tpt) REVERT: B 2840 MET cc_start: 0.9146 (mtm) cc_final: 0.8662 (mtm) REVERT: B 2895 PHE cc_start: 0.8799 (t80) cc_final: 0.8227 (t80) REVERT: B 3322 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7884 (pp) REVERT: B 3366 LEU cc_start: 0.9098 (tt) cc_final: 0.8753 (pp) REVERT: B 3439 MET cc_start: 0.3270 (ppp) cc_final: 0.2637 (pmm) REVERT: B 3689 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7550 (mpp) REVERT: B 4048 PHE cc_start: 0.8896 (t80) cc_final: 0.8544 (t80) REVERT: B 4502 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7236 (mtm) REVERT: C 81 MET cc_start: 0.7167 (tpp) cc_final: 0.6911 (tpt) REVERT: C 241 MET cc_start: 0.5965 (mmp) cc_final: 0.5502 (mpm) REVERT: C 309 MET cc_start: 0.5991 (pmm) cc_final: 0.5752 (pmm) REVERT: C 1037 LEU cc_start: 0.8875 (mt) cc_final: 0.8606 (mt) REVERT: C 1494 MET cc_start: 0.6281 (tmm) cc_final: 0.5893 (tmm) REVERT: C 2347 MET cc_start: 0.9148 (mmm) cc_final: 0.8895 (tpt) REVERT: C 3147 TYR cc_start: 0.7522 (m-80) cc_final: 0.7303 (m-80) REVERT: D 81 MET cc_start: 0.7379 (tpp) cc_final: 0.7101 (tpt) REVERT: D 241 MET cc_start: 0.6001 (mmp) cc_final: 0.5409 (mpt) REVERT: D 982 ASP cc_start: 0.8723 (t0) cc_final: 0.8259 (p0) REVERT: D 1037 LEU cc_start: 0.8781 (mt) cc_final: 0.8507 (mt) REVERT: D 1729 MET cc_start: 0.8447 (mmt) cc_final: 0.8192 (mmt) REVERT: D 2584 MET cc_start: 0.7775 (ptm) cc_final: 0.7561 (ptp) REVERT: D 2605 MET cc_start: 0.8386 (tmm) cc_final: 0.8183 (tmm) REVERT: D 3367 TYR cc_start: 0.8091 (m-10) cc_final: 0.7821 (m-10) REVERT: D 4672 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6783 (ptm) outliers start: 131 outliers final: 48 residues processed: 1009 average time/residue: 2.2865 time to fit residues: 3312.3575 Evaluate side-chains 979 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 921 time to evaluate : 12.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 2734 MET Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 3241 MET Chi-restraints excluded: chain A residue 3369 PHE Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 142 PHE Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 ASN Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 2830 ASN Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3231 MET Chi-restraints excluded: chain B residue 3322 LEU Chi-restraints excluded: chain B residue 3336 GLU Chi-restraints excluded: chain B residue 3373 LEU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 2954 PHE Chi-restraints excluded: chain C residue 3336 GLU Chi-restraints excluded: chain C residue 4511 PHE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 1495 SER Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3221 LEU Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3336 GLU Chi-restraints excluded: chain D residue 4511 PHE Chi-restraints excluded: chain D residue 4672 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 1481 optimal weight: 2.9990 chunk 1009 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 1324 optimal weight: 10.0000 chunk 733 optimal weight: 7.9990 chunk 1517 optimal weight: 10.0000 chunk 1229 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 908 optimal weight: 5.9990 chunk 1596 optimal weight: 2.9990 chunk 448 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 781 ASN ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3256 ASN A3563 GLN A3964 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 112 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3256 ASN B3563 GLN ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1503 ASN ** C2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3256 ASN C3462 GLN C3527 GLN C3563 GLN C3882 GLN C3964 GLN ** D 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1995 GLN D2729 HIS ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2995 HIS D3256 ASN D3423 ASN D3563 GLN D3964 GLN ** D4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 151000 Z= 0.406 Angle : 0.636 13.590 204000 Z= 0.321 Chirality : 0.043 0.231 22360 Planarity : 0.004 0.069 26308 Dihedral : 5.163 81.659 20261 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 1.00 % Allowed : 8.84 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.06), residues: 18336 helix: 1.84 (0.05), residues: 9652 sheet: 0.07 (0.13), residues: 1696 loop : -0.50 (0.07), residues: 6988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A2741 HIS 0.009 0.001 HIS D3732 PHE 0.082 0.002 PHE A3369 TYR 0.022 0.002 TYR B2956 ARG 0.015 0.001 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 961 time to evaluate : 12.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 CYS cc_start: 0.8303 (m) cc_final: 0.7711 (t) REVERT: A 81 MET cc_start: 0.7597 (tpp) cc_final: 0.7297 (tpt) REVERT: A 241 MET cc_start: 0.5848 (mmp) cc_final: 0.5439 (mpm) REVERT: A 309 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5608 (pmm) REVERT: A 995 MET cc_start: 0.7295 (tmm) cc_final: 0.6619 (ttp) REVERT: A 1036 THR cc_start: 0.9382 (p) cc_final: 0.9130 (p) REVERT: A 1037 LEU cc_start: 0.8726 (mt) cc_final: 0.8458 (mt) REVERT: A 3104 MET cc_start: 0.8109 (mtp) cc_final: 0.7829 (mtm) REVERT: A 3401 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8415 (tm-30) REVERT: A 3689 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8007 (mpp) REVERT: A 3854 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: A 4804 MET cc_start: 0.8923 (mmm) cc_final: 0.8540 (mmm) REVERT: E 4 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6917 (tm-30) REVERT: G 58 LYS cc_start: 0.8632 (ptmm) cc_final: 0.8259 (ptmm) REVERT: G 62 GLU cc_start: 0.8167 (pt0) cc_final: 0.7855 (pt0) REVERT: I 50 GLN cc_start: 0.9406 (mm110) cc_final: 0.9106 (mm110) REVERT: J 14 LYS cc_start: 0.9524 (tptt) cc_final: 0.9093 (tppt) REVERT: J 50 GLN cc_start: 0.9326 (mm110) cc_final: 0.8933 (mm110) REVERT: J 75 ARG cc_start: 0.8978 (tmm-80) cc_final: 0.8271 (ttp80) REVERT: J 76 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8843 (ttpp) REVERT: J 125 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6594 (mmm) REVERT: K 14 LYS cc_start: 0.9403 (tptt) cc_final: 0.8940 (tppt) REVERT: K 50 GLN cc_start: 0.9310 (mm110) cc_final: 0.8887 (mm110) REVERT: K 77 MET cc_start: 0.8688 (ppp) cc_final: 0.8464 (ppp) REVERT: K 110 MET cc_start: 0.7518 (mmm) cc_final: 0.7034 (mmt) REVERT: K 125 MET cc_start: 0.7239 (mtt) cc_final: 0.5310 (tpt) REVERT: L 50 GLN cc_start: 0.9385 (mm110) cc_final: 0.8966 (mm110) REVERT: L 75 ARG cc_start: 0.9246 (tmm-80) cc_final: 0.8684 (ttp80) REVERT: L 77 MET cc_start: 0.8755 (ppp) cc_final: 0.8371 (ppp) REVERT: L 125 MET cc_start: 0.7257 (mpp) cc_final: 0.5875 (tpt) REVERT: L 145 MET cc_start: 0.8069 (pp-130) cc_final: 0.7735 (mmp) REVERT: B 81 MET cc_start: 0.7779 (tpt) cc_final: 0.7531 (tpt) REVERT: B 309 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6223 (pmm) REVERT: B 678 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7327 (ttt) REVERT: B 899 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6161 (pm20) REVERT: B 995 MET cc_start: 0.7569 (tmm) cc_final: 0.7168 (ttp) REVERT: B 2895 PHE cc_start: 0.8884 (t80) cc_final: 0.8388 (t80) REVERT: B 3366 LEU cc_start: 0.9118 (tt) cc_final: 0.8767 (pp) REVERT: B 3472 ARG cc_start: 0.7794 (mpt180) cc_final: 0.7448 (mpt180) REVERT: B 3689 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.7768 (mpp) REVERT: C 81 MET cc_start: 0.7237 (tpp) cc_final: 0.6969 (tpt) REVERT: C 1037 LEU cc_start: 0.8925 (mt) cc_final: 0.8656 (mt) REVERT: C 1494 MET cc_start: 0.6309 (tmm) cc_final: 0.5952 (tmm) REVERT: C 2688 MET cc_start: 0.7466 (mmp) cc_final: 0.7255 (mmm) REVERT: C 4672 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6441 (pmm) REVERT: D 42 PHE cc_start: 0.8483 (t80) cc_final: 0.8273 (t80) REVERT: D 81 MET cc_start: 0.7414 (tpp) cc_final: 0.7132 (tpt) REVERT: D 114 LEU cc_start: 0.8228 (tm) cc_final: 0.7986 (tm) REVERT: D 309 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5887 (pmm) REVERT: D 964 MET cc_start: 0.2098 (OUTLIER) cc_final: 0.1433 (mpt) REVERT: D 982 ASP cc_start: 0.8750 (t0) cc_final: 0.8249 (p0) REVERT: D 1037 LEU cc_start: 0.8806 (mt) cc_final: 0.8549 (mt) REVERT: D 1729 MET cc_start: 0.8532 (mmt) cc_final: 0.8322 (mmt) REVERT: D 2605 MET cc_start: 0.8448 (tmm) cc_final: 0.8222 (tmm) REVERT: D 3095 ASN cc_start: 0.8045 (m-40) cc_final: 0.7662 (m110) REVERT: D 3147 TYR cc_start: 0.7644 (m-80) cc_final: 0.7406 (m-80) REVERT: D 3367 TYR cc_start: 0.8105 (m-10) cc_final: 0.7823 (m-10) REVERT: D 3369 PHE cc_start: 0.7390 (m-80) cc_final: 0.6945 (m-80) REVERT: D 3689 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7627 (mtp) outliers start: 153 outliers final: 58 residues processed: 1022 average time/residue: 2.2270 time to fit residues: 3271.1656 Evaluate side-chains 1000 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 929 time to evaluate : 11.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2757 MET Chi-restraints excluded: chain A residue 2830 ASN Chi-restraints excluded: chain A residue 3234 VAL Chi-restraints excluded: chain A residue 3241 MET Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 142 PHE Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1495 SER Chi-restraints excluded: chain B residue 1694 MET Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3241 MET Chi-restraints excluded: chain B residue 3336 GLU Chi-restraints excluded: chain B residue 3367 TYR Chi-restraints excluded: chain B residue 3373 LEU Chi-restraints excluded: chain B residue 3563 GLN Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2830 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 2954 PHE Chi-restraints excluded: chain C residue 3336 GLU Chi-restraints excluded: chain C residue 3563 GLN Chi-restraints excluded: chain C residue 4672 MET Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1495 SER Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 2872 VAL Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3336 GLU Chi-restraints excluded: chain D residue 3563 GLN Chi-restraints excluded: chain D residue 3689 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 598 optimal weight: 1.9990 chunk 1601 optimal weight: 3.9990 chunk 351 optimal weight: 5.9990 chunk 1044 optimal weight: 3.9990 chunk 439 optimal weight: 6.9990 chunk 1780 optimal weight: 2.9990 chunk 1477 optimal weight: 5.9990 chunk 824 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 588 optimal weight: 2.9990 chunk 934 optimal weight: 0.2980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3256 ASN ** A3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3256 ASN B3563 GLN ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3563 GLN ** D 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3256 ASN D3563 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 151000 Z= 0.187 Angle : 0.594 15.015 204000 Z= 0.296 Chirality : 0.040 0.453 22360 Planarity : 0.004 0.070 26308 Dihedral : 5.027 77.762 20261 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 0.86 % Allowed : 9.27 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.24 (0.06), residues: 18336 helix: 1.92 (0.05), residues: 9632 sheet: 0.06 (0.12), residues: 1732 loop : -0.50 (0.07), residues: 6972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP A2741 HIS 0.008 0.001 HIS D3732 PHE 0.027 0.001 PHE B3369 TYR 0.035 0.001 TYR D2956 ARG 0.016 0.000 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 953 time to evaluate : 12.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 CYS cc_start: 0.8291 (m) cc_final: 0.7700 (t) REVERT: A 81 MET cc_start: 0.7541 (tpp) cc_final: 0.7228 (tpt) REVERT: A 241 MET cc_start: 0.5838 (mmp) cc_final: 0.5450 (mpm) REVERT: A 309 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5571 (pmm) REVERT: A 317 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7334 (ptp) REVERT: A 995 MET cc_start: 0.7270 (tmm) cc_final: 0.6750 (ttt) REVERT: A 1036 THR cc_start: 0.9357 (p) cc_final: 0.9105 (p) REVERT: A 1037 LEU cc_start: 0.8719 (mt) cc_final: 0.8455 (mt) REVERT: A 1599 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8616 (ttp) REVERT: A 2843 MET cc_start: 0.9184 (ttp) cc_final: 0.8759 (ttt) REVERT: A 3104 MET cc_start: 0.8049 (mtp) cc_final: 0.7803 (mtm) REVERT: A 3366 LEU cc_start: 0.8900 (tt) cc_final: 0.8499 (pp) REVERT: A 3401 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8412 (tm-30) REVERT: A 3428 MET cc_start: 0.6405 (mmp) cc_final: 0.6137 (mmt) REVERT: A 3689 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: A 3854 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: A 4672 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6568 (pmm) REVERT: E 4 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6924 (tm-30) REVERT: G 58 LYS cc_start: 0.8540 (ptmm) cc_final: 0.8182 (ptmm) REVERT: G 62 GLU cc_start: 0.8120 (pt0) cc_final: 0.7856 (pt0) REVERT: I 50 GLN cc_start: 0.9367 (mm110) cc_final: 0.9103 (mm110) REVERT: I 110 MET cc_start: 0.8010 (mmm) cc_final: 0.7496 (mpt) REVERT: I 146 MET cc_start: 0.7672 (ppp) cc_final: 0.7461 (ppp) REVERT: J 14 LYS cc_start: 0.9515 (tptt) cc_final: 0.9082 (tppt) REVERT: J 50 GLN cc_start: 0.9299 (mm110) cc_final: 0.8901 (mm110) REVERT: J 75 ARG cc_start: 0.8977 (tmm-80) cc_final: 0.8287 (ttp80) REVERT: J 76 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8742 (ttpp) REVERT: J 92 VAL cc_start: 0.4138 (m) cc_final: 0.3863 (m) REVERT: J 125 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6515 (tpt) REVERT: K 14 LYS cc_start: 0.9398 (tptt) cc_final: 0.9012 (tppt) REVERT: K 50 GLN cc_start: 0.9296 (mm110) cc_final: 0.8872 (mm110) REVERT: K 77 MET cc_start: 0.8841 (ppp) cc_final: 0.8599 (ppp) REVERT: K 125 MET cc_start: 0.7217 (mtt) cc_final: 0.5292 (tpt) REVERT: L 50 GLN cc_start: 0.9353 (mm110) cc_final: 0.8892 (mm110) REVERT: L 75 ARG cc_start: 0.9246 (tmm-80) cc_final: 0.8667 (ttp80) REVERT: L 77 MET cc_start: 0.8825 (ppp) cc_final: 0.8501 (ppp) REVERT: L 125 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.5945 (tpt) REVERT: L 145 MET cc_start: 0.8082 (pp-130) cc_final: 0.7705 (mmp) REVERT: B 81 MET cc_start: 0.7754 (tpt) cc_final: 0.7503 (tpt) REVERT: B 241 MET cc_start: 0.6120 (mmp) cc_final: 0.5792 (mpm) REVERT: B 309 MET cc_start: 0.6386 (pmm) cc_final: 0.6024 (pmm) REVERT: B 317 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7522 (ptp) REVERT: B 899 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6198 (pm20) REVERT: B 995 MET cc_start: 0.7528 (tmm) cc_final: 0.7129 (ttp) REVERT: B 2895 PHE cc_start: 0.8888 (t80) cc_final: 0.8340 (t80) REVERT: B 3336 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: B 3366 LEU cc_start: 0.9081 (tt) cc_final: 0.8718 (pp) REVERT: B 3439 MET cc_start: 0.3320 (ppp) cc_final: 0.2654 (pmm) REVERT: B 3472 ARG cc_start: 0.7799 (mpt180) cc_final: 0.7454 (mpt180) REVERT: B 3689 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7579 (mpp) REVERT: C 81 MET cc_start: 0.7208 (tpp) cc_final: 0.6927 (tpt) REVERT: C 241 MET cc_start: 0.6046 (mmp) cc_final: 0.5632 (mpm) REVERT: C 317 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7366 (ptp) REVERT: C 1037 LEU cc_start: 0.8905 (mt) cc_final: 0.8641 (mt) REVERT: C 1494 MET cc_start: 0.6364 (tmm) cc_final: 0.6018 (tmm) REVERT: C 2688 MET cc_start: 0.7572 (mmp) cc_final: 0.7318 (mmm) REVERT: C 4672 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6427 (pmm) REVERT: D 42 PHE cc_start: 0.8461 (t80) cc_final: 0.8237 (t80) REVERT: D 81 MET cc_start: 0.7356 (tpp) cc_final: 0.7144 (tpt) REVERT: D 114 LEU cc_start: 0.8190 (tm) cc_final: 0.7944 (tm) REVERT: D 241 MET cc_start: 0.6022 (mmp) cc_final: 0.5492 (mpt) REVERT: D 309 MET cc_start: 0.5842 (pmm) cc_final: 0.5591 (pmm) REVERT: D 964 MET cc_start: 0.2105 (OUTLIER) cc_final: 0.1404 (mpt) REVERT: D 982 ASP cc_start: 0.8723 (t0) cc_final: 0.8214 (p0) REVERT: D 995 MET cc_start: 0.7351 (tmm) cc_final: 0.7089 (tmm) REVERT: D 1037 LEU cc_start: 0.8786 (mt) cc_final: 0.8533 (mt) REVERT: D 1896 MET cc_start: 0.8137 (ttp) cc_final: 0.7903 (ttm) REVERT: D 2605 MET cc_start: 0.8428 (tmm) cc_final: 0.8199 (tmm) REVERT: D 3095 ASN cc_start: 0.7987 (m-40) cc_final: 0.7593 (m110) REVERT: D 3367 TYR cc_start: 0.8087 (m-10) cc_final: 0.7801 (m-10) REVERT: D 3369 PHE cc_start: 0.7496 (m-80) cc_final: 0.7004 (m-80) REVERT: D 3491 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8393 (pp) REVERT: D 3563 GLN cc_start: 0.5840 (OUTLIER) cc_final: 0.5639 (pm20) REVERT: D 3689 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7567 (mpp) outliers start: 131 outliers final: 44 residues processed: 1010 average time/residue: 2.2964 time to fit residues: 3336.2703 Evaluate side-chains 990 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 927 time to evaluate : 12.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 3241 MET Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 142 PHE Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1495 SER Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3221 LEU Chi-restraints excluded: chain B residue 3241 MET Chi-restraints excluded: chain B residue 3336 GLU Chi-restraints excluded: chain B residue 3367 TYR Chi-restraints excluded: chain B residue 3373 LEU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3336 GLU Chi-restraints excluded: chain C residue 4672 MET Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1495 SER Chi-restraints excluded: chain D residue 2872 VAL Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3336 GLU Chi-restraints excluded: chain D residue 3491 LEU Chi-restraints excluded: chain D residue 3563 GLN Chi-restraints excluded: chain D residue 3689 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 1716 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 1014 optimal weight: 9.9990 chunk 1300 optimal weight: 8.9990 chunk 1007 optimal weight: 20.0000 chunk 1498 optimal weight: 1.9990 chunk 994 optimal weight: 5.9990 chunk 1773 optimal weight: 5.9990 chunk 1109 optimal weight: 10.0000 chunk 1081 optimal weight: 10.0000 chunk 818 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2995 HIS A3256 ASN A3563 GLN H 88 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN L 112 ASN B 781 ASN ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3233 HIS B3256 ASN ** B3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3964 GLN C 781 ASN ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2998 ASN C3233 HIS ** C3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2998 ASN D3563 GLN D3882 GLN D4961 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 151000 Z= 0.456 Angle : 0.667 14.206 204000 Z= 0.336 Chirality : 0.044 0.265 22360 Planarity : 0.004 0.073 26308 Dihedral : 5.185 79.804 20261 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 0.85 % Allowed : 9.99 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.08 (0.06), residues: 18336 helix: 1.78 (0.05), residues: 9656 sheet: 0.02 (0.13), residues: 1692 loop : -0.57 (0.07), residues: 6988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A2741 HIS 0.010 0.001 HIS D3732 PHE 0.043 0.002 PHE C2954 TYR 0.028 0.002 TYR D2939 ARG 0.018 0.001 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 964 time to evaluate : 11.528 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: A 36 CYS cc_start: 0.8294 (m) cc_final: 0.7722 (t) REVERT: A 81 MET cc_start: 0.7612 (tpp) cc_final: 0.7276 (tpt) REVERT: A 241 MET cc_start: 0.5824 (mmp) cc_final: 0.5390 (mpm) REVERT: A 309 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5754 (pmm) REVERT: A 778 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7764 (mtp) REVERT: A 995 MET cc_start: 0.7280 (tmm) cc_final: 0.6676 (ttp) REVERT: A 1036 THR cc_start: 0.9387 (p) cc_final: 0.9146 (p) REVERT: A 1037 LEU cc_start: 0.8738 (mt) cc_final: 0.8474 (mt) REVERT: A 1599 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8654 (ttp) REVERT: A 3401 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8400 (tm-30) REVERT: A 3428 MET cc_start: 0.6344 (mmp) cc_final: 0.6074 (mmt) REVERT: A 3605 MET cc_start: 0.7513 (tmm) cc_final: 0.6889 (tmm) REVERT: A 3689 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8013 (mpp) REVERT: A 3854 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: A 4672 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6635 (pmm) REVERT: G 50 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7887 (mtm110) REVERT: I 14 LYS cc_start: 0.9416 (tptt) cc_final: 0.8955 (tppt) REVERT: I 50 GLN cc_start: 0.9371 (mm110) cc_final: 0.9104 (mm110) REVERT: I 106 LEU cc_start: 0.8178 (mm) cc_final: 0.7882 (mp) REVERT: I 110 MET cc_start: 0.8189 (mmm) cc_final: 0.7534 (mpt) REVERT: J 14 LYS cc_start: 0.9511 (tptt) cc_final: 0.9077 (tppt) REVERT: J 50 GLN cc_start: 0.9287 (mm110) cc_final: 0.8912 (mm110) REVERT: J 76 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8977 (ttpp) REVERT: J 125 MET cc_start: 0.7424 (mpp) cc_final: 0.6350 (tpt) REVERT: K 14 LYS cc_start: 0.9411 (tptt) cc_final: 0.8956 (tppt) REVERT: K 50 GLN cc_start: 0.9265 (mm110) cc_final: 0.8834 (mm110) REVERT: K 110 MET cc_start: 0.7659 (mmm) cc_final: 0.7414 (mmm) REVERT: L 14 LYS cc_start: 0.9537 (tptt) cc_final: 0.9052 (tppt) REVERT: L 50 GLN cc_start: 0.9351 (mm110) cc_final: 0.8896 (mm110) REVERT: L 72 MET cc_start: 0.8856 (ptp) cc_final: 0.8530 (ptp) REVERT: L 75 ARG cc_start: 0.9274 (tmm-80) cc_final: 0.8702 (ttp80) REVERT: L 77 MET cc_start: 0.8880 (ppp) cc_final: 0.8575 (ppp) REVERT: L 125 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.5950 (tpt) REVERT: L 145 MET cc_start: 0.8130 (pp-130) cc_final: 0.7791 (mmp) REVERT: B 81 MET cc_start: 0.7811 (tpt) cc_final: 0.7568 (tpt) REVERT: B 241 MET cc_start: 0.6155 (mmp) cc_final: 0.5813 (mpm) REVERT: B 317 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7555 (ptp) REVERT: B 995 MET cc_start: 0.7564 (tmm) cc_final: 0.7236 (ttp) REVERT: B 2605 MET cc_start: 0.8513 (tmm) cc_final: 0.8287 (tmm) REVERT: B 2895 PHE cc_start: 0.8916 (t80) cc_final: 0.8343 (t80) REVERT: B 3366 LEU cc_start: 0.9083 (tt) cc_final: 0.8714 (pp) REVERT: B 3472 ARG cc_start: 0.7964 (mpt180) cc_final: 0.7575 (mpt180) REVERT: B 3689 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7762 (mpp) REVERT: C 81 MET cc_start: 0.7287 (tpp) cc_final: 0.6983 (tpt) REVERT: C 241 MET cc_start: 0.6072 (mmp) cc_final: 0.5588 (mpm) REVERT: C 309 MET cc_start: 0.6156 (pmm) cc_final: 0.5750 (pmm) REVERT: C 317 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7325 (ptp) REVERT: C 995 MET cc_start: 0.7552 (tmm) cc_final: 0.7319 (tmm) REVERT: C 1037 LEU cc_start: 0.8953 (mt) cc_final: 0.8702 (mt) REVERT: C 3369 PHE cc_start: 0.7391 (m-80) cc_final: 0.6961 (m-80) REVERT: C 4672 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6517 (pmm) REVERT: D 114 LEU cc_start: 0.8192 (tm) cc_final: 0.7952 (tm) REVERT: D 241 MET cc_start: 0.6057 (mmp) cc_final: 0.5549 (mpt) REVERT: D 309 MET cc_start: 0.6263 (pmm) cc_final: 0.6051 (pmm) REVERT: D 982 ASP cc_start: 0.8742 (t0) cc_final: 0.8265 (p0) REVERT: D 1037 LEU cc_start: 0.8823 (mt) cc_final: 0.8577 (mt) REVERT: D 1896 MET cc_start: 0.8198 (ttp) cc_final: 0.7958 (ttm) REVERT: D 3095 ASN cc_start: 0.8048 (m-40) cc_final: 0.7675 (m110) REVERT: D 3367 TYR cc_start: 0.8143 (m-10) cc_final: 0.7870 (m-10) REVERT: D 3369 PHE cc_start: 0.7426 (m-80) cc_final: 0.6868 (m-80) REVERT: D 3491 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8421 (pp) REVERT: D 3689 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7666 (mtp) REVERT: D 4672 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6662 (pmm) outliers start: 129 outliers final: 52 residues processed: 1018 average time/residue: 2.2375 time to fit residues: 3267.7691 Evaluate side-chains 1011 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 944 time to evaluate : 11.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 3241 MET Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 142 PHE Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain L residue 61 ASN Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain B residue 1495 SER Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3221 LEU Chi-restraints excluded: chain B residue 3241 MET Chi-restraints excluded: chain B residue 3336 GLU Chi-restraints excluded: chain B residue 3367 TYR Chi-restraints excluded: chain B residue 3373 LEU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3241 MET Chi-restraints excluded: chain C residue 3336 GLU Chi-restraints excluded: chain C residue 4672 MET Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1495 SER Chi-restraints excluded: chain D residue 2872 VAL Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3336 GLU Chi-restraints excluded: chain D residue 3491 LEU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4672 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 1097 optimal weight: 6.9990 chunk 708 optimal weight: 8.9990 chunk 1059 optimal weight: 50.0000 chunk 534 optimal weight: 6.9990 chunk 348 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 1127 optimal weight: 10.0000 chunk 1208 optimal weight: 9.9990 chunk 876 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 1393 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3256 ASN A3563 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN I 136 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1498 GLN ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3256 ASN ** B3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2998 ASN ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2998 ASN D3256 ASN ** D3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 151000 Z= 0.186 Angle : 0.619 17.481 204000 Z= 0.306 Chirality : 0.040 0.273 22360 Planarity : 0.004 0.079 26308 Dihedral : 5.010 75.765 20261 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 0.63 % Allowed : 10.39 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.18 (0.06), residues: 18336 helix: 1.87 (0.05), residues: 9664 sheet: 0.02 (0.12), residues: 1732 loop : -0.54 (0.07), residues: 6940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.001 TRP A2741 HIS 0.008 0.001 HIS B3732 PHE 0.030 0.001 PHE K 142 TYR 0.026 0.001 TYR J 139 ARG 0.017 0.000 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 952 time to evaluate : 12.699 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: A 36 CYS cc_start: 0.8281 (m) cc_final: 0.7692 (t) REVERT: A 81 MET cc_start: 0.7494 (tpp) cc_final: 0.7153 (tpt) REVERT: A 241 MET cc_start: 0.5688 (mmp) cc_final: 0.5277 (mpm) REVERT: A 309 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5819 (pmm) REVERT: A 995 MET cc_start: 0.7270 (tmm) cc_final: 0.6652 (ttp) REVERT: A 1036 THR cc_start: 0.9357 (p) cc_final: 0.9118 (p) REVERT: A 1037 LEU cc_start: 0.8722 (mt) cc_final: 0.8477 (mt) REVERT: A 3401 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8453 (tm-30) REVERT: A 3428 MET cc_start: 0.6232 (mmp) cc_final: 0.5951 (mmt) REVERT: A 3563 GLN cc_start: 0.5808 (OUTLIER) cc_final: 0.5494 (pm20) REVERT: A 3689 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7899 (mpp) REVERT: A 3854 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: A 4672 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6624 (pmm) REVERT: A 4707 MET cc_start: 0.8018 (ttt) cc_final: 0.7770 (ttp) REVERT: G 50 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7918 (mtm110) REVERT: I 14 LYS cc_start: 0.9404 (tptt) cc_final: 0.8924 (tppt) REVERT: I 106 LEU cc_start: 0.8198 (mm) cc_final: 0.7807 (mm) REVERT: I 110 MET cc_start: 0.8188 (mmm) cc_final: 0.7396 (mpt) REVERT: I 146 MET cc_start: 0.7578 (ppp) cc_final: 0.7178 (ppp) REVERT: J 14 LYS cc_start: 0.9508 (tptt) cc_final: 0.9062 (tppt) REVERT: J 50 GLN cc_start: 0.9266 (mm110) cc_final: 0.8895 (mm110) REVERT: J 76 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8991 (ttpp) REVERT: J 77 MET cc_start: 0.8707 (ppp) cc_final: 0.8364 (ppp) REVERT: J 125 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6463 (tpt) REVERT: K 14 LYS cc_start: 0.9401 (tptt) cc_final: 0.9009 (tppt) REVERT: K 50 GLN cc_start: 0.9218 (mm110) cc_final: 0.8770 (mm110) REVERT: K 110 MET cc_start: 0.7619 (mmm) cc_final: 0.7360 (mmm) REVERT: K 125 MET cc_start: 0.7182 (mtt) cc_final: 0.5287 (tpt) REVERT: L 14 LYS cc_start: 0.9522 (tptt) cc_final: 0.9015 (tppt) REVERT: L 50 GLN cc_start: 0.9332 (mm110) cc_final: 0.8888 (mm110) REVERT: L 72 MET cc_start: 0.8845 (ptp) cc_final: 0.8532 (ptp) REVERT: L 75 ARG cc_start: 0.9272 (tmm-80) cc_final: 0.8676 (ttp80) REVERT: L 77 MET cc_start: 0.8891 (ppp) cc_final: 0.8653 (ppp) REVERT: L 145 MET cc_start: 0.8102 (pp-130) cc_final: 0.7754 (mmp) REVERT: B 81 MET cc_start: 0.7791 (tpt) cc_final: 0.7521 (tpt) REVERT: B 241 MET cc_start: 0.6043 (mmp) cc_final: 0.5735 (mpm) REVERT: B 309 MET cc_start: 0.6457 (pmm) cc_final: 0.6084 (pmm) REVERT: B 678 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7313 (ttt) REVERT: B 995 MET cc_start: 0.7566 (tmm) cc_final: 0.7209 (ttp) REVERT: B 2895 PHE cc_start: 0.8876 (t80) cc_final: 0.8215 (t80) REVERT: B 3362 LEU cc_start: 0.8947 (pp) cc_final: 0.8706 (pt) REVERT: B 3366 LEU cc_start: 0.9061 (tt) cc_final: 0.8680 (pp) REVERT: B 3439 MET cc_start: 0.3494 (ppp) cc_final: 0.2891 (pmm) REVERT: B 3472 ARG cc_start: 0.7923 (mpt180) cc_final: 0.7563 (mpt180) REVERT: B 3689 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7556 (mpp) REVERT: B 3718 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: B 3819 MET cc_start: 0.6637 (pmm) cc_final: 0.5519 (pmm) REVERT: B 4186 MET cc_start: 0.8580 (mmm) cc_final: 0.8215 (mmp) REVERT: B 4884 MET cc_start: 0.6561 (mtp) cc_final: 0.6095 (mtm) REVERT: C 81 MET cc_start: 0.7184 (tpp) cc_final: 0.6875 (tpt) REVERT: C 241 MET cc_start: 0.5928 (mmp) cc_final: 0.5479 (mpm) REVERT: C 309 MET cc_start: 0.6038 (pmm) cc_final: 0.5828 (pmm) REVERT: C 1037 LEU cc_start: 0.8923 (mt) cc_final: 0.8665 (mt) REVERT: C 2468 MET cc_start: 0.8652 (mpp) cc_final: 0.7856 (mpp) REVERT: C 3369 PHE cc_start: 0.7368 (m-80) cc_final: 0.6914 (m-80) REVERT: C 4817 MET cc_start: 0.8875 (mmt) cc_final: 0.8548 (mmt) REVERT: D 114 LEU cc_start: 0.8174 (tm) cc_final: 0.7928 (tm) REVERT: D 241 MET cc_start: 0.6009 (mmp) cc_final: 0.5502 (mpt) REVERT: D 964 MET cc_start: 0.2076 (mpt) cc_final: 0.1559 (mpt) REVERT: D 982 ASP cc_start: 0.8740 (t0) cc_final: 0.8236 (p0) REVERT: D 995 MET cc_start: 0.7437 (tmm) cc_final: 0.7140 (tmm) REVERT: D 1037 LEU cc_start: 0.8816 (mt) cc_final: 0.8576 (mt) REVERT: D 1896 MET cc_start: 0.8078 (ttp) cc_final: 0.7852 (ttm) REVERT: D 3095 ASN cc_start: 0.7957 (m-40) cc_final: 0.7571 (m110) REVERT: D 3367 TYR cc_start: 0.8078 (m-10) cc_final: 0.7807 (m-10) REVERT: D 3369 PHE cc_start: 0.7336 (m-80) cc_final: 0.6829 (m-80) REVERT: D 3491 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8378 (pp) REVERT: D 3689 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7569 (mpp) outliers start: 94 outliers final: 44 residues processed: 998 average time/residue: 2.2299 time to fit residues: 3193.7110 Evaluate side-chains 993 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 937 time to evaluate : 12.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1495 SER Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3336 GLU Chi-restraints excluded: chain B residue 3367 TYR Chi-restraints excluded: chain B residue 3373 LEU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3718 GLU Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2830 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 2903 VAL Chi-restraints excluded: chain C residue 3336 GLU Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 1495 SER Chi-restraints excluded: chain D residue 2872 VAL Chi-restraints excluded: chain D residue 2903 VAL Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3336 GLU Chi-restraints excluded: chain D residue 3491 LEU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 1613 optimal weight: 5.9990 chunk 1699 optimal weight: 0.8980 chunk 1550 optimal weight: 3.9990 chunk 1652 optimal weight: 2.9990 chunk 1698 optimal weight: 10.0000 chunk 994 optimal weight: 10.0000 chunk 719 optimal weight: 7.9990 chunk 1297 optimal weight: 50.0000 chunk 507 optimal weight: 0.6980 chunk 1493 optimal weight: 7.9990 chunk 1563 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3256 ASN ** A3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 61 ASN I 136 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 HIS ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3256 ASN ** B3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2998 ASN D3256 ASN ** D3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 151000 Z= 0.250 Angle : 0.636 19.044 204000 Z= 0.314 Chirality : 0.041 0.290 22360 Planarity : 0.004 0.086 26308 Dihedral : 4.994 75.046 20261 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 0.63 % Allowed : 10.56 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.19 (0.06), residues: 18336 helix: 1.88 (0.05), residues: 9668 sheet: 0.03 (0.12), residues: 1732 loop : -0.55 (0.07), residues: 6936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A2741 HIS 0.010 0.001 HIS D3233 PHE 0.033 0.002 PHE A3369 TYR 0.020 0.001 TYR C2771 ARG 0.019 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 946 time to evaluate : 12.874 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: A 36 CYS cc_start: 0.8289 (m) cc_final: 0.7688 (t) REVERT: A 81 MET cc_start: 0.7506 (tpp) cc_final: 0.7164 (tpt) REVERT: A 241 MET cc_start: 0.5683 (mmp) cc_final: 0.5424 (mpm) REVERT: A 309 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5734 (pmm) REVERT: A 995 MET cc_start: 0.7292 (tmm) cc_final: 0.6687 (ttp) REVERT: A 1036 THR cc_start: 0.9352 (p) cc_final: 0.9100 (p) REVERT: A 1037 LEU cc_start: 0.8716 (mt) cc_final: 0.8452 (mt) REVERT: A 3401 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8372 (tp30) REVERT: A 3428 MET cc_start: 0.6223 (mmp) cc_final: 0.5955 (mmm) REVERT: A 3605 MET cc_start: 0.7053 (tmm) cc_final: 0.6349 (tmm) REVERT: A 3689 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7961 (mpp) REVERT: A 3854 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: A 4672 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6607 (pmm) REVERT: E 103 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: I 50 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8859 (mm-40) REVERT: I 106 LEU cc_start: 0.8227 (mm) cc_final: 0.7822 (mm) REVERT: I 110 MET cc_start: 0.8196 (mmm) cc_final: 0.7383 (mpt) REVERT: I 146 MET cc_start: 0.7647 (ppp) cc_final: 0.7370 (ppp) REVERT: J 14 LYS cc_start: 0.9507 (tptt) cc_final: 0.9059 (tppt) REVERT: J 50 GLN cc_start: 0.9248 (mm110) cc_final: 0.8864 (mm110) REVERT: J 76 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.9022 (ttpp) REVERT: J 77 MET cc_start: 0.8763 (ppp) cc_final: 0.8196 (ppp) REVERT: J 125 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6505 (tpt) REVERT: J 145 MET cc_start: 0.8114 (ppp) cc_final: 0.7707 (mmt) REVERT: K 14 LYS cc_start: 0.9403 (tptt) cc_final: 0.9000 (tppt) REVERT: K 50 GLN cc_start: 0.9179 (mm110) cc_final: 0.8739 (mm110) REVERT: K 110 MET cc_start: 0.7683 (mmm) cc_final: 0.7422 (mmm) REVERT: K 125 MET cc_start: 0.7223 (mtt) cc_final: 0.5067 (tpt) REVERT: L 14 LYS cc_start: 0.9520 (tptt) cc_final: 0.9007 (tppt) REVERT: L 50 GLN cc_start: 0.9300 (mm110) cc_final: 0.8850 (mm110) REVERT: L 72 MET cc_start: 0.8842 (ptp) cc_final: 0.8636 (ptp) REVERT: L 75 ARG cc_start: 0.9263 (tmm-80) cc_final: 0.8657 (ttp80) REVERT: L 145 MET cc_start: 0.8089 (pp-130) cc_final: 0.7686 (mmp) REVERT: B 81 MET cc_start: 0.7798 (tpt) cc_final: 0.7528 (tpt) REVERT: B 241 MET cc_start: 0.6023 (mmp) cc_final: 0.5737 (mpm) REVERT: B 309 MET cc_start: 0.6371 (pmm) cc_final: 0.5978 (pmm) REVERT: B 678 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7333 (ttt) REVERT: B 995 MET cc_start: 0.7572 (tmm) cc_final: 0.7225 (ttp) REVERT: B 2895 PHE cc_start: 0.8877 (t80) cc_final: 0.8211 (t80) REVERT: B 3439 MET cc_start: 0.3536 (ppp) cc_final: 0.2926 (pmm) REVERT: B 3472 ARG cc_start: 0.7991 (mpt180) cc_final: 0.7604 (mpt180) REVERT: B 3689 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7677 (mpp) REVERT: B 3718 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: B 4186 MET cc_start: 0.8591 (mmm) cc_final: 0.8191 (mmp) REVERT: B 4884 MET cc_start: 0.6602 (mtp) cc_final: 0.6126 (mtm) REVERT: C 81 MET cc_start: 0.7211 (tpp) cc_final: 0.6901 (tpt) REVERT: C 241 MET cc_start: 0.5883 (mmp) cc_final: 0.5472 (mpm) REVERT: C 309 MET cc_start: 0.6137 (pmm) cc_final: 0.5793 (pmm) REVERT: C 317 MET cc_start: 0.7680 (ptp) cc_final: 0.7471 (ptp) REVERT: C 995 MET cc_start: 0.7615 (tmm) cc_final: 0.7316 (tmm) REVERT: C 1037 LEU cc_start: 0.8919 (mt) cc_final: 0.8661 (mt) REVERT: C 1729 MET cc_start: 0.8499 (mmm) cc_final: 0.8253 (mmt) REVERT: C 2468 MET cc_start: 0.8674 (mpp) cc_final: 0.7901 (mpp) REVERT: C 2895 PHE cc_start: 0.9082 (t80) cc_final: 0.8823 (t80) REVERT: C 3369 PHE cc_start: 0.7368 (m-80) cc_final: 0.6912 (m-80) REVERT: C 3472 ARG cc_start: 0.7916 (mpt180) cc_final: 0.7553 (mpt180) REVERT: C 3819 MET cc_start: 0.6335 (pmm) cc_final: 0.5400 (pmm) REVERT: C 4817 MET cc_start: 0.8918 (mmt) cc_final: 0.8503 (mmt) REVERT: D 114 LEU cc_start: 0.8178 (tm) cc_final: 0.7931 (tm) REVERT: D 241 MET cc_start: 0.5999 (mmp) cc_final: 0.5492 (mpt) REVERT: D 309 MET cc_start: 0.6097 (pmm) cc_final: 0.5716 (pmm) REVERT: D 982 ASP cc_start: 0.8756 (t0) cc_final: 0.8239 (p0) REVERT: D 995 MET cc_start: 0.7413 (tmm) cc_final: 0.7149 (tmm) REVERT: D 1037 LEU cc_start: 0.8824 (mt) cc_final: 0.8592 (mt) REVERT: D 1896 MET cc_start: 0.8067 (ttp) cc_final: 0.7844 (ttm) REVERT: D 3367 TYR cc_start: 0.8030 (m-10) cc_final: 0.7743 (m-10) REVERT: D 3369 PHE cc_start: 0.7367 (m-80) cc_final: 0.6804 (m-80) REVERT: D 3491 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8360 (pp) REVERT: D 3689 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7583 (mpp) REVERT: D 4002 MET cc_start: 0.8647 (tmm) cc_final: 0.8426 (tmm) outliers start: 94 outliers final: 49 residues processed: 991 average time/residue: 2.3105 time to fit residues: 3280.1387 Evaluate side-chains 994 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 933 time to evaluate : 12.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 100 TYR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 ASN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain B residue 1168 MET Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3336 GLU Chi-restraints excluded: chain B residue 3367 TYR Chi-restraints excluded: chain B residue 3373 LEU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3718 GLU Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2830 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 2903 VAL Chi-restraints excluded: chain C residue 3336 GLU Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 1495 SER Chi-restraints excluded: chain D residue 2872 VAL Chi-restraints excluded: chain D residue 2903 VAL Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3336 GLU Chi-restraints excluded: chain D residue 3491 LEU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 1646 optimal weight: 8.9990 chunk 1085 optimal weight: 9.9990 chunk 1747 optimal weight: 10.0000 chunk 1066 optimal weight: 20.0000 chunk 829 optimal weight: 2.9990 chunk 1214 optimal weight: 20.0000 chunk 1833 optimal weight: 9.9990 chunk 1687 optimal weight: 30.0000 chunk 1459 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 1127 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2995 HIS A3256 ASN A3563 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2729 HIS ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3256 ASN ** B3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2998 ASN C3233 HIS C3256 ASN ** C3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 151000 Z= 0.405 Angle : 0.691 20.563 204000 Z= 0.341 Chirality : 0.043 0.331 22360 Planarity : 0.004 0.084 26308 Dihedral : 5.113 77.331 20261 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 0.51 % Allowed : 10.77 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.09 (0.06), residues: 18336 helix: 1.80 (0.05), residues: 9644 sheet: 0.01 (0.13), residues: 1704 loop : -0.58 (0.07), residues: 6988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP B2741 HIS 0.010 0.001 HIS D3732 PHE 0.032 0.002 PHE A2199 TYR 0.078 0.002 TYR K 100 ARG 0.020 0.001 ARG H 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36672 Ramachandran restraints generated. 18336 Oldfield, 0 Emsley, 18336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 957 time to evaluate : 12.843 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: A 36 CYS cc_start: 0.8309 (m) cc_final: 0.7713 (t) REVERT: A 81 MET cc_start: 0.7555 (tpp) cc_final: 0.7280 (tpt) REVERT: A 111 ARG cc_start: 0.7517 (tpp-160) cc_final: 0.7176 (mmp80) REVERT: A 241 MET cc_start: 0.5715 (mmp) cc_final: 0.5325 (mpm) REVERT: A 309 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5709 (pmm) REVERT: A 317 MET cc_start: 0.7536 (pmm) cc_final: 0.7119 (ptp) REVERT: A 1036 THR cc_start: 0.9381 (p) cc_final: 0.9144 (p) REVERT: A 1037 LEU cc_start: 0.8744 (mt) cc_final: 0.8497 (mt) REVERT: A 2835 ARG cc_start: 0.8449 (mmp-170) cc_final: 0.7995 (mmp80) REVERT: A 3076 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7880 (mmtm) REVERT: A 3366 LEU cc_start: 0.8921 (tt) cc_final: 0.8479 (pp) REVERT: A 3401 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8367 (tp30) REVERT: A 3428 MET cc_start: 0.6251 (mmp) cc_final: 0.5988 (mmm) REVERT: A 3472 ARG cc_start: 0.8164 (mpt180) cc_final: 0.7829 (mpt180) REVERT: A 3563 GLN cc_start: 0.5984 (OUTLIER) cc_final: 0.5642 (pm20) REVERT: A 3605 MET cc_start: 0.7098 (tmm) cc_final: 0.6432 (tmm) REVERT: A 3689 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8031 (mpp) REVERT: A 3819 MET cc_start: 0.5959 (pmm) cc_final: 0.5133 (pmm) REVERT: A 3854 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: A 4672 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6645 (pmm) REVERT: G 50 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7936 (mtm110) REVERT: I 14 LYS cc_start: 0.9409 (tptt) cc_final: 0.8932 (tppt) REVERT: I 50 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8696 (mm110) REVERT: I 106 LEU cc_start: 0.8274 (mm) cc_final: 0.8013 (mm) REVERT: I 110 MET cc_start: 0.8268 (mmm) cc_final: 0.7534 (mpt) REVERT: J 14 LYS cc_start: 0.9507 (tptt) cc_final: 0.9056 (tppt) REVERT: J 50 GLN cc_start: 0.9246 (mm110) cc_final: 0.8885 (mm110) REVERT: J 75 ARG cc_start: 0.9066 (tmm-80) cc_final: 0.8413 (ttp80) REVERT: J 76 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8870 (ttpp) REVERT: J 77 MET cc_start: 0.8833 (ppp) cc_final: 0.8339 (ppp) REVERT: J 125 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6492 (tpt) REVERT: K 14 LYS cc_start: 0.9409 (tptt) cc_final: 0.9008 (tppt) REVERT: K 50 GLN cc_start: 0.9137 (mm110) cc_final: 0.8717 (mm110) REVERT: K 125 MET cc_start: 0.7262 (mtt) cc_final: 0.5128 (tpt) REVERT: L 14 LYS cc_start: 0.9520 (tptt) cc_final: 0.8999 (tppt) REVERT: L 50 GLN cc_start: 0.9259 (mm110) cc_final: 0.8856 (mm110) REVERT: L 75 ARG cc_start: 0.9296 (tmm-80) cc_final: 0.8559 (ttp80) REVERT: L 145 MET cc_start: 0.8094 (pp-130) cc_final: 0.7723 (mmt) REVERT: B 81 MET cc_start: 0.7831 (tpt) cc_final: 0.7564 (tpt) REVERT: B 241 MET cc_start: 0.6089 (mmp) cc_final: 0.5682 (mpm) REVERT: B 309 MET cc_start: 0.6587 (pmm) cc_final: 0.6237 (pmm) REVERT: B 678 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7318 (ttt) REVERT: B 995 MET cc_start: 0.7624 (tmm) cc_final: 0.7299 (ttp) REVERT: B 2895 PHE cc_start: 0.8934 (t80) cc_final: 0.8290 (t80) REVERT: B 3472 ARG cc_start: 0.8140 (mpt180) cc_final: 0.7819 (mpt180) REVERT: B 3689 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7797 (mpp) REVERT: B 3718 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: B 3819 MET cc_start: 0.6444 (pmm) cc_final: 0.5226 (pmm) REVERT: B 4186 MET cc_start: 0.8617 (mmm) cc_final: 0.8325 (mmp) REVERT: C 81 MET cc_start: 0.7264 (tpp) cc_final: 0.6941 (tpt) REVERT: C 241 MET cc_start: 0.5844 (mmp) cc_final: 0.5530 (mpm) REVERT: C 309 MET cc_start: 0.6163 (pmm) cc_final: 0.5828 (pmm) REVERT: C 317 MET cc_start: 0.7707 (ptp) cc_final: 0.7484 (ptp) REVERT: C 995 MET cc_start: 0.7622 (tmm) cc_final: 0.7338 (tmm) REVERT: C 1037 LEU cc_start: 0.8935 (mt) cc_final: 0.8682 (mt) REVERT: C 1729 MET cc_start: 0.8502 (mmm) cc_final: 0.8296 (mmt) REVERT: C 2844 MET cc_start: 0.9026 (mtp) cc_final: 0.8744 (mtt) REVERT: C 3369 PHE cc_start: 0.7405 (m-80) cc_final: 0.6951 (m-80) REVERT: C 3472 ARG cc_start: 0.7952 (mpt180) cc_final: 0.7605 (mpt180) REVERT: C 3819 MET cc_start: 0.6310 (pmm) cc_final: 0.5403 (pmm) REVERT: D 114 LEU cc_start: 0.8183 (tm) cc_final: 0.7940 (tm) REVERT: D 241 MET cc_start: 0.6055 (mmp) cc_final: 0.5669 (ttm) REVERT: D 309 MET cc_start: 0.6245 (pmm) cc_final: 0.5850 (pmm) REVERT: D 982 ASP cc_start: 0.8741 (t0) cc_final: 0.8232 (p0) REVERT: D 995 MET cc_start: 0.7377 (tmm) cc_final: 0.7139 (tmm) REVERT: D 1037 LEU cc_start: 0.8843 (mt) cc_final: 0.8603 (mt) REVERT: D 1896 MET cc_start: 0.8136 (ttp) cc_final: 0.7891 (ttm) REVERT: D 1975 MET cc_start: 0.8386 (ppp) cc_final: 0.8038 (ptp) REVERT: D 3273 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8482 (mtt) REVERT: D 3367 TYR cc_start: 0.8056 (m-10) cc_final: 0.7764 (m-10) REVERT: D 3369 PHE cc_start: 0.7429 (m-80) cc_final: 0.6830 (m-80) REVERT: D 3491 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8360 (pp) REVERT: D 3689 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7657 (mpp) REVERT: D 4502 MET cc_start: 0.7676 (mtm) cc_final: 0.7428 (mtm) outliers start: 75 outliers final: 48 residues processed: 996 average time/residue: 2.3062 time to fit residues: 3304.2836 Evaluate side-chains 1007 residues out of total 16192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 946 time to evaluate : 12.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 142 PHE Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1168 MET Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3336 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3718 GLU Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2830 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 2903 VAL Chi-restraints excluded: chain C residue 3336 GLU Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 1495 SER Chi-restraints excluded: chain D residue 2872 VAL Chi-restraints excluded: chain D residue 2903 VAL Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3336 GLU Chi-restraints excluded: chain D residue 3491 LEU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1840 random chunks: chunk 895 optimal weight: 1.9990 chunk 1159 optimal weight: 7.9990 chunk 1554 optimal weight: 0.8980 chunk 447 optimal weight: 9.9990 chunk 1345 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 405 optimal weight: 0.6980 chunk 1462 optimal weight: 7.9990 chunk 611 optimal weight: 10.0000 chunk 1501 optimal weight: 0.0570 chunk 185 optimal weight: 0.5980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2995 HIS A3256 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3256 ASN ** B3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2998 ASN C3256 ASN ** C3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.056294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042303 restraints weight = 1125976.442| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.58 r_work: 0.2903 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.403 151000 Z= 0.380 Angle : 0.746 59.183 204000 Z= 0.391 Chirality : 0.042 0.608 22360 Planarity : 0.005 0.155 26308 Dihedral : 5.111 77.218 20261 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 0.48 % Allowed : 10.87 % Favored : 88.65 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.10 (0.06), residues: 18336 helix: 1.81 (0.05), residues: 9640 sheet: -0.00 (0.13), residues: 1704 loop : -0.58 (0.07), residues: 6992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP B2741 HIS 0.009 0.001 HIS H 26 PHE 0.254 0.002 PHE K 142 TYR 0.063 0.002 TYR K 100 ARG 0.017 0.000 ARG H 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51069.43 seconds wall clock time: 887 minutes 17.93 seconds (53237.93 seconds total)