Starting phenix.real_space_refine on Tue Mar 19 10:31:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkk_32566/03_2024/7wkk_32566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkk_32566/03_2024/7wkk_32566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkk_32566/03_2024/7wkk_32566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkk_32566/03_2024/7wkk_32566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkk_32566/03_2024/7wkk_32566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkk_32566/03_2024/7wkk_32566.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 55365 2.51 5 N 18728 2.21 5 O 18728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 92821 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1684, 8339 Classifications: {'peptide': 1684} Incomplete info: {'truncation_to_alanine': 1493} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1628} Chain breaks: 20 Unresolved chain link angles: 55 Unresolved non-hydrogen bonds: 5355 Unresolved non-hydrogen angles: 6843 Unresolved non-hydrogen dihedrals: 4399 Unresolved non-hydrogen chiralities: 539 Planarities with less than four sites: {'GLN:plan1': 108, 'ASP:plan': 79, 'TYR:plan': 50, 'ASN:plan1': 51, 'TRP:plan': 17, 'HIS:plan': 46, 'PHE:plan': 58, 'GLU:plan': 110, 'ARG:plan': 103} Unresolved non-hydrogen planarities: 2858 Chain: "B" Number of atoms: 7347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1482, 7347 Classifications: {'peptide': 1482} Incomplete info: {'truncation_to_alanine': 1329} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1431} Chain breaks: 16 Unresolved chain link angles: 50 Unresolved non-hydrogen bonds: 4731 Unresolved non-hydrogen angles: 6071 Unresolved non-hydrogen dihedrals: 3921 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 89, 'HIS:plan': 43, 'TYR:plan': 47, 'ASN:plan1': 42, 'TRP:plan': 19, 'ASP:plan': 58, 'PHE:plan': 60, 'GLU:plan': 90, 'ARG:plan': 75} Unresolved non-hydrogen planarities: 2466 Chain: "C" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 3144 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 565} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 9 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 2124 Unresolved non-hydrogen angles: 2701 Unresolved non-hydrogen dihedrals: 1765 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'GLN:plan1': 37, 'HIS:plan': 13, 'TYR:plan': 27, 'ASN:plan1': 29, 'TRP:plan': 4, 'ASP:plan': 36, 'PHE:plan': 33, 'GLU:plan': 48, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1243 Chain: "D" Number of atoms: 5524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 5524 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 991} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 43, 'TRANS': 1068} Chain breaks: 16 Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 3568 Unresolved non-hydrogen angles: 4569 Unresolved non-hydrogen dihedrals: 2966 Unresolved non-hydrogen chiralities: 326 Planarities with less than four sites: {'GLN:plan1': 69, 'ASP:plan': 62, 'TYR:plan': 36, 'ASN:plan1': 39, 'TRP:plan': 13, 'HIS:plan': 32, 'PHE:plan': 45, 'GLU:plan': 72, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1966 Chain: "E" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 3105 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 558} Link IDs: {'PTRANS': 13, 'TRANS': 611} Chain breaks: 11 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2105 Unresolved non-hydrogen angles: 2671 Unresolved non-hydrogen dihedrals: 1747 Unresolved non-hydrogen chiralities: 171 Planarities with less than four sites: {'GLN:plan1': 38, 'HIS:plan': 11, 'TYR:plan': 27, 'ASN:plan1': 30, 'TRP:plan': 4, 'ASP:plan': 33, 'PHE:plan': 32, 'GLU:plan': 47, 'ARG:plan': 47} Unresolved non-hydrogen planarities: 1236 Chain: "F" Number of atoms: 5417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 5417 Classifications: {'peptide': 1094} Incomplete info: {'truncation_to_alanine': 968} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1057} Chain breaks: 17 Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 3463 Unresolved non-hydrogen angles: 4432 Unresolved non-hydrogen dihedrals: 2872 Unresolved non-hydrogen chiralities: 318 Planarities with less than four sites: {'GLN:plan1': 64, 'ASP:plan': 58, 'TYR:plan': 35, 'ASN:plan1': 43, 'TRP:plan': 13, 'HIS:plan': 32, 'PHE:plan': 41, 'GLU:plan': 77, 'ARG:plan': 57} Unresolved non-hydrogen planarities: 1920 Chain: "G" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1063 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 722 Unresolved non-hydrogen angles: 911 Unresolved non-hydrogen dihedrals: 589 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 7, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 402 Chain: "H" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 813 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 706 Unresolved non-hydrogen dihedrals: 449 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 20, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 329 Chain: "I" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 853 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 4, 'TRANS': 166} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 687 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 307 Chain: "J" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 963 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 540 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 356 Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 778 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 529 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 17, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 304 Chain: "K" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 829 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 4, 'TRANS': 161} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 528 Unresolved non-hydrogen angles: 665 Unresolved non-hydrogen dihedrals: 426 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 294 Chain: "M" Number of atoms: 4296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 4296 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 766} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 828} Chain breaks: 7 Unresolved chain link angles: 40 Unresolved non-hydrogen bonds: 2679 Unresolved non-hydrogen angles: 3433 Unresolved non-hydrogen dihedrals: 2208 Unresolved non-hydrogen chiralities: 255 Planarities with less than four sites: {'GLN:plan1': 50, 'HIS:plan': 24, 'TYR:plan': 23, 'ASN:plan1': 39, 'TRP:plan': 8, 'ASP:plan': 48, 'PHE:plan': 35, 'GLU:plan': 53, 'ARG:plan': 42} Unresolved non-hydrogen planarities: 1446 Chain: "a" Number of atoms: 8268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1669, 8268 Classifications: {'peptide': 1669} Incomplete info: {'truncation_to_alanine': 1485} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1615} Chain breaks: 21 Unresolved chain link angles: 53 Unresolved non-hydrogen bonds: 5335 Unresolved non-hydrogen angles: 6818 Unresolved non-hydrogen dihedrals: 4382 Unresolved non-hydrogen chiralities: 538 Planarities with less than four sites: {'GLN:plan1': 107, 'ASP:plan': 79, 'TYR:plan': 50, 'ASN:plan1': 50, 'TRP:plan': 17, 'HIS:plan': 46, 'PHE:plan': 58, 'GLU:plan': 110, 'ARG:plan': 103} Unresolved non-hydrogen planarities: 2851 Chain: "b" Number of atoms: 7347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1482, 7347 Classifications: {'peptide': 1482} Incomplete info: {'truncation_to_alanine': 1329} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1431} Chain breaks: 16 Unresolved chain link angles: 50 Unresolved non-hydrogen bonds: 4731 Unresolved non-hydrogen angles: 6071 Unresolved non-hydrogen dihedrals: 3921 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 89, 'HIS:plan': 43, 'TYR:plan': 47, 'ASN:plan1': 42, 'TRP:plan': 19, 'ASP:plan': 58, 'PHE:plan': 60, 'GLU:plan': 90, 'ARG:plan': 75} Unresolved non-hydrogen planarities: 2466 Chain: "c" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 3144 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 565} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 9 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 2124 Unresolved non-hydrogen angles: 2701 Unresolved non-hydrogen dihedrals: 1765 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'GLN:plan1': 37, 'HIS:plan': 13, 'TYR:plan': 27, 'ASN:plan1': 29, 'TRP:plan': 4, 'ASP:plan': 36, 'PHE:plan': 33, 'GLU:plan': 48, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1243 Chain: "d" Number of atoms: 5563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 5563 Classifications: {'peptide': 1123} Incomplete info: {'truncation_to_alanine': 997} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 1077} Chain breaks: 17 Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 3586 Unresolved non-hydrogen angles: 4592 Unresolved non-hydrogen dihedrals: 2979 Unresolved non-hydrogen chiralities: 327 Planarities with less than four sites: {'GLN:plan1': 70, 'ASP:plan': 62, 'TYR:plan': 36, 'ASN:plan1': 40, 'TRP:plan': 13, 'HIS:plan': 32, 'PHE:plan': 45, 'GLU:plan': 74, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1981 Chain: "e" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 3105 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 558} Link IDs: {'PTRANS': 13, 'TRANS': 611} Chain breaks: 11 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2105 Unresolved non-hydrogen angles: 2671 Unresolved non-hydrogen dihedrals: 1747 Unresolved non-hydrogen chiralities: 171 Planarities with less than four sites: {'GLN:plan1': 38, 'HIS:plan': 11, 'TYR:plan': 27, 'ASN:plan1': 30, 'TRP:plan': 4, 'ASP:plan': 33, 'PHE:plan': 32, 'GLU:plan': 47, 'ARG:plan': 47} Unresolved non-hydrogen planarities: 1236 Chain: "f" Number of atoms: 5432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 5432 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 970} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1060} Chain breaks: 17 Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 3472 Unresolved non-hydrogen angles: 4443 Unresolved non-hydrogen dihedrals: 2879 Unresolved non-hydrogen chiralities: 318 Planarities with less than four sites: {'GLN:plan1': 64, 'ASP:plan': 59, 'TYR:plan': 35, 'ASN:plan1': 43, 'TRP:plan': 13, 'HIS:plan': 32, 'PHE:plan': 41, 'GLU:plan': 77, 'ARG:plan': 58} Unresolved non-hydrogen planarities: 1928 Chain: "g" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1063 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 722 Unresolved non-hydrogen angles: 911 Unresolved non-hydrogen dihedrals: 589 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 7, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 402 Chain: "h" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 813 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 706 Unresolved non-hydrogen dihedrals: 449 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 20, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 329 Chain: "i" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 853 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 4, 'TRANS': 166} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 687 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 307 Chain: "j" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 963 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 540 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 356 Chain: "l" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 778 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 529 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 17, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 304 Chain: "k" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 829 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 4, 'TRANS': 161} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 528 Unresolved non-hydrogen angles: 665 Unresolved non-hydrogen dihedrals: 426 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 294 Chain: "m" Number of atoms: 4296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 4296 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 766} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 828} Chain breaks: 7 Unresolved chain link angles: 40 Unresolved non-hydrogen bonds: 2679 Unresolved non-hydrogen angles: 3433 Unresolved non-hydrogen dihedrals: 2208 Unresolved non-hydrogen chiralities: 255 Planarities with less than four sites: {'GLN:plan1': 50, 'HIS:plan': 24, 'TYR:plan': 23, 'ASN:plan1': 39, 'TRP:plan': 8, 'ASP:plan': 48, 'PHE:plan': 35, 'GLU:plan': 53, 'ARG:plan': 42} Unresolved non-hydrogen planarities: 1446 Chain: "O" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 1805 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 310} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 334} Chain breaks: 5 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 1100 Unresolved non-hydrogen angles: 1436 Unresolved non-hydrogen dihedrals: 960 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 13, 'ASP:plan': 15, 'PHE:plan': 20, 'GLU:plan': 15, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 575 Chain: "N" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 2143 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 387} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1435 Unresolved non-hydrogen angles: 1860 Unresolved non-hydrogen dihedrals: 1235 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 7, 'TYR:plan': 20, 'ASN:plan1': 7, 'TRP:plan': 9, 'HIS:plan': 16, 'PHE:plan': 27, 'GLU:plan': 17, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 759 Chain: "o" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 1805 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 310} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 334} Chain breaks: 5 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 1100 Unresolved non-hydrogen angles: 1436 Unresolved non-hydrogen dihedrals: 960 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 13, 'ASP:plan': 15, 'PHE:plan': 20, 'GLU:plan': 15, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 575 Chain: "n" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 2143 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 387} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1435 Unresolved non-hydrogen angles: 1860 Unresolved non-hydrogen dihedrals: 1235 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 7, 'TYR:plan': 20, 'ASN:plan1': 7, 'TRP:plan': 9, 'HIS:plan': 16, 'PHE:plan': 27, 'GLU:plan': 17, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 759 Time building chain proxies: 44.83, per 1000 atoms: 0.48 Number of scatterers: 92821 At special positions: 0 Unit cell: (352.298, 306.527, 362.007, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 18728 8.00 N 18728 7.00 C 55365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.06 Conformation dependent library (CDL) restraints added in 18.2 seconds 36404 Ramachandran restraints generated. 18202 Oldfield, 0 Emsley, 18202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 35818 Finding SS restraints... Secondary structure from input PDB file: 866 helices and 92 sheets defined 71.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.80 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 32 through 46 removed outlier: 4.166A pdb=" N HIS A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 118 Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 126 through 153 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 210 through 239 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 299 through 302 removed outlier: 3.784A pdb=" N MET A 302 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.888A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.810A pdb=" N GLN A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.752A pdb=" N VAL A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 382 through 400 Proline residue: A 397 - end of helix removed outlier: 3.774A pdb=" N MET A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 424 removed outlier: 3.593A pdb=" N VAL A 404 " --> pdb=" O MET A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 447 removed outlier: 3.577A pdb=" N TYR A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'A' and resid 489 through 498 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.736A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'A' and resid 551 through 569 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.628A pdb=" N GLU A 617 " --> pdb=" O LEU A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 removed outlier: 3.667A pdb=" N GLN A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 653 through 668 removed outlier: 3.508A pdb=" N SER A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 695 removed outlier: 3.612A pdb=" N GLU A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 713 Processing helix chain 'A' and resid 729 through 740 Processing helix chain 'A' and resid 752 through 773 removed outlier: 4.020A pdb=" N TRP A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 removed outlier: 4.176A pdb=" N PHE A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 781 " --> pdb=" O PRO A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 781' Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 810 through 830 removed outlier: 3.771A pdb=" N TYR A 830 " --> pdb=" O GLN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 868 removed outlier: 4.333A pdb=" N ASN A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 881 removed outlier: 3.700A pdb=" N LEU A 879 " --> pdb=" O PRO A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 removed outlier: 3.530A pdb=" N TYR A 899 " --> pdb=" O ASN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 903 Processing helix chain 'A' and resid 906 through 922 removed outlier: 3.848A pdb=" N ALA A 910 " --> pdb=" O ASN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 936 removed outlier: 3.752A pdb=" N GLN A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 953 Processing helix chain 'A' and resid 971 through 994 removed outlier: 3.853A pdb=" N MET A 994 " --> pdb=" O THR A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.867A pdb=" N PHE A1002 " --> pdb=" O ASN A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1015 Processing helix chain 'A' and resid 1021 through 1025 Processing helix chain 'A' and resid 1028 through 1039 removed outlier: 3.762A pdb=" N SER A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 removed outlier: 4.058A pdb=" N TRP A1051 " --> pdb=" O PRO A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1070 removed outlier: 3.626A pdb=" N CYS A1070 " --> pdb=" O GLN A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1085 removed outlier: 4.396A pdb=" N GLY A1075 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Proline residue: A1076 - end of helix removed outlier: 3.840A pdb=" N GLN A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1093 Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1142 Processing helix chain 'A' and resid 1178 through 1187 removed outlier: 3.904A pdb=" N ILE A1187 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1214 Processing helix chain 'A' and resid 1226 through 1240 Processing helix chain 'A' and resid 1249 through 1294 Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1301 through 1322 removed outlier: 3.800A pdb=" N ASP A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1328 No H-bonds generated for 'chain 'A' and resid 1326 through 1328' Processing helix chain 'A' and resid 1329 through 1352 removed outlier: 4.004A pdb=" N VAL A1333 " --> pdb=" O LEU A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1409 Processing helix chain 'A' and resid 1413 through 1430 Processing helix chain 'A' and resid 1457 through 1472 removed outlier: 3.551A pdb=" N TYR A1472 " --> pdb=" O ILE A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1487 removed outlier: 3.942A pdb=" N MET A1477 " --> pdb=" O GLY A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1505 Processing helix chain 'A' and resid 1509 through 1518 Processing helix chain 'A' and resid 1519 through 1539 Processing helix chain 'A' and resid 1546 through 1561 removed outlier: 3.750A pdb=" N TYR A1550 " --> pdb=" O LEU A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1575 Processing helix chain 'A' and resid 1576 through 1584 Processing helix chain 'A' and resid 1585 through 1589 Processing helix chain 'A' and resid 1611 through 1633 Proline residue: A1621 - end of helix Processing helix chain 'A' and resid 1637 through 1651 removed outlier: 3.871A pdb=" N ALA A1641 " --> pdb=" O HIS A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1660 Processing helix chain 'A' and resid 1665 through 1683 Processing helix chain 'A' and resid 1698 through 1722 removed outlier: 4.282A pdb=" N LEU A1718 " --> pdb=" O CYS A1714 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN A1719 " --> pdb=" O LEU A1715 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A1720 " --> pdb=" O ALA A1716 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1733 removed outlier: 3.511A pdb=" N SER A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A1733 " --> pdb=" O GLN A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1767 Processing helix chain 'A' and resid 1811 through 1841 Processing helix chain 'A' and resid 1848 through 1855 Processing helix chain 'A' and resid 1868 through 1913 Processing helix chain 'A' and resid 1958 through 1970 Processing helix chain 'A' and resid 1971 through 1990 removed outlier: 4.965A pdb=" N LYS A1987 " --> pdb=" O SER A1983 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL A1988 " --> pdb=" O LEU A1984 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A1989 " --> pdb=" O TYR A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1993 through 2007 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 27 through 38 Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.691A pdb=" N TYR B 49 " --> pdb=" O LEU B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 113 through 145 Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.594A pdb=" N LYS B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 196 through 225 Processing helix chain 'B' and resid 228 through 242 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.721A pdb=" N VAL B 254 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.742A pdb=" N VAL B 262 " --> pdb=" O MET B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 299 through 311 Processing helix chain 'B' and resid 318 through 334 removed outlier: 4.694A pdb=" N VAL B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.650A pdb=" N ARG B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 367 Processing helix chain 'B' and resid 371 through 392 Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.571A pdb=" N SER B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN B 398 " --> pdb=" O GLN B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 411 Processing helix chain 'B' and resid 415 through 423 removed outlier: 3.979A pdb=" N LEU B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 438 removed outlier: 4.032A pdb=" N LEU B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 455 removed outlier: 3.869A pdb=" N LEU B 447 " --> pdb=" O ARG B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 Processing helix chain 'B' and resid 537 through 553 Processing helix chain 'B' and resid 557 through 577 Proline residue: B 567 - end of helix removed outlier: 3.812A pdb=" N LEU B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 586 through 601 removed outlier: 4.152A pdb=" N TYR B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 623 Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.537A pdb=" N THR B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 672 removed outlier: 4.058A pdb=" N LEU B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 690 Processing helix chain 'B' and resid 693 through 699 removed outlier: 3.603A pdb=" N SER B 697 " --> pdb=" O SER B 694 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 698 " --> pdb=" O THR B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 710 removed outlier: 3.502A pdb=" N GLU B 710 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 715 removed outlier: 3.959A pdb=" N ASN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 742 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 768 through 779 Processing helix chain 'B' and resid 779 through 790 removed outlier: 4.337A pdb=" N THR B 783 " --> pdb=" O ILE B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 822 Processing helix chain 'B' and resid 831 through 837 Processing helix chain 'B' and resid 844 through 852 Processing helix chain 'B' and resid 853 through 855 No H-bonds generated for 'chain 'B' and resid 853 through 855' Processing helix chain 'B' and resid 859 through 876 Processing helix chain 'B' and resid 879 through 885 Processing helix chain 'B' and resid 887 through 901 Processing helix chain 'B' and resid 905 through 923 Processing helix chain 'B' and resid 923 through 932 removed outlier: 3.815A pdb=" N LEU B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B 932 " --> pdb=" O GLU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 961 Processing helix chain 'B' and resid 971 through 988 Processing helix chain 'B' and resid 990 through 1000 removed outlier: 3.581A pdb=" N LYS B1000 " --> pdb=" O VAL B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1009 Processing helix chain 'B' and resid 1023 through 1044 removed outlier: 3.674A pdb=" N LEU B1027 " --> pdb=" O GLU B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1063 Processing helix chain 'B' and resid 1064 through 1083 Processing helix chain 'B' and resid 1089 through 1110 Processing helix chain 'B' and resid 1118 through 1139 removed outlier: 4.004A pdb=" N VAL B1139 " --> pdb=" O ALA B1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1163 Processing helix chain 'B' and resid 1171 through 1186 Processing helix chain 'B' and resid 1188 through 1210 removed outlier: 3.582A pdb=" N VAL B1192 " --> pdb=" O ASP B1188 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B1193 " --> pdb=" O GLN B1189 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS B1194 " --> pdb=" O GLN B1190 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N THR B1195 " --> pdb=" O LEU B1191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B1210 " --> pdb=" O VAL B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1217 Processing helix chain 'B' and resid 1219 through 1245 Processing helix chain 'B' and resid 1269 through 1290 removed outlier: 4.011A pdb=" N ASP B1273 " --> pdb=" O LYS B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1293 through 1303 Processing helix chain 'B' and resid 1304 through 1320 removed outlier: 3.618A pdb=" N ILE B1308 " --> pdb=" O PRO B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1322 through 1337 Processing helix chain 'B' and resid 1339 through 1349 Processing helix chain 'B' and resid 1350 through 1356 Processing helix chain 'B' and resid 1358 through 1364 removed outlier: 4.086A pdb=" N VAL B1362 " --> pdb=" O PRO B1358 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR B1363 " --> pdb=" O LEU B1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 1388 through 1432 removed outlier: 7.901A pdb=" N TYR B1408 " --> pdb=" O LYS B1404 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ASN B1409 " --> pdb=" O THR B1405 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER B1412 " --> pdb=" O TYR B1408 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU B1413 " --> pdb=" O ASN B1409 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLU B1423 " --> pdb=" O GLY B1419 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG B1424 " --> pdb=" O VAL B1420 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B1432 " --> pdb=" O CYS B1428 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1456 removed outlier: 3.698A pdb=" N ASN B1456 " --> pdb=" O LEU B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1457 through 1465 Processing helix chain 'B' and resid 1465 through 1489 removed outlier: 3.605A pdb=" N LYS B1470 " --> pdb=" O PRO B1466 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B1489 " --> pdb=" O SER B1485 " (cutoff:3.500A) Processing helix chain 'B' and resid 1532 through 1557 Processing helix chain 'B' and resid 1596 through 1616 Processing helix chain 'B' and resid 1634 through 1662 Processing helix chain 'B' and resid 1666 through 1693 Processing helix chain 'B' and resid 1726 through 1738 Processing helix chain 'C' and resid 34 through 46 Processing helix chain 'C' and resid 98 through 149 Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 204 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.712A pdb=" N ASP C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 248 through 277 Processing helix chain 'C' and resid 290 through 302 removed outlier: 3.817A pdb=" N ILE C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 330 Processing helix chain 'C' and resid 331 through 342 removed outlier: 3.612A pdb=" N ALA C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 347 Processing helix chain 'C' and resid 348 through 358 Processing helix chain 'C' and resid 365 through 379 Processing helix chain 'C' and resid 380 through 383 Processing helix chain 'C' and resid 385 through 397 Processing helix chain 'C' and resid 410 through 422 Processing helix chain 'C' and resid 439 through 448 Processing helix chain 'C' and resid 449 through 454 removed outlier: 3.556A pdb=" N HIS C 453 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 454 " --> pdb=" O GLY C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 454' Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.692A pdb=" N LEU C 483 " --> pdb=" O PHE C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.843A pdb=" N LEU C 500 " --> pdb=" O ALA C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 538 Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.500A pdb=" N ALA C 548 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 565 through 578 Processing helix chain 'C' and resid 580 through 585 Processing helix chain 'C' and resid 598 through 603 removed outlier: 4.075A pdb=" N PHE C 602 " --> pdb=" O ALA C 598 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 603 " --> pdb=" O ILE C 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 598 through 603' Processing helix chain 'C' and resid 606 through 620 Processing helix chain 'C' and resid 622 through 633 Processing helix chain 'C' and resid 635 through 648 Processing helix chain 'C' and resid 649 through 652 removed outlier: 3.852A pdb=" N SER C 652 " --> pdb=" O PRO C 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 649 through 652' Processing helix chain 'C' and resid 660 through 678 Processing helix chain 'C' and resid 685 through 706 Processing helix chain 'C' and resid 708 through 719 Processing helix chain 'C' and resid 726 through 738 removed outlier: 4.150A pdb=" N GLU C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 766 removed outlier: 3.906A pdb=" N ASN C 745 " --> pdb=" O GLU C 741 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER C 747 " --> pdb=" O ARG C 743 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLU C 748 " --> pdb=" O HIS C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 797 Processing helix chain 'C' and resid 807 through 820 Processing helix chain 'D' and resid 10 through 34 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.653A pdb=" N ILE D 90 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 313 through 325 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 481 through 486 removed outlier: 3.636A pdb=" N GLN D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 522 removed outlier: 3.674A pdb=" N ASN D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 536 Processing helix chain 'D' and resid 538 through 550 removed outlier: 3.798A pdb=" N LEU D 548 " --> pdb=" O THR D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 555 No H-bonds generated for 'chain 'D' and resid 553 through 555' Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.661A pdb=" N SER D 561 " --> pdb=" O ARG D 557 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 565 " --> pdb=" O SER D 561 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY D 571 " --> pdb=" O PHE D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 668 Processing helix chain 'D' and resid 669 through 673 removed outlier: 3.724A pdb=" N ASP D 673 " --> pdb=" O ASN D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 718 Processing helix chain 'D' and resid 719 through 723 Processing helix chain 'D' and resid 761 through 798 Processing helix chain 'D' and resid 799 through 806 removed outlier: 3.519A pdb=" N ASP D 806 " --> pdb=" O LEU D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 817 removed outlier: 3.680A pdb=" N ILE D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 826 Processing helix chain 'D' and resid 827 through 845 removed outlier: 4.181A pdb=" N THR D 831 " --> pdb=" O ASP D 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 859 Processing helix chain 'D' and resid 867 through 883 removed outlier: 3.636A pdb=" N ARG D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS D 883 " --> pdb=" O GLN D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 904 removed outlier: 3.843A pdb=" N ILE D 904 " --> pdb=" O GLU D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 920 Processing helix chain 'D' and resid 922 through 938 removed outlier: 3.545A pdb=" N VAL D 926 " --> pdb=" O PHE D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 948 Processing helix chain 'D' and resid 960 through 979 removed outlier: 3.857A pdb=" N CYS D 971 " --> pdb=" O ASN D 967 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE D 972 " --> pdb=" O SER D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1026 removed outlier: 3.795A pdb=" N ARG D1026 " --> pdb=" O LYS D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1043 Processing helix chain 'D' and resid 1045 through 1051 Processing helix chain 'D' and resid 1056 through 1068 Processing helix chain 'D' and resid 1070 through 1085 removed outlier: 3.762A pdb=" N ASN D1085 " --> pdb=" O TYR D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1101 Processing helix chain 'D' and resid 1107 through 1117 Processing helix chain 'D' and resid 1134 through 1161 Processing helix chain 'D' and resid 1169 through 1178 Processing helix chain 'D' and resid 1181 through 1189 Processing helix chain 'D' and resid 1195 through 1207 Processing helix chain 'D' and resid 1210 through 1229 Processing helix chain 'D' and resid 1236 through 1253 removed outlier: 4.067A pdb=" N ILE D1251 " --> pdb=" O SER D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1260 through 1276 Processing helix chain 'D' and resid 1280 through 1289 Processing helix chain 'D' and resid 1292 through 1306 Processing helix chain 'D' and resid 1308 through 1314 removed outlier: 3.836A pdb=" N SER D1312 " --> pdb=" O ASP D1308 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1334 Processing helix chain 'D' and resid 1345 through 1364 Processing helix chain 'D' and resid 1367 through 1388 Processing helix chain 'E' and resid 34 through 46 Processing helix chain 'E' and resid 98 through 147 Processing helix chain 'E' and resid 180 through 197 Processing helix chain 'E' and resid 205 through 217 Processing helix chain 'E' and resid 218 through 233 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 248 through 278 Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 292 through 301 Processing helix chain 'E' and resid 320 through 328 Processing helix chain 'E' and resid 331 through 342 removed outlier: 3.792A pdb=" N ALA E 335 " --> pdb=" O ASP E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 358 Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.681A pdb=" N ARG E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 383 Processing helix chain 'E' and resid 385 through 397 Processing helix chain 'E' and resid 410 through 421 Processing helix chain 'E' and resid 438 through 447 Processing helix chain 'E' and resid 449 through 455 removed outlier: 3.815A pdb=" N HIS E 453 " --> pdb=" O TYR E 449 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE E 454 " --> pdb=" O GLY E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 470 removed outlier: 3.571A pdb=" N THR E 470 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 483 removed outlier: 3.560A pdb=" N LEU E 483 " --> pdb=" O PHE E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 500 Processing helix chain 'E' and resid 528 through 539 removed outlier: 4.205A pdb=" N LYS E 539 " --> pdb=" O LEU E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 553 Processing helix chain 'E' and resid 554 through 558 removed outlier: 4.389A pdb=" N ASN E 557 " --> pdb=" O PHE E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 579 Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 597 through 603 removed outlier: 3.810A pdb=" N LYS E 601 " --> pdb=" O GLY E 597 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE E 602 " --> pdb=" O ALA E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 621 removed outlier: 3.791A pdb=" N ILE E 609 " --> pdb=" O ASP E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 633 Processing helix chain 'E' and resid 635 through 648 removed outlier: 3.801A pdb=" N VAL E 639 " --> pdb=" O ASN E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 651 No H-bonds generated for 'chain 'E' and resid 649 through 651' Processing helix chain 'E' and resid 660 through 677 Processing helix chain 'E' and resid 685 through 706 Processing helix chain 'E' and resid 707 through 719 Processing helix chain 'E' and resid 724 through 726 No H-bonds generated for 'chain 'E' and resid 724 through 726' Processing helix chain 'E' and resid 727 through 736 removed outlier: 3.566A pdb=" N PHE E 735 " --> pdb=" O ARG E 731 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG E 736 " --> pdb=" O VAL E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 766 removed outlier: 4.484A pdb=" N SER E 747 " --> pdb=" O ARG E 743 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU E 748 " --> pdb=" O HIS E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 800 Processing helix chain 'E' and resid 805 through 819 removed outlier: 3.704A pdb=" N MET E 819 " --> pdb=" O MET E 815 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 32 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 86 through 93 removed outlier: 3.588A pdb=" N ILE F 90 " --> pdb=" O PRO F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 329 through 334 removed outlier: 3.563A pdb=" N LYS F 334 " --> pdb=" O ASN F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 521 Processing helix chain 'F' and resid 526 through 536 Processing helix chain 'F' and resid 538 through 549 Processing helix chain 'F' and resid 553 through 555 No H-bonds generated for 'chain 'F' and resid 553 through 555' Processing helix chain 'F' and resid 556 through 571 Processing helix chain 'F' and resid 654 through 674 removed outlier: 5.668A pdb=" N ASN F 670 " --> pdb=" O ARG F 666 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE F 671 " --> pdb=" O ILE F 667 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP F 673 " --> pdb=" O GLY F 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 719 removed outlier: 3.605A pdb=" N LEU F 701 " --> pdb=" O THR F 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 767 through 797 Processing helix chain 'F' and resid 799 through 807 removed outlier: 3.658A pdb=" N LEU F 807 " --> pdb=" O VAL F 803 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 818 Processing helix chain 'F' and resid 819 through 826 Processing helix chain 'F' and resid 827 through 845 removed outlier: 3.626A pdb=" N THR F 831 " --> pdb=" O ASP F 827 " (cutoff:3.500A) Processing helix chain 'F' and resid 849 through 860 Processing helix chain 'F' and resid 869 through 881 Processing helix chain 'F' and resid 888 through 904 removed outlier: 3.539A pdb=" N ILE F 904 " --> pdb=" O GLU F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 909 through 920 Processing helix chain 'F' and resid 922 through 938 removed outlier: 3.542A pdb=" N VAL F 926 " --> pdb=" O PHE F 922 " (cutoff:3.500A) Processing helix chain 'F' and resid 941 through 949 Processing helix chain 'F' and resid 955 through 985 removed outlier: 3.788A pdb=" N CYS F 971 " --> pdb=" O ASN F 967 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE F 972 " --> pdb=" O SER F 968 " (cutoff:3.500A) Processing helix chain 'F' and resid 1010 through 1025 Processing helix chain 'F' and resid 1029 through 1043 Processing helix chain 'F' and resid 1045 through 1051 Processing helix chain 'F' and resid 1056 through 1068 Processing helix chain 'F' and resid 1070 through 1085 removed outlier: 4.481A pdb=" N TYR F1074 " --> pdb=" O ASN F1070 " (cutoff:3.500A) Processing helix chain 'F' and resid 1087 through 1101 Processing helix chain 'F' and resid 1107 through 1124 Processing helix chain 'F' and resid 1134 through 1162 Processing helix chain 'F' and resid 1167 through 1178 removed outlier: 3.528A pdb=" N GLN F1178 " --> pdb=" O GLN F1174 " (cutoff:3.500A) Processing helix chain 'F' and resid 1181 through 1188 Processing helix chain 'F' and resid 1189 through 1194 Processing helix chain 'F' and resid 1195 through 1207 Processing helix chain 'F' and resid 1210 through 1229 removed outlier: 3.733A pdb=" N VAL F1214 " --> pdb=" O ASP F1210 " (cutoff:3.500A) Processing helix chain 'F' and resid 1230 through 1232 No H-bonds generated for 'chain 'F' and resid 1230 through 1232' Processing helix chain 'F' and resid 1233 through 1253 removed outlier: 4.150A pdb=" N ILE F1251 " --> pdb=" O SER F1247 " (cutoff:3.500A) Processing helix chain 'F' and resid 1262 through 1275 Processing helix chain 'F' and resid 1280 through 1289 Processing helix chain 'F' and resid 1292 through 1307 Processing helix chain 'F' and resid 1309 through 1314 Processing helix chain 'F' and resid 1318 through 1334 Processing helix chain 'F' and resid 1342 through 1363 Processing helix chain 'F' and resid 1367 through 1388 Processing helix chain 'G' and resid 157 through 169 Processing helix chain 'G' and resid 320 through 325 Processing helix chain 'G' and resid 333 through 344 Processing helix chain 'G' and resid 356 through 425 removed outlier: 3.709A pdb=" N LEU G 361 " --> pdb=" O GLY G 357 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 448 Processing helix chain 'G' and resid 456 through 474 Processing helix chain 'G' and resid 490 through 520 removed outlier: 4.196A pdb=" N HIS G 494 " --> pdb=" O GLU G 490 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER G 507 " --> pdb=" O SER G 503 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE G 508 " --> pdb=" O HIS G 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 447 removed outlier: 3.685A pdb=" N ARG H 396 " --> pdb=" O GLN H 392 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU H 429 " --> pdb=" O GLN H 425 " (cutoff:3.500A) Proline residue: H 434 - end of helix Processing helix chain 'H' and resid 458 through 487 Processing helix chain 'H' and resid 495 through 527 Processing helix chain 'I' and resid 283 through 309 removed outlier: 3.735A pdb=" N GLU I 290 " --> pdb=" O CYS I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 369 removed outlier: 3.821A pdb=" N GLN I 318 " --> pdb=" O MET I 314 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU I 319 " --> pdb=" O LEU I 315 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU I 340 " --> pdb=" O GLN I 336 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA I 341 " --> pdb=" O ARG I 337 " (cutoff:3.500A) Proline residue: I 366 - end of helix Processing helix chain 'I' and resid 373 through 411 removed outlier: 3.918A pdb=" N VAL I 389 " --> pdb=" O GLN I 385 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN I 390 " --> pdb=" O GLN I 386 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN I 392 " --> pdb=" O GLU I 388 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 452 removed outlier: 4.430A pdb=" N SER I 420 " --> pdb=" O PRO I 416 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU I 452 " --> pdb=" O LYS I 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 169 Processing helix chain 'J' and resid 320 through 325 Processing helix chain 'J' and resid 333 through 343 Processing helix chain 'J' and resid 358 through 424 removed outlier: 4.060A pdb=" N GLY J 401 " --> pdb=" O MET J 397 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN J 402 " --> pdb=" O ALA J 398 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 474 Processing helix chain 'J' and resid 489 through 520 removed outlier: 4.210A pdb=" N GLN J 493 " --> pdb=" O ARG J 489 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS J 494 " --> pdb=" O GLU J 490 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER J 507 " --> pdb=" O SER J 503 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE J 508 " --> pdb=" O HIS J 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 360 through 449 removed outlier: 4.152A pdb=" N LYS L 364 " --> pdb=" O ASN L 360 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG L 396 " --> pdb=" O GLN L 392 " (cutoff:3.500A) Proline residue: L 434 - end of helix Processing helix chain 'L' and resid 458 through 487 removed outlier: 3.561A pdb=" N ALA L 487 " --> pdb=" O LEU L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 495 through 527 removed outlier: 3.776A pdb=" N VAL L 527 " --> pdb=" O LYS L 523 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 309 removed outlier: 4.550A pdb=" N GLU K 290 " --> pdb=" O CYS K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 365 removed outlier: 3.948A pdb=" N GLN K 318 " --> pdb=" O MET K 314 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU K 319 " --> pdb=" O LEU K 315 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN K 326 " --> pdb=" O LYS K 322 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU K 340 " --> pdb=" O GLN K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 411 removed outlier: 3.626A pdb=" N PHE K 387 " --> pdb=" O LEU K 383 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL K 389 " --> pdb=" O GLN K 385 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN K 390 " --> pdb=" O GLN K 386 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN K 392 " --> pdb=" O GLU K 388 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 452 removed outlier: 3.885A pdb=" N SER K 420 " --> pdb=" O PRO K 416 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU K 452 " --> pdb=" O LYS K 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 34 Processing helix chain 'M' and resid 38 through 43 Processing helix chain 'M' and resid 57 through 61 Processing helix chain 'M' and resid 86 through 93 removed outlier: 3.626A pdb=" N ILE M 90 " --> pdb=" O PRO M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 96 No H-bonds generated for 'chain 'M' and resid 94 through 96' Processing helix chain 'M' and resid 106 through 109 Processing helix chain 'M' and resid 186 through 190 removed outlier: 3.797A pdb=" N SER M 189 " --> pdb=" O ASP M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 325 Processing helix chain 'M' and resid 329 through 334 removed outlier: 3.804A pdb=" N LYS M 334 " --> pdb=" O ASN M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 481 through 486 removed outlier: 3.559A pdb=" N GLN M 485 " --> pdb=" O PRO M 481 " (cutoff:3.500A) Processing helix chain 'M' and resid 509 through 521 Processing helix chain 'M' and resid 526 through 536 Processing helix chain 'M' and resid 538 through 550 removed outlier: 3.609A pdb=" N LEU M 548 " --> pdb=" O THR M 544 " (cutoff:3.500A) Processing helix chain 'M' and resid 553 through 555 No H-bonds generated for 'chain 'M' and resid 553 through 555' Processing helix chain 'M' and resid 556 through 570 Processing helix chain 'M' and resid 654 through 669 Processing helix chain 'M' and resid 670 through 672 No H-bonds generated for 'chain 'M' and resid 670 through 672' Processing helix chain 'M' and resid 697 through 719 Processing helix chain 'M' and resid 770 through 798 Processing helix chain 'M' and resid 799 through 807 removed outlier: 3.508A pdb=" N LEU M 807 " --> pdb=" O VAL M 803 " (cutoff:3.500A) Processing helix chain 'M' and resid 808 through 818 Processing helix chain 'M' and resid 819 through 826 Processing helix chain 'M' and resid 827 through 845 removed outlier: 3.892A pdb=" N THR M 831 " --> pdb=" O ASP M 827 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP M 845 " --> pdb=" O CYS M 841 " (cutoff:3.500A) Processing helix chain 'M' and resid 849 through 860 Processing helix chain 'M' and resid 867 through 882 removed outlier: 3.746A pdb=" N ARG M 882 " --> pdb=" O LEU M 878 " (cutoff:3.500A) Processing helix chain 'M' and resid 886 through 904 removed outlier: 3.824A pdb=" N ILE M 904 " --> pdb=" O GLU M 900 " (cutoff:3.500A) Processing helix chain 'M' and resid 909 through 920 Processing helix chain 'M' and resid 922 through 938 Processing helix chain 'M' and resid 941 through 949 Processing helix chain 'M' and resid 959 through 984 removed outlier: 4.126A pdb=" N CYS M 971 " --> pdb=" O ASN M 967 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE M 972 " --> pdb=" O SER M 968 " (cutoff:3.500A) Processing helix chain 'M' and resid 1011 through 1025 Processing helix chain 'M' and resid 1029 through 1043 Processing helix chain 'M' and resid 1045 through 1051 Processing helix chain 'M' and resid 1056 through 1068 Processing helix chain 'a' and resid 14 through 29 Processing helix chain 'a' and resid 34 through 46 removed outlier: 3.917A pdb=" N SER a 38 " --> pdb=" O GLU a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 52 Processing helix chain 'a' and resid 60 through 69 Processing helix chain 'a' and resid 91 through 102 Processing helix chain 'a' and resid 104 through 119 Processing helix chain 'a' and resid 126 through 153 Processing helix chain 'a' and resid 163 through 180 removed outlier: 3.558A pdb=" N GLN a 180 " --> pdb=" O ASP a 176 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 193 Processing helix chain 'a' and resid 194 through 205 removed outlier: 3.619A pdb=" N GLU a 205 " --> pdb=" O LYS a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 239 Processing helix chain 'a' and resid 242 through 254 Processing helix chain 'a' and resid 265 through 279 Processing helix chain 'a' and resid 290 through 296 Processing helix chain 'a' and resid 303 through 316 removed outlier: 3.717A pdb=" N ILE a 307 " --> pdb=" O ASP a 303 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 342 removed outlier: 3.616A pdb=" N GLN a 342 " --> pdb=" O ARG a 338 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 350 Processing helix chain 'a' and resid 352 through 363 removed outlier: 3.623A pdb=" N MET a 356 " --> pdb=" O ALA a 352 " (cutoff:3.500A) Processing helix chain 'a' and resid 364 through 372 Processing helix chain 'a' and resid 376 through 381 removed outlier: 3.615A pdb=" N CYS a 380 " --> pdb=" O GLU a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 382 through 400 Proline residue: a 397 - end of helix Processing helix chain 'a' and resid 400 through 424 Processing helix chain 'a' and resid 434 through 449 removed outlier: 4.163A pdb=" N LYS a 449 " --> pdb=" O GLU a 445 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 461 Processing helix chain 'a' and resid 489 through 498 Processing helix chain 'a' and resid 503 through 518 removed outlier: 3.991A pdb=" N LEU a 508 " --> pdb=" O ALA a 504 " (cutoff:3.500A) Proline residue: a 509 - end of helix Processing helix chain 'a' and resid 520 through 534 Processing helix chain 'a' and resid 551 through 568 Processing helix chain 'a' and resid 587 through 608 Processing helix chain 'a' and resid 608 through 618 Processing helix chain 'a' and resid 622 through 631 Processing helix chain 'a' and resid 636 through 652 removed outlier: 3.536A pdb=" N LYS a 640 " --> pdb=" O PRO a 636 " (cutoff:3.500A) Processing helix chain 'a' and resid 653 through 668 removed outlier: 3.924A pdb=" N SER a 659 " --> pdb=" O GLU a 655 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN a 668 " --> pdb=" O LEU a 664 " (cutoff:3.500A) Processing helix chain 'a' and resid 683 through 691 Processing helix chain 'a' and resid 691 through 696 Processing helix chain 'a' and resid 698 through 713 removed outlier: 3.552A pdb=" N ARG a 702 " --> pdb=" O TYR a 698 " (cutoff:3.500A) Processing helix chain 'a' and resid 729 through 740 Processing helix chain 'a' and resid 740 through 745 removed outlier: 4.473A pdb=" N ARG a 745 " --> pdb=" O PHE a 741 " (cutoff:3.500A) Processing helix chain 'a' and resid 752 through 772 removed outlier: 4.203A pdb=" N TRP a 756 " --> pdb=" O ALA a 752 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP a 772 " --> pdb=" O LYS a 768 " (cutoff:3.500A) Processing helix chain 'a' and resid 799 through 807 Processing helix chain 'a' and resid 810 through 829 Processing helix chain 'a' and resid 835 through 866 removed outlier: 4.372A pdb=" N ASN a 858 " --> pdb=" O LEU a 854 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG a 859 " --> pdb=" O GLN a 855 " (cutoff:3.500A) Processing helix chain 'a' and resid 875 through 881 Processing helix chain 'a' and resid 891 through 899 Processing helix chain 'a' and resid 900 through 904 removed outlier: 4.408A pdb=" N ASN a 904 " --> pdb=" O CYS a 901 " (cutoff:3.500A) Processing helix chain 'a' and resid 906 through 922 removed outlier: 3.541A pdb=" N ALA a 910 " --> pdb=" O ASN a 906 " (cutoff:3.500A) Processing helix chain 'a' and resid 923 through 936 removed outlier: 3.828A pdb=" N GLN a 927 " --> pdb=" O ASN a 923 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU a 928 " --> pdb=" O SER a 924 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LYS a 929 " --> pdb=" O LYS a 925 " (cutoff:3.500A) Processing helix chain 'a' and resid 937 through 953 Processing helix chain 'a' and resid 971 through 993 Processing helix chain 'a' and resid 998 through 1005 removed outlier: 3.631A pdb=" N GLY a1005 " --> pdb=" O MET a1001 " (cutoff:3.500A) Processing helix chain 'a' and resid 1011 through 1015 Processing helix chain 'a' and resid 1021 through 1025 Processing helix chain 'a' and resid 1029 through 1039 Processing helix chain 'a' and resid 1047 through 1053 removed outlier: 3.840A pdb=" N TRP a1051 " --> pdb=" O PRO a1047 " (cutoff:3.500A) Processing helix chain 'a' and resid 1053 through 1070 removed outlier: 3.551A pdb=" N ALA a1057 " --> pdb=" O THR a1053 " (cutoff:3.500A) Processing helix chain 'a' and resid 1073 through 1084 Processing helix chain 'a' and resid 1086 through 1093 Processing helix chain 'a' and resid 1102 through 1128 Processing helix chain 'a' and resid 1130 through 1142 Processing helix chain 'a' and resid 1178 through 1187 removed outlier: 3.567A pdb=" N ILE a1187 " --> pdb=" O ILE a1183 " (cutoff:3.500A) Processing helix chain 'a' and resid 1203 through 1214 Processing helix chain 'a' and resid 1226 through 1240 Processing helix chain 'a' and resid 1249 through 1294 Processing helix chain 'a' and resid 1296 through 1300 Processing helix chain 'a' and resid 1301 through 1321 Processing helix chain 'a' and resid 1329 through 1352 removed outlier: 4.211A pdb=" N VAL a1333 " --> pdb=" O LEU a1329 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY a1335 " --> pdb=" O PRO a1331 " (cutoff:3.500A) Processing helix chain 'a' and resid 1392 through 1409 Processing helix chain 'a' and resid 1413 through 1430 Processing helix chain 'a' and resid 1457 through 1472 removed outlier: 3.691A pdb=" N TYR a1472 " --> pdb=" O ILE a1468 " (cutoff:3.500A) Processing helix chain 'a' and resid 1473 through 1487 removed outlier: 4.203A pdb=" N MET a1477 " --> pdb=" O GLY a1473 " (cutoff:3.500A) Processing helix chain 'a' and resid 1488 through 1506 Processing helix chain 'a' and resid 1509 through 1518 Processing helix chain 'a' and resid 1519 through 1539 removed outlier: 3.552A pdb=" N VAL a1523 " --> pdb=" O GLY a1519 " (cutoff:3.500A) Processing helix chain 'a' and resid 1546 through 1561 removed outlier: 3.607A pdb=" N TYR a1550 " --> pdb=" O LEU a1546 " (cutoff:3.500A) Processing helix chain 'a' and resid 1566 through 1575 Processing helix chain 'a' and resid 1576 through 1584 removed outlier: 3.656A pdb=" N CYS a1584 " --> pdb=" O ARG a1580 " (cutoff:3.500A) Processing helix chain 'a' and resid 1611 through 1633 Proline residue: a1621 - end of helix Processing helix chain 'a' and resid 1637 through 1651 Processing helix chain 'a' and resid 1651 through 1660 Processing helix chain 'a' and resid 1665 through 1683 Processing helix chain 'a' and resid 1684 through 1691 removed outlier: 4.087A pdb=" N LEU a1688 " --> pdb=" O LEU a1684 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU a1690 " --> pdb=" O GLY a1686 " (cutoff:3.500A) Processing helix chain 'a' and resid 1698 through 1722 removed outlier: 4.036A pdb=" N LEU a1718 " --> pdb=" O CYS a1714 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN a1719 " --> pdb=" O LEU a1715 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG a1720 " --> pdb=" O ALA a1716 " (cutoff:3.500A) Processing helix chain 'a' and resid 1724 through 1732 removed outlier: 3.879A pdb=" N ARG a1728 " --> pdb=" O SER a1724 " (cutoff:3.500A) Processing helix chain 'a' and resid 1742 through 1768 Processing helix chain 'a' and resid 1811 through 1841 Processing helix chain 'a' and resid 1848 through 1855 Processing helix chain 'a' and resid 1868 through 1913 Processing helix chain 'a' and resid 1958 through 1970 Processing helix chain 'a' and resid 1971 through 1985 removed outlier: 3.539A pdb=" N GLN a1975 " --> pdb=" O GLY a1971 " (cutoff:3.500A) Processing helix chain 'a' and resid 1986 through 1989 Processing helix chain 'a' and resid 1993 through 2007 Processing helix chain 'b' and resid 12 through 20 Processing helix chain 'b' and resid 27 through 38 Processing helix chain 'b' and resid 38 through 45 Processing helix chain 'b' and resid 46 through 49 removed outlier: 3.691A pdb=" N TYR b 49 " --> pdb=" O LEU b 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 46 through 49' Processing helix chain 'b' and resid 53 through 63 Processing helix chain 'b' and resid 67 through 82 Processing helix chain 'b' and resid 84 through 99 Processing helix chain 'b' and resid 105 through 109 Processing helix chain 'b' and resid 113 through 145 Processing helix chain 'b' and resid 153 through 166 Processing helix chain 'b' and resid 168 through 182 removed outlier: 3.595A pdb=" N LYS b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 192 Processing helix chain 'b' and resid 196 through 225 Processing helix chain 'b' and resid 228 through 242 Processing helix chain 'b' and resid 250 through 254 removed outlier: 3.720A pdb=" N VAL b 254 " --> pdb=" O HIS b 251 " (cutoff:3.500A) Processing helix chain 'b' and resid 255 through 257 No H-bonds generated for 'chain 'b' and resid 255 through 257' Processing helix chain 'b' and resid 258 through 276 removed outlier: 3.742A pdb=" N VAL b 262 " --> pdb=" O MET b 258 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 289 Processing helix chain 'b' and resid 290 through 294 Processing helix chain 'b' and resid 299 through 311 Processing helix chain 'b' and resid 318 through 334 removed outlier: 4.695A pdb=" N VAL b 322 " --> pdb=" O HIS b 318 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN b 334 " --> pdb=" O ARG b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 339 through 352 removed outlier: 3.650A pdb=" N ARG b 343 " --> pdb=" O THR b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 353 through 367 Processing helix chain 'b' and resid 371 through 392 Processing helix chain 'b' and resid 394 through 400 removed outlier: 3.571A pdb=" N SER b 397 " --> pdb=" O GLU b 394 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN b 398 " --> pdb=" O GLN b 395 " (cutoff:3.500A) Processing helix chain 'b' and resid 401 through 411 Processing helix chain 'b' and resid 415 through 423 removed outlier: 3.979A pdb=" N LEU b 419 " --> pdb=" O ASN b 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 428 through 438 removed outlier: 4.031A pdb=" N LEU b 432 " --> pdb=" O GLY b 428 " (cutoff:3.500A) Processing helix chain 'b' and resid 443 through 455 removed outlier: 3.870A pdb=" N LEU b 447 " --> pdb=" O ARG b 443 " (cutoff:3.500A) Processing helix chain 'b' and resid 459 through 469 Processing helix chain 'b' and resid 537 through 553 Processing helix chain 'b' and resid 557 through 577 Proline residue: b 567 - end of helix removed outlier: 3.812A pdb=" N LEU b 571 " --> pdb=" O PRO b 567 " (cutoff:3.500A) Processing helix chain 'b' and resid 579 through 583 Processing helix chain 'b' and resid 586 through 601 removed outlier: 4.151A pdb=" N TYR b 594 " --> pdb=" O THR b 590 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET b 595 " --> pdb=" O SER b 591 " (cutoff:3.500A) Processing helix chain 'b' and resid 607 through 623 Processing helix chain 'b' and resid 625 through 637 removed outlier: 3.537A pdb=" N THR b 636 " --> pdb=" O ASP b 632 " (cutoff:3.500A) Processing helix chain 'b' and resid 660 through 672 removed outlier: 4.058A pdb=" N LEU b 664 " --> pdb=" O GLY b 660 " (cutoff:3.500A) Processing helix chain 'b' and resid 674 through 690 Processing helix chain 'b' and resid 693 through 699 removed outlier: 3.603A pdb=" N SER b 697 " --> pdb=" O SER b 694 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN b 698 " --> pdb=" O THR b 695 " (cutoff:3.500A) Processing helix chain 'b' and resid 700 through 710 removed outlier: 3.503A pdb=" N GLU b 710 " --> pdb=" O PHE b 706 " (cutoff:3.500A) Processing helix chain 'b' and resid 710 through 715 removed outlier: 3.959A pdb=" N ASN b 714 " --> pdb=" O GLU b 710 " (cutoff:3.500A) Processing helix chain 'b' and resid 724 through 742 Processing helix chain 'b' and resid 757 through 767 Processing helix chain 'b' and resid 768 through 779 Processing helix chain 'b' and resid 779 through 790 removed outlier: 4.337A pdb=" N THR b 783 " --> pdb=" O ILE b 779 " (cutoff:3.500A) Processing helix chain 'b' and resid 799 through 822 Processing helix chain 'b' and resid 831 through 837 Processing helix chain 'b' and resid 844 through 852 Processing helix chain 'b' and resid 853 through 855 No H-bonds generated for 'chain 'b' and resid 853 through 855' Processing helix chain 'b' and resid 859 through 876 Processing helix chain 'b' and resid 879 through 885 Processing helix chain 'b' and resid 887 through 901 Processing helix chain 'b' and resid 905 through 923 Processing helix chain 'b' and resid 923 through 932 removed outlier: 3.815A pdb=" N LEU b 931 " --> pdb=" O ILE b 927 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN b 932 " --> pdb=" O GLU b 928 " (cutoff:3.500A) Processing helix chain 'b' and resid 952 through 961 Processing helix chain 'b' and resid 971 through 988 Processing helix chain 'b' and resid 990 through 1000 removed outlier: 3.582A pdb=" N LYS b1000 " --> pdb=" O VAL b 996 " (cutoff:3.500A) Processing helix chain 'b' and resid 1002 through 1009 Processing helix chain 'b' and resid 1023 through 1044 removed outlier: 3.674A pdb=" N LEU b1027 " --> pdb=" O GLU b1023 " (cutoff:3.500A) Processing helix chain 'b' and resid 1053 through 1063 Processing helix chain 'b' and resid 1064 through 1083 Processing helix chain 'b' and resid 1089 through 1110 Processing helix chain 'b' and resid 1118 through 1139 removed outlier: 4.004A pdb=" N VAL b1139 " --> pdb=" O ALA b1135 " (cutoff:3.500A) Processing helix chain 'b' and resid 1144 through 1163 Processing helix chain 'b' and resid 1171 through 1186 Processing helix chain 'b' and resid 1188 through 1210 removed outlier: 3.582A pdb=" N VAL b1192 " --> pdb=" O ASP b1188 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU b1193 " --> pdb=" O GLN b1189 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS b1194 " --> pdb=" O GLN b1190 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N THR b1195 " --> pdb=" O LEU b1191 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS b1210 " --> pdb=" O VAL b1206 " (cutoff:3.500A) Processing helix chain 'b' and resid 1213 through 1217 Processing helix chain 'b' and resid 1219 through 1245 Processing helix chain 'b' and resid 1269 through 1290 removed outlier: 4.010A pdb=" N ASP b1273 " --> pdb=" O LYS b1269 " (cutoff:3.500A) Processing helix chain 'b' and resid 1293 through 1303 Processing helix chain 'b' and resid 1304 through 1320 removed outlier: 3.618A pdb=" N ILE b1308 " --> pdb=" O PRO b1304 " (cutoff:3.500A) Processing helix chain 'b' and resid 1322 through 1337 Processing helix chain 'b' and resid 1339 through 1349 Processing helix chain 'b' and resid 1350 through 1356 Processing helix chain 'b' and resid 1358 through 1364 removed outlier: 4.085A pdb=" N VAL b1362 " --> pdb=" O PRO b1358 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR b1363 " --> pdb=" O LEU b1359 " (cutoff:3.500A) Processing helix chain 'b' and resid 1388 through 1432 removed outlier: 7.901A pdb=" N TYR b1408 " --> pdb=" O LYS b1404 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASN b1409 " --> pdb=" O THR b1405 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER b1412 " --> pdb=" O TYR b1408 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU b1413 " --> pdb=" O ASN b1409 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU b1423 " --> pdb=" O GLY b1419 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ARG b1424 " --> pdb=" O VAL b1420 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL b1432 " --> pdb=" O CYS b1428 " (cutoff:3.500A) Processing helix chain 'b' and resid 1438 through 1456 removed outlier: 3.699A pdb=" N ASN b1456 " --> pdb=" O LEU b1452 " (cutoff:3.500A) Processing helix chain 'b' and resid 1457 through 1465 Processing helix chain 'b' and resid 1465 through 1489 removed outlier: 3.605A pdb=" N LYS b1470 " --> pdb=" O PRO b1466 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER b1489 " --> pdb=" O SER b1485 " (cutoff:3.500A) Processing helix chain 'b' and resid 1532 through 1557 Processing helix chain 'b' and resid 1596 through 1616 Processing helix chain 'b' and resid 1634 through 1662 Processing helix chain 'b' and resid 1666 through 1693 Processing helix chain 'b' and resid 1726 through 1738 Processing helix chain 'c' and resid 34 through 46 Processing helix chain 'c' and resid 98 through 149 Processing helix chain 'c' and resid 180 through 198 Processing helix chain 'c' and resid 204 through 216 Processing helix chain 'c' and resid 218 through 233 Processing helix chain 'c' and resid 242 through 247 Processing helix chain 'c' and resid 248 through 277 Processing helix chain 'c' and resid 290 through 302 removed outlier: 3.924A pdb=" N ILE c 300 " --> pdb=" O SER c 296 " (cutoff:3.500A) Processing helix chain 'c' and resid 319 through 329 Processing helix chain 'c' and resid 331 through 342 Processing helix chain 'c' and resid 342 through 347 Processing helix chain 'c' and resid 348 through 359 removed outlier: 3.579A pdb=" N ASN c 359 " --> pdb=" O GLU c 355 " (cutoff:3.500A) Processing helix chain 'c' and resid 365 through 379 Processing helix chain 'c' and resid 380 through 383 Processing helix chain 'c' and resid 385 through 397 Processing helix chain 'c' and resid 410 through 422 Processing helix chain 'c' and resid 439 through 447 Processing helix chain 'c' and resid 449 through 454 removed outlier: 3.762A pdb=" N HIS c 453 " --> pdb=" O TYR c 449 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE c 454 " --> pdb=" O GLY c 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 449 through 454' Processing helix chain 'c' and resid 459 through 469 Processing helix chain 'c' and resid 472 through 483 removed outlier: 3.765A pdb=" N LEU c 483 " --> pdb=" O PHE c 479 " (cutoff:3.500A) Processing helix chain 'c' and resid 483 through 501 removed outlier: 4.093A pdb=" N CYS c 488 " --> pdb=" O GLU c 484 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N HIS c 489 " --> pdb=" O ARG c 485 " (cutoff:3.500A) Processing helix chain 'c' and resid 530 through 538 Processing helix chain 'c' and resid 544 through 553 Processing helix chain 'c' and resid 554 through 558 removed outlier: 3.913A pdb=" N ASN c 557 " --> pdb=" O PHE c 554 " (cutoff:3.500A) Processing helix chain 'c' and resid 565 through 578 Processing helix chain 'c' and resid 580 through 585 Processing helix chain 'c' and resid 598 through 602 Processing helix chain 'c' and resid 606 through 620 removed outlier: 3.593A pdb=" N LYS c 620 " --> pdb=" O VAL c 616 " (cutoff:3.500A) Processing helix chain 'c' and resid 622 through 633 Processing helix chain 'c' and resid 635 through 648 Processing helix chain 'c' and resid 649 through 652 removed outlier: 4.081A pdb=" N SER c 652 " --> pdb=" O PRO c 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 649 through 652' Processing helix chain 'c' and resid 660 through 678 Processing helix chain 'c' and resid 685 through 706 Processing helix chain 'c' and resid 708 through 719 removed outlier: 3.756A pdb=" N LYS c 719 " --> pdb=" O ILE c 715 " (cutoff:3.500A) Processing helix chain 'c' and resid 727 through 738 Processing helix chain 'c' and resid 739 through 766 removed outlier: 3.552A pdb=" N ASN c 745 " --> pdb=" O GLU c 741 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER c 747 " --> pdb=" O ARG c 743 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU c 748 " --> pdb=" O HIS c 744 " (cutoff:3.500A) Processing helix chain 'c' and resid 779 through 797 removed outlier: 3.561A pdb=" N ALA c 797 " --> pdb=" O LEU c 793 " (cutoff:3.500A) Processing helix chain 'c' and resid 807 through 820 Processing helix chain 'd' and resid 10 through 34 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'd' and resid 57 through 61 Processing helix chain 'd' and resid 86 through 93 Processing helix chain 'd' and resid 94 through 96 No H-bonds generated for 'chain 'd' and resid 94 through 96' Processing helix chain 'd' and resid 106 through 108 No H-bonds generated for 'chain 'd' and resid 106 through 108' Processing helix chain 'd' and resid 313 through 325 Processing helix chain 'd' and resid 329 through 334 Processing helix chain 'd' and resid 481 through 486 removed outlier: 3.588A pdb=" N GLN d 485 " --> pdb=" O PRO d 481 " (cutoff:3.500A) Processing helix chain 'd' and resid 509 through 521 Processing helix chain 'd' and resid 526 through 536 Processing helix chain 'd' and resid 538 through 550 removed outlier: 3.582A pdb=" N LEU d 548 " --> pdb=" O THR d 544 " (cutoff:3.500A) Processing helix chain 'd' and resid 553 through 555 No H-bonds generated for 'chain 'd' and resid 553 through 555' Processing helix chain 'd' and resid 556 through 570 Processing helix chain 'd' and resid 654 through 668 removed outlier: 3.605A pdb=" N ILE d 668 " --> pdb=" O PHE d 664 " (cutoff:3.500A) Processing helix chain 'd' and resid 669 through 673 Processing helix chain 'd' and resid 697 through 720 removed outlier: 3.812A pdb=" N GLN d 720 " --> pdb=" O ASP d 716 " (cutoff:3.500A) Processing helix chain 'd' and resid 761 through 797 Processing helix chain 'd' and resid 799 through 807 removed outlier: 3.521A pdb=" N LEU d 807 " --> pdb=" O VAL d 803 " (cutoff:3.500A) Processing helix chain 'd' and resid 808 through 817 Processing helix chain 'd' and resid 819 through 826 Processing helix chain 'd' and resid 827 through 845 removed outlier: 4.245A pdb=" N THR d 831 " --> pdb=" O ASP d 827 " (cutoff:3.500A) Processing helix chain 'd' and resid 851 through 859 Processing helix chain 'd' and resid 867 through 881 Processing helix chain 'd' and resid 882 through 884 No H-bonds generated for 'chain 'd' and resid 882 through 884' Processing helix chain 'd' and resid 886 through 903 removed outlier: 3.523A pdb=" N LYS d 890 " --> pdb=" O ASN d 886 " (cutoff:3.500A) Processing helix chain 'd' and resid 909 through 920 Processing helix chain 'd' and resid 922 through 938 removed outlier: 3.818A pdb=" N ASP d 938 " --> pdb=" O ALA d 934 " (cutoff:3.500A) Processing helix chain 'd' and resid 942 through 949 Processing helix chain 'd' and resid 959 through 983 removed outlier: 4.044A pdb=" N CYS d 971 " --> pdb=" O ASN d 967 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE d 972 " --> pdb=" O SER d 968 " (cutoff:3.500A) Processing helix chain 'd' and resid 1012 through 1026 removed outlier: 3.644A pdb=" N ARG d1026 " --> pdb=" O LYS d1022 " (cutoff:3.500A) Processing helix chain 'd' and resid 1029 through 1044 Processing helix chain 'd' and resid 1045 through 1052 Processing helix chain 'd' and resid 1056 through 1068 Processing helix chain 'd' and resid 1070 through 1085 removed outlier: 3.519A pdb=" N ASN d1085 " --> pdb=" O TYR d1081 " (cutoff:3.500A) Processing helix chain 'd' and resid 1087 through 1101 removed outlier: 3.523A pdb=" N ALA d1091 " --> pdb=" O ASN d1087 " (cutoff:3.500A) Processing helix chain 'd' and resid 1107 through 1118 Processing helix chain 'd' and resid 1134 through 1161 Processing helix chain 'd' and resid 1169 through 1178 Processing helix chain 'd' and resid 1181 through 1189 Processing helix chain 'd' and resid 1190 through 1194 Processing helix chain 'd' and resid 1195 through 1206 Processing helix chain 'd' and resid 1210 through 1228 Processing helix chain 'd' and resid 1236 through 1253 Processing helix chain 'd' and resid 1260 through 1276 Processing helix chain 'd' and resid 1280 through 1289 Processing helix chain 'd' and resid 1292 through 1306 Processing helix chain 'd' and resid 1308 through 1314 removed outlier: 4.073A pdb=" N SER d1312 " --> pdb=" O ASP d1308 " (cutoff:3.500A) Processing helix chain 'd' and resid 1318 through 1333 Processing helix chain 'd' and resid 1345 through 1364 Processing helix chain 'd' and resid 1367 through 1387 Processing helix chain 'e' and resid 34 through 46 Processing helix chain 'e' and resid 98 through 147 Processing helix chain 'e' and resid 180 through 197 Processing helix chain 'e' and resid 205 through 217 removed outlier: 3.542A pdb=" N ASP e 217 " --> pdb=" O ALA e 213 " (cutoff:3.500A) Processing helix chain 'e' and resid 218 through 233 Processing helix chain 'e' and resid 242 through 247 Processing helix chain 'e' and resid 248 through 278 Processing helix chain 'e' and resid 278 through 283 removed outlier: 3.543A pdb=" N GLN e 283 " --> pdb=" O LEU e 279 " (cutoff:3.500A) Processing helix chain 'e' and resid 292 through 299 Processing helix chain 'e' and resid 320 through 329 Processing helix chain 'e' and resid 331 through 342 removed outlier: 3.868A pdb=" N ALA e 335 " --> pdb=" O ASP e 331 " (cutoff:3.500A) Processing helix chain 'e' and resid 349 through 358 Processing helix chain 'e' and resid 369 through 379 Processing helix chain 'e' and resid 380 through 383 Processing helix chain 'e' and resid 385 through 397 Processing helix chain 'e' and resid 410 through 421 Processing helix chain 'e' and resid 438 through 447 Processing helix chain 'e' and resid 451 through 455 Processing helix chain 'e' and resid 459 through 470 removed outlier: 3.591A pdb=" N TYR e 463 " --> pdb=" O GLN e 459 " (cutoff:3.500A) Processing helix chain 'e' and resid 472 through 483 removed outlier: 3.763A pdb=" N LEU e 483 " --> pdb=" O PHE e 479 " (cutoff:3.500A) Processing helix chain 'e' and resid 486 through 500 Processing helix chain 'e' and resid 528 through 538 Processing helix chain 'e' and resid 544 through 553 Processing helix chain 'e' and resid 554 through 556 No H-bonds generated for 'chain 'e' and resid 554 through 556' Processing helix chain 'e' and resid 565 through 579 Processing helix chain 'e' and resid 581 through 585 Processing helix chain 'e' and resid 598 through 602 Processing helix chain 'e' and resid 605 through 620 removed outlier: 4.394A pdb=" N ILE e 609 " --> pdb=" O ASP e 605 " (cutoff:3.500A) Processing helix chain 'e' and resid 622 through 633 removed outlier: 3.550A pdb=" N ALA e 626 " --> pdb=" O LEU e 622 " (cutoff:3.500A) Processing helix chain 'e' and resid 635 through 648 removed outlier: 3.635A pdb=" N VAL e 639 " --> pdb=" O ASN e 635 " (cutoff:3.500A) Processing helix chain 'e' and resid 649 through 651 No H-bonds generated for 'chain 'e' and resid 649 through 651' Processing helix chain 'e' and resid 660 through 677 Processing helix chain 'e' and resid 685 through 706 Processing helix chain 'e' and resid 707 through 719 Processing helix chain 'e' and resid 724 through 726 No H-bonds generated for 'chain 'e' and resid 724 through 726' Processing helix chain 'e' and resid 727 through 735 removed outlier: 3.678A pdb=" N PHE e 735 " --> pdb=" O ARG e 731 " (cutoff:3.500A) Processing helix chain 'e' and resid 739 through 766 removed outlier: 4.380A pdb=" N SER e 747 " --> pdb=" O ARG e 743 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU e 748 " --> pdb=" O HIS e 744 " (cutoff:3.500A) Processing helix chain 'e' and resid 786 through 799 Processing helix chain 'e' and resid 805 through 819 removed outlier: 3.645A pdb=" N ASN e 809 " --> pdb=" O SER e 805 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 35 Processing helix chain 'f' and resid 39 through 43 Processing helix chain 'f' and resid 86 through 93 Processing helix chain 'f' and resid 94 through 96 No H-bonds generated for 'chain 'f' and resid 94 through 96' Processing helix chain 'f' and resid 106 through 108 No H-bonds generated for 'chain 'f' and resid 106 through 108' Processing helix chain 'f' and resid 313 through 325 Processing helix chain 'f' and resid 329 through 334 Processing helix chain 'f' and resid 509 through 521 Processing helix chain 'f' and resid 526 through 536 Processing helix chain 'f' and resid 537 through 550 removed outlier: 3.574A pdb=" N ALA f 541 " --> pdb=" O GLN f 537 " (cutoff:3.500A) Processing helix chain 'f' and resid 553 through 555 No H-bonds generated for 'chain 'f' and resid 553 through 555' Processing helix chain 'f' and resid 556 through 570 removed outlier: 3.823A pdb=" N SER f 561 " --> pdb=" O ARG f 557 " (cutoff:3.500A) Processing helix chain 'f' and resid 654 through 674 removed outlier: 5.488A pdb=" N ASN f 670 " --> pdb=" O ARG f 666 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE f 671 " --> pdb=" O ILE f 667 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP f 673 " --> pdb=" O GLY f 669 " (cutoff:3.500A) Processing helix chain 'f' and resid 697 through 719 Processing helix chain 'f' and resid 767 through 798 Processing helix chain 'f' and resid 799 through 804 removed outlier: 3.694A pdb=" N VAL f 803 " --> pdb=" O GLN f 799 " (cutoff:3.500A) Processing helix chain 'f' and resid 805 through 807 No H-bonds generated for 'chain 'f' and resid 805 through 807' Processing helix chain 'f' and resid 808 through 816 Processing helix chain 'f' and resid 819 through 826 Processing helix chain 'f' and resid 827 through 845 removed outlier: 3.907A pdb=" N THR f 831 " --> pdb=" O ASP f 827 " (cutoff:3.500A) Processing helix chain 'f' and resid 849 through 860 Processing helix chain 'f' and resid 869 through 882 removed outlier: 3.529A pdb=" N ARG f 882 " --> pdb=" O LEU f 878 " (cutoff:3.500A) Processing helix chain 'f' and resid 888 through 904 removed outlier: 3.780A pdb=" N ILE f 904 " --> pdb=" O GLU f 900 " (cutoff:3.500A) Processing helix chain 'f' and resid 909 through 920 Processing helix chain 'f' and resid 922 through 938 Processing helix chain 'f' and resid 941 through 949 Processing helix chain 'f' and resid 955 through 985 removed outlier: 3.859A pdb=" N CYS f 971 " --> pdb=" O ASN f 967 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE f 972 " --> pdb=" O SER f 968 " (cutoff:3.500A) Processing helix chain 'f' and resid 1010 through 1025 Processing helix chain 'f' and resid 1029 through 1043 Processing helix chain 'f' and resid 1045 through 1052 Processing helix chain 'f' and resid 1056 through 1068 Processing helix chain 'f' and resid 1070 through 1085 removed outlier: 4.383A pdb=" N TYR f1074 " --> pdb=" O ASN f1070 " (cutoff:3.500A) Processing helix chain 'f' and resid 1087 through 1101 Processing helix chain 'f' and resid 1107 through 1124 Processing helix chain 'f' and resid 1134 through 1163 removed outlier: 3.833A pdb=" N SER f1163 " --> pdb=" O THR f1159 " (cutoff:3.500A) Processing helix chain 'f' and resid 1167 through 1178 removed outlier: 3.579A pdb=" N GLN f1178 " --> pdb=" O GLN f1174 " (cutoff:3.500A) Processing helix chain 'f' and resid 1181 through 1188 Processing helix chain 'f' and resid 1189 through 1194 removed outlier: 4.032A pdb=" N PHE f1193 " --> pdb=" O TYR f1189 " (cutoff:3.500A) Processing helix chain 'f' and resid 1195 through 1207 Processing helix chain 'f' and resid 1210 through 1229 removed outlier: 3.581A pdb=" N VAL f1214 " --> pdb=" O ASP f1210 " (cutoff:3.500A) Processing helix chain 'f' and resid 1233 through 1253 removed outlier: 3.797A pdb=" N ILE f1251 " --> pdb=" O SER f1247 " (cutoff:3.500A) Processing helix chain 'f' and resid 1262 through 1275 Processing helix chain 'f' and resid 1280 through 1289 Processing helix chain 'f' and resid 1292 through 1306 Processing helix chain 'f' and resid 1309 through 1314 Processing helix chain 'f' and resid 1318 through 1333 Processing helix chain 'f' and resid 1342 through 1363 Processing helix chain 'f' and resid 1367 through 1388 Processing helix chain 'g' and resid 157 through 169 removed outlier: 3.604A pdb=" N TRP g 169 " --> pdb=" O ILE g 165 " (cutoff:3.500A) Processing helix chain 'g' and resid 320 through 326 removed outlier: 3.772A pdb=" N GLN g 326 " --> pdb=" O LYS g 322 " (cutoff:3.500A) Processing helix chain 'g' and resid 333 through 343 Processing helix chain 'g' and resid 357 through 425 removed outlier: 3.582A pdb=" N GLY g 401 " --> pdb=" O MET g 397 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN g 402 " --> pdb=" O ALA g 398 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG g 425 " --> pdb=" O GLN g 421 " (cutoff:3.500A) Processing helix chain 'g' and resid 432 through 448 Processing helix chain 'g' and resid 456 through 474 Processing helix chain 'g' and resid 489 through 520 removed outlier: 4.061A pdb=" N GLN g 493 " --> pdb=" O ARG g 489 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS g 494 " --> pdb=" O GLU g 490 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER g 507 " --> pdb=" O SER g 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE g 508 " --> pdb=" O HIS g 504 " (cutoff:3.500A) Processing helix chain 'h' and resid 360 through 447 removed outlier: 3.654A pdb=" N LYS h 364 " --> pdb=" O ASN h 360 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG h 396 " --> pdb=" O GLN h 392 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU h 429 " --> pdb=" O GLN h 425 " (cutoff:3.500A) Proline residue: h 434 - end of helix Processing helix chain 'h' and resid 458 through 487 Processing helix chain 'h' and resid 495 through 527 Processing helix chain 'i' and resid 283 through 309 removed outlier: 4.351A pdb=" N GLU i 290 " --> pdb=" O CYS i 286 " (cutoff:3.500A) Processing helix chain 'i' and resid 312 through 369 removed outlier: 3.551A pdb=" N LYS i 316 " --> pdb=" O LYS i 312 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN i 318 " --> pdb=" O MET i 314 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU i 319 " --> pdb=" O LEU i 315 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU i 340 " --> pdb=" O GLN i 336 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA i 341 " --> pdb=" O ARG i 337 " (cutoff:3.500A) Proline residue: i 366 - end of helix removed outlier: 3.667A pdb=" N LEU i 369 " --> pdb=" O THR i 365 " (cutoff:3.500A) Processing helix chain 'i' and resid 373 through 411 removed outlier: 3.955A pdb=" N VAL i 389 " --> pdb=" O GLN i 385 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN i 390 " --> pdb=" O GLN i 386 " (cutoff:3.500A) Processing helix chain 'i' and resid 416 through 451 removed outlier: 4.168A pdb=" N SER i 420 " --> pdb=" O PRO i 416 " (cutoff:3.500A) Processing helix chain 'j' and resid 157 through 169 Processing helix chain 'j' and resid 175 through 179 removed outlier: 3.590A pdb=" N THR j 178 " --> pdb=" O PHE j 175 " (cutoff:3.500A) Processing helix chain 'j' and resid 320 through 326 removed outlier: 3.810A pdb=" N GLN j 326 " --> pdb=" O LYS j 322 " (cutoff:3.500A) Processing helix chain 'j' and resid 333 through 344 Processing helix chain 'j' and resid 356 through 425 removed outlier: 3.518A pdb=" N LEU j 361 " --> pdb=" O GLY j 357 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG j 425 " --> pdb=" O GLN j 421 " (cutoff:3.500A) Processing helix chain 'j' and resid 456 through 474 Processing helix chain 'j' and resid 490 through 520 removed outlier: 3.873A pdb=" N HIS j 494 " --> pdb=" O GLU j 490 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE j 508 " --> pdb=" O HIS j 504 " (cutoff:3.500A) Processing helix chain 'l' and resid 360 through 449 removed outlier: 3.523A pdb=" N GLN l 392 " --> pdb=" O ARG l 388 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG l 396 " --> pdb=" O GLN l 392 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU l 429 " --> pdb=" O GLN l 425 " (cutoff:3.500A) Proline residue: l 434 - end of helix Processing helix chain 'l' and resid 458 through 487 Processing helix chain 'l' and resid 495 through 527 removed outlier: 3.693A pdb=" N TRP l 512 " --> pdb=" O ASP l 508 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP l 514 " --> pdb=" O LEU l 510 " (cutoff:3.500A) Processing helix chain 'k' and resid 283 through 309 removed outlier: 4.321A pdb=" N GLU k 290 " --> pdb=" O CYS k 286 " (cutoff:3.500A) Processing helix chain 'k' and resid 312 through 365 removed outlier: 3.962A pdb=" N GLN k 318 " --> pdb=" O MET k 314 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU k 319 " --> pdb=" O LEU k 315 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU k 340 " --> pdb=" O GLN k 336 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA k 341 " --> pdb=" O ARG k 337 " (cutoff:3.500A) Processing helix chain 'k' and resid 374 through 411 removed outlier: 3.513A pdb=" N PHE k 387 " --> pdb=" O LEU k 383 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL k 389 " --> pdb=" O GLN k 385 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN k 392 " --> pdb=" O GLU k 388 " (cutoff:3.500A) Processing helix chain 'k' and resid 417 through 452 Processing helix chain 'm' and resid 19 through 34 Processing helix chain 'm' and resid 38 through 43 Processing helix chain 'm' and resid 57 through 61 Processing helix chain 'm' and resid 86 through 93 removed outlier: 3.626A pdb=" N ILE m 90 " --> pdb=" O PRO m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 94 through 96 No H-bonds generated for 'chain 'm' and resid 94 through 96' Processing helix chain 'm' and resid 106 through 109 Processing helix chain 'm' and resid 186 through 190 removed outlier: 3.796A pdb=" N SER m 189 " --> pdb=" O ASP m 186 " (cutoff:3.500A) Processing helix chain 'm' and resid 313 through 325 Processing helix chain 'm' and resid 329 through 334 removed outlier: 3.805A pdb=" N LYS m 334 " --> pdb=" O ASN m 331 " (cutoff:3.500A) Processing helix chain 'm' and resid 481 through 486 removed outlier: 3.558A pdb=" N GLN m 485 " --> pdb=" O PRO m 481 " (cutoff:3.500A) Processing helix chain 'm' and resid 509 through 521 Processing helix chain 'm' and resid 526 through 536 Processing helix chain 'm' and resid 538 through 550 removed outlier: 3.609A pdb=" N LEU m 548 " --> pdb=" O THR m 544 " (cutoff:3.500A) Processing helix chain 'm' and resid 553 through 555 No H-bonds generated for 'chain 'm' and resid 553 through 555' Processing helix chain 'm' and resid 556 through 570 Processing helix chain 'm' and resid 654 through 669 Processing helix chain 'm' and resid 670 through 672 No H-bonds generated for 'chain 'm' and resid 670 through 672' Processing helix chain 'm' and resid 697 through 719 Processing helix chain 'm' and resid 770 through 798 Processing helix chain 'm' and resid 799 through 807 removed outlier: 3.507A pdb=" N LEU m 807 " --> pdb=" O VAL m 803 " (cutoff:3.500A) Processing helix chain 'm' and resid 808 through 818 Processing helix chain 'm' and resid 819 through 826 Processing helix chain 'm' and resid 827 through 845 removed outlier: 3.892A pdb=" N THR m 831 " --> pdb=" O ASP m 827 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP m 845 " --> pdb=" O CYS m 841 " (cutoff:3.500A) Processing helix chain 'm' and resid 849 through 860 Processing helix chain 'm' and resid 867 through 882 removed outlier: 3.746A pdb=" N ARG m 882 " --> pdb=" O LEU m 878 " (cutoff:3.500A) Processing helix chain 'm' and resid 886 through 904 removed outlier: 3.824A pdb=" N ILE m 904 " --> pdb=" O GLU m 900 " (cutoff:3.500A) Processing helix chain 'm' and resid 909 through 920 Processing helix chain 'm' and resid 922 through 938 Processing helix chain 'm' and resid 941 through 949 Processing helix chain 'm' and resid 959 through 984 removed outlier: 4.125A pdb=" N CYS m 971 " --> pdb=" O ASN m 967 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE m 972 " --> pdb=" O SER m 968 " (cutoff:3.500A) Processing helix chain 'm' and resid 1011 through 1025 Processing helix chain 'm' and resid 1029 through 1043 Processing helix chain 'm' and resid 1045 through 1051 Processing helix chain 'm' and resid 1056 through 1068 Processing helix chain 'O' and resid 35 through 40 removed outlier: 3.875A pdb=" N SER O 40 " --> pdb=" O PRO O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 148 Processing helix chain 'N' and resid 2 through 37 Proline residue: N 26 - end of helix removed outlier: 3.647A pdb=" N ARG N 37 " --> pdb=" O ILE N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 55 Processing helix chain 'N' and resid 56 through 81 Processing helix chain 'N' and resid 90 through 98 Processing helix chain 'N' and resid 100 through 125 Processing helix chain 'N' and resid 154 through 176 Processing helix chain 'N' and resid 189 through 223 Proline residue: N 199 - end of helix Processing helix chain 'N' and resid 257 through 284 Processing helix chain 'N' and resid 295 through 301 removed outlier: 4.315A pdb=" N GLU N 300 " --> pdb=" O GLU N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 309 Processing helix chain 'N' and resid 312 through 330 Processing helix chain 'N' and resid 330 through 338 Processing helix chain 'N' and resid 347 through 373 removed outlier: 3.516A pdb=" N GLU N 373 " --> pdb=" O ILE N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 540 Processing helix chain 'N' and resid 543 through 562 removed outlier: 4.266A pdb=" N HIS N 547 " --> pdb=" O ASP N 543 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE N 562 " --> pdb=" O VAL N 558 " (cutoff:3.500A) Processing helix chain 'N' and resid 570 through 594 removed outlier: 4.629A pdb=" N SER N 575 " --> pdb=" O GLN N 571 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER N 576 " --> pdb=" O THR N 572 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE N 580 " --> pdb=" O SER N 576 " (cutoff:3.500A) Processing helix chain 'N' and resid 616 through 636 Processing helix chain 'N' and resid 637 through 642 Processing helix chain 'N' and resid 645 through 657 removed outlier: 3.584A pdb=" N LYS N 651 " --> pdb=" O GLU N 647 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 40 removed outlier: 3.875A pdb=" N SER o 40 " --> pdb=" O PRO o 36 " (cutoff:3.500A) Processing helix chain 'o' and resid 142 through 148 Processing helix chain 'n' and resid 2 through 37 Proline residue: n 26 - end of helix removed outlier: 3.648A pdb=" N ARG n 37 " --> pdb=" O ILE n 33 " (cutoff:3.500A) Processing helix chain 'n' and resid 42 through 55 Processing helix chain 'n' and resid 56 through 81 Processing helix chain 'n' and resid 90 through 98 Processing helix chain 'n' and resid 100 through 125 Processing helix chain 'n' and resid 154 through 176 Processing helix chain 'n' and resid 189 through 223 Proline residue: n 199 - end of helix Processing helix chain 'n' and resid 257 through 284 Processing helix chain 'n' and resid 295 through 301 removed outlier: 4.316A pdb=" N GLU n 300 " --> pdb=" O GLU n 297 " (cutoff:3.500A) Processing helix chain 'n' and resid 302 through 309 Processing helix chain 'n' and resid 312 through 330 Processing helix chain 'n' and resid 330 through 338 Processing helix chain 'n' and resid 347 through 373 removed outlier: 3.517A pdb=" N GLU n 373 " --> pdb=" O ILE n 369 " (cutoff:3.500A) Processing helix chain 'n' and resid 534 through 540 Processing helix chain 'n' and resid 543 through 562 removed outlier: 4.265A pdb=" N HIS n 547 " --> pdb=" O ASP n 543 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE n 562 " --> pdb=" O VAL n 558 " (cutoff:3.500A) Processing helix chain 'n' and resid 570 through 594 removed outlier: 4.629A pdb=" N SER n 575 " --> pdb=" O GLN n 571 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER n 576 " --> pdb=" O THR n 572 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE n 580 " --> pdb=" O SER n 576 " (cutoff:3.500A) Processing helix chain 'n' and resid 616 through 636 Processing helix chain 'n' and resid 637 through 642 Processing helix chain 'n' and resid 645 through 657 removed outlier: 3.584A pdb=" N LYS n 651 " --> pdb=" O GLU n 647 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 784 through 787 Processing sheet with id=AA2, first strand: chain 'A' and resid 1215 through 1217 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 477 Processing sheet with id=AA4, first strand: chain 'B' and resid 499 through 500 removed outlier: 3.898A pdb=" N LYS B 499 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AA6, first strand: chain 'C' and resid 586 through 588 Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 54 removed outlier: 5.384A pdb=" N LEU D 381 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER D 365 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS D 383 " --> pdb=" O TYR D 363 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 100 through 105 Processing sheet with id=AA9, first strand: chain 'D' and resid 142 through 146 Processing sheet with id=AB1, first strand: chain 'D' and resid 142 through 146 Processing sheet with id=AB2, first strand: chain 'D' and resid 209 through 214 removed outlier: 6.440A pdb=" N SER D 223 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE D 212 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE D 221 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE D 220 " --> pdb=" O VAL D 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.948A pdb=" N GLN D 275 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 294 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER D 311 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 296 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 402 through 408 removed outlier: 6.609A pdb=" N ALA D 415 " --> pdb=" O HIS D 403 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA D 405 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU D 413 " --> pdb=" O ALA D 405 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR D 407 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 411 " --> pdb=" O TYR D 407 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 492 through 498 removed outlier: 3.543A pdb=" N LYS D 492 " --> pdb=" O LYS D 507 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 575 through 577 removed outlier: 4.446A pdb=" N GLN D 575 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL D 652 " --> pdb=" O GLN D 575 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 677 through 684 Processing sheet with id=AB8, first strand: chain 'E' and resid 514 through 515 Processing sheet with id=AB9, first strand: chain 'E' and resid 586 through 588 Processing sheet with id=AC1, first strand: chain 'F' and resid 52 through 54 removed outlier: 6.516A pdb=" N THR F 52 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU F 381 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER F 365 " --> pdb=" O LEU F 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 81 through 84 removed outlier: 4.035A pdb=" N ARG F 493 " --> pdb=" O VAL F 458 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 100 through 105 Processing sheet with id=AC4, first strand: chain 'F' and resid 142 through 146 removed outlier: 3.617A pdb=" N SER F 142 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 142 through 146 removed outlier: 3.617A pdb=" N SER F 142 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 209 through 214 removed outlier: 6.623A pdb=" N SER F 223 " --> pdb=" O LEU F 210 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE F 212 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE F 221 " --> pdb=" O ILE F 212 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE F 220 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.824A pdb=" N ILE F 294 " --> pdb=" O SER F 311 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER F 311 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL F 296 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 402 through 408 removed outlier: 6.737A pdb=" N VAL F 402 " --> pdb=" O SER F 417 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER F 417 " --> pdb=" O VAL F 402 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS F 404 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 677 through 684 Processing sheet with id=AD1, first strand: chain 'G' and resid 181 through 185 removed outlier: 4.233A pdb=" N GLY G 181 " --> pdb=" O MET G 355 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET G 355 " --> pdb=" O GLY G 181 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE G 183 " --> pdb=" O VAL G 353 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 183 through 185 removed outlier: 3.737A pdb=" N PHE J 183 " --> pdb=" O VAL J 353 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 52 through 54 removed outlier: 5.436A pdb=" N LEU M 381 " --> pdb=" O SER M 365 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER M 365 " --> pdb=" O LEU M 381 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS M 383 " --> pdb=" O TYR M 363 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 81 through 83 removed outlier: 3.807A pdb=" N LYS M 492 " --> pdb=" O LYS M 507 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG M 493 " --> pdb=" O VAL M 458 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 100 through 105 Processing sheet with id=AD6, first strand: chain 'M' and resid 142 through 146 removed outlier: 7.396A pdb=" N ILE M 157 " --> pdb=" O PHE M 176 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE M 176 " --> pdb=" O ILE M 157 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 142 through 146 removed outlier: 7.396A pdb=" N ILE M 157 " --> pdb=" O PHE M 176 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE M 176 " --> pdb=" O ILE M 157 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 209 through 214 removed outlier: 3.864A pdb=" N SER M 211 " --> pdb=" O SER M 223 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE M 220 " --> pdb=" O VAL M 232 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 273 through 278 removed outlier: 5.723A pdb=" N ASP M 298 " --> pdb=" O ARG M 308 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ARG M 308 " --> pdb=" O ASP M 298 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 402 through 408 removed outlier: 6.713A pdb=" N VAL M 402 " --> pdb=" O SER M 417 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER M 417 " --> pdb=" O VAL M 402 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS M 404 " --> pdb=" O ALA M 415 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 677 through 684 Processing sheet with id=AE3, first strand: chain 'a' and resid 784 through 787 Processing sheet with id=AE4, first strand: chain 'a' and resid 1215 through 1217 Processing sheet with id=AE5, first strand: chain 'b' and resid 473 through 477 Processing sheet with id=AE6, first strand: chain 'b' and resid 499 through 500 removed outlier: 3.897A pdb=" N LYS b 499 " --> pdb=" O ILE b 513 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 313 through 314 Processing sheet with id=AE8, first strand: chain 'c' and resid 586 through 588 Processing sheet with id=AE9, first strand: chain 'd' and resid 52 through 54 removed outlier: 5.566A pdb=" N LEU d 381 " --> pdb=" O SER d 365 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER d 365 " --> pdb=" O LEU d 381 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'd' and resid 100 through 105 Processing sheet with id=AF2, first strand: chain 'd' and resid 142 through 146 removed outlier: 3.632A pdb=" N SER d 175 " --> pdb=" O GLN d 193 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 142 through 146 Processing sheet with id=AF4, first strand: chain 'd' and resid 209 through 214 removed outlier: 3.542A pdb=" N SER d 211 " --> pdb=" O SER d 223 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE d 220 " --> pdb=" O VAL d 232 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 275 through 278 removed outlier: 3.680A pdb=" N GLN d 275 " --> pdb=" O ARG d 288 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE d 294 " --> pdb=" O SER d 311 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER d 311 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL d 296 " --> pdb=" O VAL d 309 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 402 through 408 removed outlier: 6.913A pdb=" N ALA d 415 " --> pdb=" O HIS d 403 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA d 405 " --> pdb=" O LEU d 413 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU d 413 " --> pdb=" O ALA d 405 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR d 407 " --> pdb=" O VAL d 411 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL d 411 " --> pdb=" O TYR d 407 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU d 418 " --> pdb=" O ASN d 422 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASN d 422 " --> pdb=" O GLU d 418 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 493 through 498 Processing sheet with id=AF8, first strand: chain 'd' and resid 575 through 577 removed outlier: 4.071A pdb=" N GLN d 575 " --> pdb=" O VAL d 652 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL d 652 " --> pdb=" O GLN d 575 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 677 through 684 Processing sheet with id=AG1, first strand: chain 'e' and resid 514 through 515 Processing sheet with id=AG2, first strand: chain 'e' and resid 586 through 588 Processing sheet with id=AG3, first strand: chain 'f' and resid 52 through 54 removed outlier: 5.444A pdb=" N LEU f 381 " --> pdb=" O SER f 365 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER f 365 " --> pdb=" O LEU f 381 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS f 383 " --> pdb=" O TYR f 363 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'f' and resid 81 through 84 removed outlier: 4.105A pdb=" N ARG f 493 " --> pdb=" O VAL f 458 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA f 454 " --> pdb=" O LEU f 497 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'f' and resid 100 through 105 Processing sheet with id=AG6, first strand: chain 'f' and resid 142 through 146 removed outlier: 3.740A pdb=" N SER f 142 " --> pdb=" O SER f 164 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'f' and resid 142 through 146 removed outlier: 3.740A pdb=" N SER f 142 " --> pdb=" O SER f 164 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'f' and resid 209 through 214 removed outlier: 6.315A pdb=" N SER f 223 " --> pdb=" O LEU f 210 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE f 212 " --> pdb=" O PHE f 221 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE f 221 " --> pdb=" O ILE f 212 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE f 220 " --> pdb=" O VAL f 232 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'f' and resid 275 through 279 removed outlier: 6.602A pdb=" N ILE f 294 " --> pdb=" O SER f 311 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER f 311 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL f 296 " --> pdb=" O VAL f 309 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'f' and resid 402 through 408 removed outlier: 6.832A pdb=" N VAL f 402 " --> pdb=" O SER f 417 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER f 417 " --> pdb=" O VAL f 402 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS f 404 " --> pdb=" O ALA f 415 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'f' and resid 677 through 684 Processing sheet with id=AH3, first strand: chain 'g' and resid 180 through 185 removed outlier: 4.740A pdb=" N GLY g 181 " --> pdb=" O MET g 355 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET g 355 " --> pdb=" O GLY g 181 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE g 183 " --> pdb=" O VAL g 353 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'j' and resid 183 through 185 Processing sheet with id=AH5, first strand: chain 'm' and resid 52 through 54 removed outlier: 5.435A pdb=" N LEU m 381 " --> pdb=" O SER m 365 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER m 365 " --> pdb=" O LEU m 381 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS m 383 " --> pdb=" O TYR m 363 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'm' and resid 81 through 83 removed outlier: 3.806A pdb=" N LYS m 492 " --> pdb=" O LYS m 507 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG m 493 " --> pdb=" O VAL m 458 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'm' and resid 100 through 105 Processing sheet with id=AH8, first strand: chain 'm' and resid 142 through 146 removed outlier: 7.397A pdb=" N ILE m 157 " --> pdb=" O PHE m 176 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE m 176 " --> pdb=" O ILE m 157 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'm' and resid 142 through 146 removed outlier: 7.397A pdb=" N ILE m 157 " --> pdb=" O PHE m 176 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE m 176 " --> pdb=" O ILE m 157 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'm' and resid 209 through 214 removed outlier: 3.863A pdb=" N SER m 211 " --> pdb=" O SER m 223 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE m 220 " --> pdb=" O VAL m 232 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'm' and resid 273 through 278 removed outlier: 5.723A pdb=" N ASP m 298 " --> pdb=" O ARG m 308 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ARG m 308 " --> pdb=" O ASP m 298 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'm' and resid 402 through 408 removed outlier: 6.714A pdb=" N VAL m 402 " --> pdb=" O SER m 417 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER m 417 " --> pdb=" O VAL m 402 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS m 404 " --> pdb=" O ALA m 415 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'm' and resid 677 through 684 Processing sheet with id=AI5, first strand: chain 'O' and resid 2 through 3 removed outlier: 6.064A pdb=" N CYS O 2 " --> pdb=" O ASP O 384 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR O 380 " --> pdb=" O SER O 359 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE O 357 " --> pdb=" O VAL O 382 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL O 356 " --> pdb=" O VAL O 351 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL O 351 " --> pdb=" O VAL O 356 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR O 337 " --> pdb=" O ALA O 350 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'O' and resid 16 through 21 removed outlier: 7.084A pdb=" N VAL O 26 " --> pdb=" O LEU O 18 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU O 20 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 161 through 163 Processing sheet with id=AI8, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AI9, first strand: chain 'O' and resid 253 through 256 removed outlier: 3.742A pdb=" N SER O 253 " --> pdb=" O ALA O 266 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 296 through 299 removed outlier: 4.169A pdb=" N PHE O 315 " --> pdb=" O TRP O 328 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 402 through 408 removed outlier: 5.064A pdb=" N ILE O 403 " --> pdb=" O LYS O 420 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS O 420 " --> pdb=" O ILE O 403 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG O 436 " --> pdb=" O PRO O 447 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG O 438 " --> pdb=" O LEU O 445 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU O 445 " --> pdb=" O ARG O 438 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 459 through 464 Processing sheet with id=AJ4, first strand: chain 'o' and resid 2 through 3 removed outlier: 6.064A pdb=" N CYS o 2 " --> pdb=" O ASP o 384 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR o 380 " --> pdb=" O SER o 359 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE o 357 " --> pdb=" O VAL o 382 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL o 356 " --> pdb=" O VAL o 351 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL o 351 " --> pdb=" O VAL o 356 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR o 337 " --> pdb=" O ALA o 350 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'o' and resid 16 through 21 removed outlier: 7.085A pdb=" N VAL o 26 " --> pdb=" O LEU o 18 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU o 20 " --> pdb=" O GLU o 24 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU o 24 " --> pdb=" O GLU o 20 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'o' and resid 161 through 163 Processing sheet with id=AJ7, first strand: chain 'o' and resid 203 through 205 Processing sheet with id=AJ8, first strand: chain 'o' and resid 253 through 256 removed outlier: 3.742A pdb=" N SER o 253 " --> pdb=" O ALA o 266 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'o' and resid 296 through 299 removed outlier: 4.169A pdb=" N PHE o 315 " --> pdb=" O TRP o 328 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'o' and resid 402 through 408 removed outlier: 5.064A pdb=" N ILE o 403 " --> pdb=" O LYS o 420 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS o 420 " --> pdb=" O ILE o 403 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG o 436 " --> pdb=" O PRO o 447 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG o 438 " --> pdb=" O LEU o 445 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU o 445 " --> pdb=" O ARG o 438 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'o' and resid 459 through 464 10448 hydrogen bonds defined for protein. 30597 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: 76.12 Time building geometry restraints manager: 36.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.56: 92558 1.56 - 1.91: 0 1.91 - 2.25: 0 2.25 - 2.59: 0 2.59 - 2.94: 1 Bond restraints: 92559 Sorted by residual: bond pdb=" C LEU D 979 " pdb=" N GLY D1014 " ideal model delta sigma weight residual 1.329 2.939 -1.610 1.40e-02 5.10e+03 1.32e+04 bond pdb=" C SER K 415 " pdb=" N PRO K 416 " ideal model delta sigma weight residual 1.334 1.490 -0.156 2.34e-02 1.83e+03 4.43e+01 bond pdb=" C GLU A 809 " pdb=" N SER A 810 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.07e-02 2.33e+03 1.36e+01 bond pdb=" C PRO d1366 " pdb=" N ALA d1367 " ideal model delta sigma weight residual 1.323 1.272 0.050 1.64e-02 3.72e+03 9.37e+00 bond pdb=" N ILE f 651 " pdb=" CA ILE f 651 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.13e+00 ... (remaining 92554 not shown) Histogram of bond angle deviations from ideal: 58.81 - 76.09: 1 76.09 - 93.36: 0 93.36 - 110.64: 31772 110.64 - 127.91: 96882 127.91 - 145.19: 17 Bond angle restraints: 128672 Sorted by residual: angle pdb=" O LEU D 979 " pdb=" C LEU D 979 " pdb=" N GLY D1014 " ideal model delta sigma weight residual 122.59 58.81 63.78 1.33e+00 5.65e-01 2.30e+03 angle pdb=" C SER K 415 " pdb=" N PRO K 416 " pdb=" CA PRO K 416 " ideal model delta sigma weight residual 119.84 145.19 -25.35 1.25e+00 6.40e-01 4.11e+02 angle pdb=" C LEU D 979 " pdb=" N GLY D1014 " pdb=" CA GLY D1014 " ideal model delta sigma weight residual 121.70 103.67 18.03 1.80e+00 3.09e-01 1.00e+02 angle pdb=" CA LEU D 979 " pdb=" C LEU D 979 " pdb=" N GLY D1014 " ideal model delta sigma weight residual 116.84 104.34 12.50 1.71e+00 3.42e-01 5.34e+01 angle pdb=" N LEU i 412 " pdb=" CA LEU i 412 " pdb=" C LEU i 412 " ideal model delta sigma weight residual 113.50 105.09 8.41 1.65e+00 3.67e-01 2.60e+01 ... (remaining 128667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.72: 52364 7.72 - 15.44: 1773 15.44 - 23.15: 120 23.15 - 30.87: 22 30.87 - 38.59: 5 Dihedral angle restraints: 54284 sinusoidal: 0 harmonic: 54284 Sorted by residual: dihedral pdb=" CA GLN m 537 " pdb=" C GLN m 537 " pdb=" N GLU m 538 " pdb=" CA GLU m 538 " ideal model delta harmonic sigma weight residual -180.00 -141.41 -38.59 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" CA GLN M 537 " pdb=" C GLN M 537 " pdb=" N GLU M 538 " pdb=" CA GLU M 538 " ideal model delta harmonic sigma weight residual -180.00 -141.45 -38.55 0 5.00e+00 4.00e-02 5.95e+01 dihedral pdb=" CA ILE f 115 " pdb=" C ILE f 115 " pdb=" N ASP f 116 " pdb=" CA ASP f 116 " ideal model delta harmonic sigma weight residual -180.00 -144.36 -35.64 0 5.00e+00 4.00e-02 5.08e+01 ... (remaining 54281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 13361 0.042 - 0.083: 3649 0.083 - 0.125: 839 0.125 - 0.166: 54 0.166 - 0.208: 6 Chirality restraints: 17909 Sorted by residual: chirality pdb=" CA LEU k 412 " pdb=" N LEU k 412 " pdb=" C LEU k 412 " pdb=" CB LEU k 412 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE l 446 " pdb=" N ILE l 446 " pdb=" C ILE l 446 " pdb=" CB ILE l 446 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA LEU L 448 " pdb=" N LEU L 448 " pdb=" C LEU L 448 " pdb=" CB LEU L 448 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 17906 not shown) Planarity restraints: 18466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 979 " -0.177 2.00e-02 2.50e+03 2.70e-01 7.27e+02 pdb=" C LEU D 979 " 0.429 2.00e-02 2.50e+03 pdb=" O LEU D 979 " -0.274 2.00e-02 2.50e+03 pdb=" N GLY D1014 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU a1553 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C GLU a1553 " -0.046 2.00e-02 2.50e+03 pdb=" O GLU a1553 " 0.017 2.00e-02 2.50e+03 pdb=" N SER a1554 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1338 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.88e+00 pdb=" C PHE A1338 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A1338 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A1339 " -0.014 2.00e-02 2.50e+03 ... (remaining 18463 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1469 2.69 - 3.24: 105706 3.24 - 3.80: 146405 3.80 - 4.35: 149168 4.35 - 4.90: 241053 Nonbonded interactions: 643801 Sorted by model distance: nonbonded pdb=" N GLY A1021 " pdb=" O CYS A1025 " model vdw 2.138 2.520 nonbonded pdb=" O GLN F 537 " pdb=" N ASN F 539 " model vdw 2.157 2.520 nonbonded pdb=" O THR A1634 " pdb=" N GLN A1636 " model vdw 2.172 2.520 nonbonded pdb=" O ILE D 171 " pdb=" N LEU D 199 " model vdw 2.187 2.520 nonbonded pdb=" O CYS O 2 " pdb=" N ASP O 384 " model vdw 2.229 2.520 ... (remaining 643796 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 13 through 462 or resid 488 through 534 or resid 550 throu \ gh 1692 or resid 1697 through 2007)) selection = (chain 'a' and (resid 13 through 1841 or resid 1847 through 2007)) } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'C' and (resid 33 through 147 or resid 179 through 198 or resid 205 throu \ gh 233 or resid 241 through 289 or resid 291 through 301 or resid 319 through 34 \ 3 or resid 348 through 422 or resid 438 through 653 or resid 659 through 677 or \ resid 684 through 778 or resid 786 through 819)) selection = (chain 'E' and (resid 33 through 277 or resid 285 or resid 291 through 422 or re \ sid 438 through 501 or resid 529 through 798 or resid 807 through 819)) selection = (chain 'c' and (resid 33 through 147 or resid 179 through 198 or resid 205 throu \ gh 233 or resid 241 through 289 or resid 291 through 301 or resid 319 through 34 \ 3 or resid 348 through 422 or resid 438 through 653 or resid 659 through 677 or \ resid 684 through 778 or resid 786 through 819)) selection = (chain 'e' and (resid 33 through 277 or resid 285 or resid 291 through 422 or re \ sid 438 through 501 or resid 529 through 798 or resid 807 through 819)) } ncs_group { reference = (chain 'D' and (resid 13 through 33 or resid 39 through 56 or resid 76 through 1 \ 47 or resid 157 through 235 or resid 244 through 250 or resid 273 through 432 or \ resid 440 through 459 or resid 486 through 576 or resid 650 through 721 or resi \ d 766 through 859 or resid 868 through 884 or resid 887 through 1253 or resid 12 \ 61 through 1388)) selection = (chain 'F' and (resid 13 through 190 or resid 192 through 389 or resid 398 throu \ gh 845 or resid 850 through 859 or resid 868 through 949 or resid 959 through 97 \ 9 or resid 1014 through 1118 or resid 1133 through 1161 or resid 1168 through 12 \ 30 or resid 1235 through 1334 or resid 1344 through 1388)) selection = (chain 'd' and (resid 13 through 33 or resid 39 through 56 or resid 76 through 1 \ 47 or resid 157 through 235 or resid 244 through 250 or resid 273 through 432 or \ resid 440 through 459 or resid 486 through 576 or resid 650 through 721 or resi \ d 766 through 859 or resid 868 through 884 or resid 887 through 949 or resid 959 \ through 979 or resid 1014 through 1253 or resid 1261 through 1388)) selection = (chain 'f' and (resid 13 through 33 or resid 39 through 190 or resid 192 through \ 389 or resid 398 through 845 or resid 850 through 859 or resid 868 through 949 \ or resid 959 through 979 or resid 1014 through 1118 or resid 1133 through 1161 o \ r resid 1168 through 1230 or resid 1235 through 1334 or resid 1344 through 1388) \ ) } ncs_group { reference = (chain 'G' and (resid 156 through 429 or resid 456 through 520)) selection = chain 'J' selection = (chain 'g' and (resid 156 through 429 or resid 456 through 520)) selection = chain 'j' } ncs_group { reference = (chain 'H' and (resid 359 through 449 or resid 457 through 527)) selection = chain 'L' selection = (chain 'h' and (resid 359 through 449 or resid 457 through 527)) selection = chain 'l' } ncs_group { reference = (chain 'I' and (resid 282 through 367 or resid 373 through 452)) selection = chain 'K' selection = (chain 'i' and (resid 282 through 367 or resid 373 through 452)) selection = chain 'k' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 29.630 Check model and map are aligned: 1.010 Set scattering table: 0.650 Process input model: 256.620 Find NCS groups from input model: 7.170 Set up NCS constraints: 0.750 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 308.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 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 : 0.006 1.610 92559 Z= 0.333 Angle : 0.625 63.778 128672 Z= 0.435 Chirality : 0.039 0.208 17909 Planarity : 0.004 0.270 18466 Dihedral : 4.937 38.588 18466 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.74 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.36 (0.05), residues: 18202 helix: -1.36 (0.04), residues: 12292 sheet: -0.80 (0.13), residues: 1363 loop : -1.81 (0.09), residues: 4547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36404 Ramachandran restraints generated. 18202 Oldfield, 0 Emsley, 18202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36404 Ramachandran restraints generated. 18202 Oldfield, 0 Emsley, 18202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.835 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.6559 time to fit residues: 627.2490 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1569 optimal weight: 0.8980 chunk 1409 optimal weight: 40.0000 chunk 781 optimal weight: 40.0000 chunk 481 optimal weight: 30.0000 chunk 950 optimal weight: 30.0000 chunk 752 optimal weight: 6.9990 chunk 1457 optimal weight: 70.0000 chunk 563 optimal weight: 10.0000 chunk 885 optimal weight: 50.0000 chunk 1084 optimal weight: 50.0000 chunk 1688 optimal weight: 50.0000 overall best weight: 15.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 92559 Z= 0.334 Angle : 0.630 11.845 128672 Z= 0.411 Chirality : 0.043 0.238 17909 Planarity : 0.005 0.031 18466 Dihedral : 5.694 41.811 18466 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % 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: -1.45 (0.06), residues: 18204 helix: -0.50 (0.04), residues: 12374 sheet: -0.84 (0.14), residues: 1316 loop : -1.90 (0.09), residues: 4514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 8.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.7077 time to fit residues: 675.1081 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 938 optimal weight: 20.0000 chunk 523 optimal weight: 20.0000 chunk 1405 optimal weight: 50.0000 chunk 1149 optimal weight: 50.0000 chunk 465 optimal weight: 20.0000 chunk 1691 optimal weight: 50.0000 chunk 1826 optimal weight: 30.0000 chunk 1506 optimal weight: 10.0000 chunk 1677 optimal weight: 50.0000 chunk 576 optimal weight: 3.9990 chunk 1356 optimal weight: 4.9990 overall best weight: 11.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 92559 Z= 0.243 Angle : 0.503 10.179 128672 Z= 0.326 Chirality : 0.040 0.194 17909 Planarity : 0.003 0.023 18466 Dihedral : 4.931 36.083 18466 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.06), residues: 18204 helix: 0.31 (0.05), residues: 12393 sheet: -0.86 (0.14), residues: 1323 loop : -1.83 (0.09), residues: 4488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.865 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.6790 time to fit residues: 649.7806 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1670 optimal weight: 30.0000 chunk 1271 optimal weight: 2.9990 chunk 877 optimal weight: 6.9990 chunk 187 optimal weight: 50.0000 chunk 807 optimal weight: 0.9990 chunk 1135 optimal weight: 4.9990 chunk 1697 optimal weight: 50.0000 chunk 1796 optimal weight: 40.0000 chunk 886 optimal weight: 30.0000 chunk 1608 optimal weight: 50.0000 chunk 484 optimal weight: 50.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 92559 Z= 0.197 Angle : 0.444 9.386 128672 Z= 0.285 Chirality : 0.039 0.168 17909 Planarity : 0.003 0.025 18466 Dihedral : 4.381 33.371 18466 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.06 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.06), residues: 18204 helix: 1.17 (0.05), residues: 12407 sheet: -0.84 (0.14), residues: 1292 loop : -1.69 (0.09), residues: 4505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.985 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.6903 time to fit residues: 657.2325 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1496 optimal weight: 20.0000 chunk 1020 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 1337 optimal weight: 30.0000 chunk 741 optimal weight: 50.0000 chunk 1533 optimal weight: 50.0000 chunk 1242 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 917 optimal weight: 60.0000 chunk 1612 optimal weight: 50.0000 chunk 453 optimal weight: 50.0000 overall best weight: 17.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 92559 Z= 0.361 Angle : 0.628 9.536 128672 Z= 0.412 Chirality : 0.043 0.217 17909 Planarity : 0.004 0.027 18466 Dihedral : 5.720 34.880 18466 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.28 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % 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: -1.10 (0.06), residues: 18204 helix: -0.06 (0.04), residues: 12302 sheet: -0.96 (0.14), residues: 1224 loop : -2.24 (0.09), residues: 4678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.881 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.7129 time to fit residues: 680.3011 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 604 optimal weight: 0.0970 chunk 1618 optimal weight: 6.9990 chunk 355 optimal weight: 8.9990 chunk 1055 optimal weight: 7.9990 chunk 443 optimal weight: 5.9990 chunk 1798 optimal weight: 9.9990 chunk 1493 optimal weight: 6.9990 chunk 832 optimal weight: 50.0000 chunk 149 optimal weight: 30.0000 chunk 594 optimal weight: 30.0000 chunk 944 optimal weight: 5.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 92559 Z= 0.136 Angle : 0.393 8.312 128672 Z= 0.249 Chirality : 0.038 0.146 17909 Planarity : 0.002 0.021 18466 Dihedral : 4.232 32.508 18466 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.42 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.06), residues: 18204 helix: 1.48 (0.05), residues: 12401 sheet: -0.99 (0.14), residues: 1316 loop : -1.72 (0.09), residues: 4487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.941 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.6836 time to fit residues: 656.8496 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1734 optimal weight: 0.0870 chunk 202 optimal weight: 50.0000 chunk 1024 optimal weight: 50.0000 chunk 1313 optimal weight: 1.9990 chunk 1017 optimal weight: 8.9990 chunk 1514 optimal weight: 20.0000 chunk 1004 optimal weight: 20.0000 chunk 1791 optimal weight: 30.0000 chunk 1121 optimal weight: 30.0000 chunk 1092 optimal weight: 0.0060 chunk 827 optimal weight: 10.0000 overall best weight: 4.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 92559 Z= 0.111 Angle : 0.356 6.847 128672 Z= 0.225 Chirality : 0.037 0.142 17909 Planarity : 0.002 0.018 18466 Dihedral : 3.699 30.453 18466 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.46 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % 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: 1.89 (0.07), residues: 18204 helix: 2.38 (0.05), residues: 12436 sheet: -0.87 (0.14), residues: 1280 loop : -1.42 (0.10), residues: 4488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.972 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.7015 time to fit residues: 668.4771 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1108 optimal weight: 0.0170 chunk 715 optimal weight: 70.0000 chunk 1070 optimal weight: 50.0000 chunk 539 optimal weight: 0.9980 chunk 352 optimal weight: 20.0000 chunk 347 optimal weight: 0.9990 chunk 1139 optimal weight: 0.7980 chunk 1220 optimal weight: 7.9990 chunk 885 optimal weight: 50.0000 chunk 166 optimal weight: 20.0000 chunk 1408 optimal weight: 50.0000 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.019 92559 Z= 0.077 Angle : 0.318 7.247 128672 Z= 0.199 Chirality : 0.037 0.139 17909 Planarity : 0.001 0.018 18466 Dihedral : 3.272 27.984 18466 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.69 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % 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: 2.75 (0.07), residues: 18204 helix: 3.06 (0.05), residues: 12458 sheet: -0.80 (0.14), residues: 1327 loop : -1.13 (0.10), residues: 4419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.915 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.7078 time to fit residues: 676.3687 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1629 optimal weight: 10.0000 chunk 1716 optimal weight: 30.0000 chunk 1566 optimal weight: 50.0000 chunk 1669 optimal weight: 50.0000 chunk 1004 optimal weight: 20.0000 chunk 727 optimal weight: 80.0000 chunk 1311 optimal weight: 30.0000 chunk 512 optimal weight: 20.0000 chunk 1508 optimal weight: 20.0000 chunk 1579 optimal weight: 5.9990 chunk 1663 optimal weight: 50.0000 overall best weight: 15.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 92559 Z= 0.316 Angle : 0.554 9.562 128672 Z= 0.364 Chirality : 0.041 0.228 17909 Planarity : 0.003 0.025 18466 Dihedral : 4.688 28.849 18466 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.06), residues: 18204 helix: 1.32 (0.05), residues: 12392 sheet: -1.00 (0.14), residues: 1240 loop : -1.72 (0.09), residues: 4572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 8.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.7207 time to fit residues: 687.9282 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 7.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1096 optimal weight: 1.9990 chunk 1765 optimal weight: 30.0000 chunk 1077 optimal weight: 50.0000 chunk 837 optimal weight: 50.0000 chunk 1227 optimal weight: 7.9990 chunk 1852 optimal weight: 50.0000 chunk 1704 optimal weight: 40.0000 chunk 1474 optimal weight: 50.0000 chunk 153 optimal weight: 30.0000 chunk 1139 optimal weight: 30.0000 chunk 904 optimal weight: 2.9990 overall best weight: 14.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 92559 Z= 0.289 Angle : 0.542 8.599 128672 Z= 0.355 Chirality : 0.041 0.172 17909 Planarity : 0.004 0.029 18466 Dihedral : 5.133 32.710 18466 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.82 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.06), residues: 18204 helix: 0.62 (0.05), residues: 12326 sheet: -1.16 (0.14), residues: 1207 loop : -2.04 (0.09), residues: 4671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 36408 Ramachandran restraints generated. 18204 Oldfield, 0 Emsley, 18204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 8.584 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.7224 time to fit residues: 691.2228 Evaluate side-chains 492 residues out of total 16678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 8.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1171 optimal weight: 40.0000 chunk 1570 optimal weight: 9.9990 chunk 451 optimal weight: 40.0000 chunk 1359 optimal weight: 2.9990 chunk 217 optimal weight: 50.0000 chunk 409 optimal weight: 30.0000 chunk 1477 optimal weight: 50.0000 chunk 618 optimal weight: 40.0000 chunk 1516 optimal weight: 9.9990 chunk 187 optimal weight: 50.0000 chunk 272 optimal weight: 30.0000 overall best weight: 16.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.081669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.073388 restraints weight = 740467.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.072393 restraints weight = 874423.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.071049 restraints weight = 831054.957| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 92559 Z= 0.337 Angle : 0.596 9.532 128672 Z= 0.392 Chirality : 0.042 0.214 17909 Planarity : 0.004 0.030 18466 Dihedral : 5.509 32.702 18466 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.63 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.06), residues: 18204 helix: 0.13 (0.05), residues: 12295 sheet: -1.25 (0.15), residues: 1166 loop : -2.36 (0.09), residues: 4743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 14 PHE 0.000 0.000 PHE A 50 TYR 0.000 0.000 TYR A 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14193.51 seconds wall clock time: 248 minutes 14.11 seconds (14894.11 seconds total)