Starting phenix.real_space_refine on Wed Mar 27 01:22:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agw_15426/03_2024/8agw_15426_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agw_15426/03_2024/8agw_15426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agw_15426/03_2024/8agw_15426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agw_15426/03_2024/8agw_15426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agw_15426/03_2024/8agw_15426_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agw_15426/03_2024/8agw_15426_updated.pdb" } resolution = 2.6 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= 0.021 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 3643 5.49 5 Mg 13 5.21 5 S 168 5.16 5 C 80649 2.51 5 N 27422 2.21 5 O 38367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150269 Number of models: 1 Model: "" Number of chains: 68 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "B" Number of atoms: 1555 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "C" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1416 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "E" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "G" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1272 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "I" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "J" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 518 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "M" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "N" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1169 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "Q" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "V" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 78} Chain: "X" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Z" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 410 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 824 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "d" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 207 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "f" Number of atoms: 68802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3216, 68782 Classifications: {'RNA': 3216} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 220, 'rna3p_pur': 1449, 'rna3p_pyr': 1217} Link IDs: {'rna2p': 550, 'rna3p': 2665} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 3216, 68782 Classifications: {'RNA': 3216} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 221, 'rna3p_pur': 1449, 'rna3p_pyr': 1216} Link IDs: {'rna2p': 551, 'rna3p': 2664} Chain breaks: 3 bond proxies already assigned to first conformer: 76966 Chain: "h" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "i" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p_pur': 63, 'rna3p_pyr': 66} Link IDs: {'rna2p': 28, 'rna3p': 129} Chain: "j" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1874 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 234} Chain: "k" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2351 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 157} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "o" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "p" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "q" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1508 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "r" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1764 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "s" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1346 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "t" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "u" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "a" Number of atoms: 6573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6573 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 29, 'TRANS': 818} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 166 Chain: "e" Number of atoms: 11512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 11512 Classifications: {'peptide': 1527} Incomplete info: {'truncation_to_alanine': 270} Link IDs: {'PTRANS': 38, 'TRANS': 1488} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 978 Unresolved non-hydrogen angles: 1247 Unresolved non-hydrogen dihedrals: 813 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 12, 'ASN:plan1': 23, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 27, 'GLU:plan': 25, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 566 Chain: "g" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1651 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "x" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1579 Classifications: {'RNA': 74} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 28, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 57} Chain breaks: 1 Chain: "y" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 62} Chain breaks: 1 Chain: "z" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 728 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 182 Chain: "0" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "w" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1709 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' MG': 3, 'SPD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20901 SG CYS T 44 120.513 171.542 212.336 1.00 54.16 S ATOM 20919 SG CYS T 47 122.601 168.887 211.244 1.00 59.61 S ATOM 21191 SG CYS T 84 123.795 171.359 214.072 1.00 57.91 S ATOM 23302 SG CYS W 19 85.265 189.341 170.011 1.00 40.18 S ATOM 23327 SG CYS W 22 83.521 189.431 166.726 1.00 41.00 S ATOM 23427 SG CYS W 34 87.252 189.424 166.777 1.00 38.42 S ATOM 23445 SG CYS W 37 85.293 192.516 167.939 1.00 40.17 S ATOM 25002 SG CYS Z 96 133.617 140.708 76.316 1.00 54.37 S ATOM 25028 SG CYS Z 99 130.986 139.026 78.319 1.00 53.18 S ATOM 25115 SG CYS Z 110 130.864 138.505 74.638 1.00 52.08 S ATOM 25161 SG CYS Z 115 129.811 141.729 75.887 1.00 52.77 S ATOM 25359 SG CYS b 12 132.816 248.124 110.214 1.00 63.95 S ATOM 25394 SG CYS b 17 134.107 251.660 109.325 1.00 72.10 S ATOM 25858 SG CYS b 74 136.310 249.131 111.452 1.00 60.93 S ATOM 25880 SG CYS b 77 133.215 250.977 112.630 1.00 66.15 S ATOM 26403 SG CYS c 39 139.163 169.015 205.522 1.00 58.71 S ATOM 26426 SG CYS c 42 138.536 166.031 207.607 1.00 62.48 S ATOM 26535 SG CYS c 57 136.323 166.560 204.613 1.00 55.64 S ATOM 26553 SG CYS c 60 135.905 169.021 207.373 1.00 57.82 S ATOM A0W6Y SG CYS e1527 39.677 126.087 188.089 1.00285.10 S ATOM A0W7I SG CYS e1530 37.227 123.647 187.047 1.00279.23 S ATOM A0WCA SG CYS e1551 37.894 126.832 184.962 1.00286.27 S ATOM A0WCV SG CYS e1554 36.095 127.540 188.043 1.00284.05 S ATOM A0W2W SG CYS e1508 41.513 120.465 177.471 1.00285.58 S ATOM A0W3F SG CYS e1511 41.384 119.120 174.083 1.00284.14 S ATOM A0W98 SG CYS e1538 43.230 122.737 174.360 1.00281.30 S Residues with excluded nonbonded symmetry interactions: 198 residue: pdb=" N AVAL B 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 3 " occ=0.50 residue: pdb=" N AGLU B 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2AGLU B 4 " occ=0.50 residue: pdb=" N APRO B 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO B 5 " occ=0.50 residue: pdb=" N AVAL B 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 6 " occ=0.50 residue: pdb=" N AVAL B 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 7 " occ=0.50 residue: pdb=" N AVAL B 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 8 " occ=0.50 residue: pdb=" N AILE B 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE B 9 " occ=0.50 residue: pdb=" N AASP B 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2AASP B 10 " occ=0.50 residue: pdb=" N AGLY B 11 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 11 " occ=0.50 residue: pdb=" N ALYS B 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS B 12 " occ=0.50 residue: pdb=" N AGLY B 13 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 13 " occ=0.50 residue: pdb=" N AHIS B 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2AHIS B 14 " occ=0.50 ... (remaining 186 not shown) Time building chain proxies: 80.36, per 1000 atoms: 0.53 Number of scatterers: 150269 At special positions: 0 Unit cell: (232.98, 316.641, 262.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 168 16.00 P 3643 15.00 Mg 13 11.99 O 38367 8.00 N 27422 7.00 C 80649 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: 57.73 Conformation dependent library (CDL) restraints added in 10.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 47 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 84 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 44 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 22 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 19 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 37 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 34 " pdb=" ZN Z 201 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 99 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 110 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 115 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 96 " pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 12 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 17 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 39 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 57 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 60 " pdb=" ZN e2001 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1551 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1554 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1530 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1527 " pdb=" ZN e2002 " pdb="ZN ZN e2002 " - pdb=" ND1 HIS e1535 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1508 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1511 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1538 " Number of angles added : 33 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17498 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 363 helices and 84 sheets defined 49.2% alpha, 12.5% beta 1188 base pairs and 2007 stacking pairs defined. Time for finding SS restraints: 88.92 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.805A pdb=" N TYR A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.753A pdb=" N TRP A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.844A pdb=" N GLN A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 88' Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 139 through 145 removed outlier: 4.410A pdb=" N ASP A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 removed outlier: 5.055A pdb=" N TRP A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N CYS A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 153' Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 186 through 196 Processing helix chain 'B' and resid 15 through 30 removed outlier: 3.689A pdb=" N ALYS B 25 " --> pdb=" O ASER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 removed outlier: 4.078A pdb=" N ALYS B 60 " --> pdb=" O AASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 4.022A pdb=" N AGLY B 69 " --> pdb=" O AASN B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix No H-bonds generated for 'chain 'B' and resid 65 through 70' Processing helix chain 'B' and resid 75 through 89 removed outlier: 3.835A pdb=" N AMET B 87 " --> pdb=" O AALA B 83 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASER B 89 " --> pdb=" O AARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 removed outlier: 3.927A pdb=" N AARG B 101 " --> pdb=" O AALA B 97 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALEU B 102 " --> pdb=" O AALA B 98 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALYS B 103 " --> pdb=" O ALEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.914A pdb=" N ALYS B 114 " --> pdb=" O APRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 151 through 186 removed outlier: 3.814A pdb=" N ALYS B 170 " --> pdb=" O AGLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.729A pdb=" N SER C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ALA C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 25 through 37 removed outlier: 3.639A pdb=" N GLU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 84 through 106 Processing helix chain 'C' and resid 169 through 183 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.765A pdb=" N GLY C 73 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 75 " --> pdb=" O GLN C 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.961A pdb=" N LYS D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Proline residue: D 60 - end of helix Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.812A pdb=" N GLN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 147 through 154 removed outlier: 4.145A pdb=" N ARG D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 154' Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.909A pdb=" N VAL E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP E 23 " --> pdb=" O LYS E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 28 through 36 removed outlier: 5.178A pdb=" N ASN E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 48 Processing helix chain 'E' and resid 60 through 73 Processing helix chain 'E' and resid 77 through 82 removed outlier: 3.709A pdb=" N ARG E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 77 through 82' Processing helix chain 'E' and resid 84 through 113 Proline residue: E 90 - end of helix removed outlier: 6.827A pdb=" N VAL E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.686A pdb=" N VAL E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 157 Processing helix chain 'F' and resid 33 through 49 Processing helix chain 'F' and resid 98 through 114 Processing helix chain 'F' and resid 117 through 122 removed outlier: 5.662A pdb=" N HIS F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 4.881A pdb=" N PHE F 143 " --> pdb=" O TYR F 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 32 removed outlier: 4.512A pdb=" N TYR G 30 " --> pdb=" O HIS G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 4.286A pdb=" N ILE G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LYS G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 97' Processing helix chain 'G' and resid 99 through 121 removed outlier: 3.890A pdb=" N GLN G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 4.166A pdb=" N ASN H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY H 26 " --> pdb=" O PRO H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 72 through 88 Processing helix chain 'I' and resid 66 through 71 removed outlier: 5.400A pdb=" N LYS I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 removed outlier: 3.883A pdb=" N LEU I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Proline residue: I 127 - end of helix Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'J' and resid 33 through 43 Processing helix chain 'J' and resid 45 through 50 removed outlier: 3.562A pdb=" N ILE J 49 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 50' Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.644A pdb=" N ILE K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU K 64 " --> pdb=" O TYR K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 78 removed outlier: 3.734A pdb=" N LYS K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP K 78 " --> pdb=" O LYS K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 Processing helix chain 'K' and resid 131 through 140 removed outlier: 3.835A pdb=" N ASN K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 22 Processing helix chain 'L' and resid 23 through 32 removed outlier: 4.027A pdb=" N VAL L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 100 through 105 removed outlier: 3.567A pdb=" N LEU L 104 " --> pdb=" O HIS L 100 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 105' Processing helix chain 'L' and resid 112 through 123 Processing helix chain 'M' and resid 58 through 67 removed outlier: 5.381A pdb=" N VAL M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS M 67 " --> pdb=" O ALA M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 81 removed outlier: 3.569A pdb=" N LEU M 80 " --> pdb=" O ASN M 76 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 76 through 81' Processing helix chain 'M' and resid 92 through 97 removed outlier: 5.471A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 125 removed outlier: 3.596A pdb=" N VAL M 113 " --> pdb=" O GLU M 109 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY M 125 " --> pdb=" O ARG M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'N' and resid 2 through 7 removed outlier: 4.160A pdb=" N THR N 6 " --> pdb=" O PRO N 2 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS N 7 " --> pdb=" O SER N 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 7' Processing helix chain 'N' and resid 41 through 49 Processing helix chain 'N' and resid 64 through 69 removed outlier: 4.420A pdb=" N PHE N 68 " --> pdb=" O GLN N 64 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP N 69 " --> pdb=" O GLN N 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 64 through 69' Processing helix chain 'N' and resid 74 through 83 removed outlier: 4.577A pdb=" N TRP N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THR N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU N 81 " --> pdb=" O LYS N 77 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Proline residue: N 83 - end of helix Processing helix chain 'N' and resid 86 through 94 removed outlier: 4.083A pdb=" N ALA N 94 " --> pdb=" O TYR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 Processing helix chain 'N' and resid 131 through 142 Processing helix chain 'O' and resid 11 through 20 removed outlier: 4.643A pdb=" N ASN O 19 " --> pdb=" O LYS O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 59 removed outlier: 3.532A pdb=" N ASN O 42 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 26 through 37 Processing helix chain 'P' and resid 49 through 64 Processing helix chain 'P' and resid 73 through 82 removed outlier: 3.829A pdb=" N THR P 79 " --> pdb=" O ASN P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.972A pdb=" N LEU P 104 " --> pdb=" O ILE P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 21 removed outlier: 3.857A pdb=" N ARG Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 45 Processing helix chain 'Q' and resid 52 through 61 Processing helix chain 'R' and resid 21 through 26 removed outlier: 5.154A pdb=" N HIS R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.852A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET R 87 " --> pdb=" O GLU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 4.187A pdb=" N VAL R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 45 removed outlier: 4.453A pdb=" N PHE S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR S 44 " --> pdb=" O ASP S 40 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 66 removed outlier: 3.621A pdb=" N TYR T 62 " --> pdb=" O ARG T 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA T 63 " --> pdb=" O PRO T 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR T 64 " --> pdb=" O ARG T 60 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER T 66 " --> pdb=" O TYR T 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 58 through 66' Processing helix chain 'T' and resid 81 through 113 removed outlier: 3.752A pdb=" N GLU T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 12 removed outlier: 4.178A pdb=" N THR U 11 " --> pdb=" O TYR U 7 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS U 12 " --> pdb=" O GLU U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 38 removed outlier: 3.564A pdb=" N GLN U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU U 36 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER U 37 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 71 removed outlier: 4.591A pdb=" N THR U 46 " --> pdb=" O PRO U 42 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 82 removed outlier: 5.176A pdb=" N ALA U 82 " --> pdb=" O LYS U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 91 Processing helix chain 'U' and resid 93 through 99 Processing helix chain 'U' and resid 101 through 111 Processing helix chain 'V' and resid 25 through 30 removed outlier: 4.459A pdb=" N LYS V 29 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS V 30 " --> pdb=" O ILE V 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 25 through 30' Processing helix chain 'V' and resid 34 through 49 Processing helix chain 'V' and resid 51 through 64 Processing helix chain 'V' and resid 65 through 77 Processing helix chain 'V' and resid 79 through 100 Processing helix chain 'W' and resid 4 through 11 removed outlier: 3.650A pdb=" N GLY W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS W 10 " --> pdb=" O PRO W 6 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG W 11 " --> pdb=" O SER W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 58 Processing helix chain 'W' and resid 65 through 77 removed outlier: 5.841A pdb=" N HIS W 69 " --> pdb=" O ARG W 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER W 71 " --> pdb=" O LEU W 67 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 17 removed outlier: 3.795A pdb=" N ARG X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 69 Processing helix chain 'Y' and resid 6 through 21 removed outlier: 5.317A pdb=" N ARG Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 30 removed outlier: 4.499A pdb=" N ARG Y 28 " --> pdb=" O PRO Y 24 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG Y 30 " --> pdb=" O TRP Y 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 24 through 30' Processing helix chain 'Z' and resid 79 through 91 removed outlier: 3.872A pdb=" N TYR Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 48 Processing helix chain 'c' and resid 19 through 35 removed outlier: 3.578A pdb=" N GLN c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 92 removed outlier: 4.150A pdb=" N GLU c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA c 92 " --> pdb=" O GLU c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 25 removed outlier: 5.694A pdb=" N TRP d 8 " --> pdb=" O MET d 4 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 11 removed outlier: 4.394A pdb=" N GLY j 11 " --> pdb=" O ASN j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 39 removed outlier: 5.744A pdb=" N ARG j 37 " --> pdb=" O ASP j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 108 removed outlier: 4.097A pdb=" N VAL j 107 " --> pdb=" O PRO j 103 " (cutoff:3.500A) Proline residue: j 108 - end of helix No H-bonds generated for 'chain 'j' and resid 103 through 108' Processing helix chain 'j' and resid 181 through 193 removed outlier: 4.174A pdb=" N LEU j 191 " --> pdb=" O HIS j 187 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS j 192 " --> pdb=" O LYS j 188 " (cutoff:3.500A) Processing helix chain 'j' and resid 200 through 205 removed outlier: 3.825A pdb=" N MET j 204 " --> pdb=" O ARG j 200 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASN j 205 " --> pdb=" O GLY j 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 200 through 205' Processing helix chain 'j' and resid 173 through 178 removed outlier: 3.642A pdb=" N ASP j 176 " --> pdb=" O GLY j 173 " (cutoff:3.500A) Proline residue: j 178 - end of helix Processing helix chain 'k' and resid 111 through 120 removed outlier: 4.414A pdb=" N ARG k 117 " --> pdb=" O GLU k 113 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE k 118 " --> pdb=" O VAL k 114 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR k 119 " --> pdb=" O LYS k 115 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS k 120 " --> pdb=" O ARG k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 139 removed outlier: 3.972A pdb=" N ALA k 138 " --> pdb=" O SER k 134 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN k 139 " --> pdb=" O ALA k 135 " (cutoff:3.500A) Processing helix chain 'k' and resid 142 through 154 removed outlier: 4.412A pdb=" N ARG k 146 " --> pdb=" O ALA k 142 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU k 147 " --> pdb=" O GLY k 143 " (cutoff:3.500A) Processing helix chain 'k' and resid 165 through 170 removed outlier: 4.239A pdb=" N THR k 169 " --> pdb=" O GLN k 165 " (cutoff:3.500A) Proline residue: k 170 - end of helix No H-bonds generated for 'chain 'k' and resid 165 through 170' Processing helix chain 'k' and resid 187 through 199 Processing helix chain 'k' and resid 204 through 209 removed outlier: 4.181A pdb=" N VAL k 208 " --> pdb=" O ALA k 204 " (cutoff:3.500A) Processing helix chain 'k' and resid 228 through 233 Processing helix chain 'k' and resid 347 through 352 removed outlier: 6.411A pdb=" N LEU k 351 " --> pdb=" O SER k 347 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU k 352 " --> pdb=" O ARG k 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 347 through 352' Processing helix chain 'k' and resid 372 through 381 Processing helix chain 'l' and resid 31 through 46 removed outlier: 3.787A pdb=" N SER l 41 " --> pdb=" O THR l 37 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS l 44 " --> pdb=" O THR l 40 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN l 45 " --> pdb=" O SER l 41 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS l 46 " --> pdb=" O VAL l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 131 removed outlier: 3.923A pdb=" N ALA l 130 " --> pdb=" O ILE l 126 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL l 131 " --> pdb=" O ALA l 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 139 Processing helix chain 'l' and resid 154 through 159 removed outlier: 4.896A pdb=" N SER l 158 " --> pdb=" O THR l 154 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE l 159 " --> pdb=" O ASP l 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 154 through 159' Processing helix chain 'l' and resid 161 through 173 Processing helix chain 'l' and resid 174 through 185 removed outlier: 4.235A pdb=" N LYS l 185 " --> pdb=" O VAL l 181 " (cutoff:3.500A) Processing helix chain 'l' and resid 191 through 196 removed outlier: 3.777A pdb=" N ARG l 195 " --> pdb=" O LYS l 191 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN l 196 " --> pdb=" O GLY l 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 191 through 196' Processing helix chain 'l' and resid 214 through 221 removed outlier: 4.755A pdb=" N ASN l 221 " --> pdb=" O LYS l 217 " (cutoff:3.500A) Processing helix chain 'l' and resid 234 through 240 Proline residue: l 240 - end of helix Processing helix chain 'l' and resid 251 through 262 removed outlier: 4.669A pdb=" N ASP l 259 " --> pdb=" O PHE l 255 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN l 260 " --> pdb=" O THR l 256 " (cutoff:3.500A) Processing helix chain 'l' and resid 285 through 292 Processing helix chain 'l' and resid 293 through 299 removed outlier: 3.687A pdb=" N ALA l 298 " --> pdb=" O GLU l 294 " (cutoff:3.500A) Processing helix chain 'l' and resid 320 through 328 Processing helix chain 'l' and resid 329 through 338 removed outlier: 4.450A pdb=" N VAL l 333 " --> pdb=" O PRO l 329 " (cutoff:3.500A) Processing helix chain 'l' and resid 352 through 361 Processing helix chain 'm' and resid 9 through 16 Processing helix chain 'm' and resid 20 through 26 Processing helix chain 'm' and resid 29 through 37 removed outlier: 3.682A pdb=" N ARG m 35 " --> pdb=" O TYR m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 87 removed outlier: 4.613A pdb=" N LEU m 83 " --> pdb=" O TYR m 79 " (cutoff:3.500A) Proline residue: m 84 - end of helix Processing helix chain 'm' and resid 94 through 114 Processing helix chain 'm' and resid 115 through 120 removed outlier: 4.700A pdb=" N TYR m 119 " --> pdb=" O LEU m 115 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS m 120 " --> pdb=" O ASP m 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 115 through 120' Processing helix chain 'm' and resid 157 through 170 removed outlier: 3.763A pdb=" N GLY m 161 " --> pdb=" O ALA m 157 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY m 170 " --> pdb=" O ALA m 166 " (cutoff:3.500A) Processing helix chain 'm' and resid 191 through 201 removed outlier: 3.619A pdb=" N LEU m 195 " --> pdb=" O ASP m 191 " (cutoff:3.500A) Processing helix chain 'm' and resid 202 through 215 removed outlier: 3.708A pdb=" N TYR m 207 " --> pdb=" O HIS m 203 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP m 214 " --> pdb=" O GLU m 210 " (cutoff:3.500A) Processing helix chain 'm' and resid 216 through 223 removed outlier: 4.783A pdb=" N PHE m 223 " --> pdb=" O PHE m 219 " (cutoff:3.500A) Processing helix chain 'm' and resid 224 through 230 Processing helix chain 'm' and resid 234 through 250 removed outlier: 4.367A pdb=" N ASP m 238 " --> pdb=" O ASP m 234 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 273 removed outlier: 3.767A pdb=" N GLU m 268 " --> pdb=" O GLN m 264 " (cutoff:3.500A) Processing helix chain 'm' and resid 278 through 294 Processing helix chain 'n' and resid 80 through 85 removed outlier: 3.994A pdb=" N VAL n 84 " --> pdb=" O ASN n 80 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE n 85 " --> pdb=" O ALA n 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 80 through 85' Processing helix chain 'n' and resid 102 through 107 removed outlier: 3.963A pdb=" N PHE n 106 " --> pdb=" O ASN n 102 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA n 107 " --> pdb=" O VAL n 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 102 through 107' Processing helix chain 'n' and resid 131 through 150 removed outlier: 3.875A pdb=" N LYS n 143 " --> pdb=" O LYS n 139 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA n 144 " --> pdb=" O VAL n 140 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA n 147 " --> pdb=" O LYS n 143 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU n 148 " --> pdb=" O ALA n 144 " (cutoff:3.500A) Processing helix chain 'n' and resid 154 through 162 removed outlier: 5.285A pdb=" N SER n 162 " --> pdb=" O TYR n 158 " (cutoff:3.500A) Processing helix chain 'o' and resid 27 through 73 Processing helix chain 'o' and resid 96 through 107 Processing helix chain 'o' and resid 120 through 131 removed outlier: 4.041A pdb=" N LEU o 126 " --> pdb=" O ALA o 122 " (cutoff:3.500A) Processing helix chain 'o' and resid 140 through 151 Processing helix chain 'o' and resid 165 through 173 removed outlier: 4.157A pdb=" N ILE o 169 " --> pdb=" O ASP o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 180 through 191 removed outlier: 4.171A pdb=" N VAL o 191 " --> pdb=" O GLU o 187 " (cutoff:3.500A) Processing helix chain 'o' and resid 194 through 203 removed outlier: 5.109A pdb=" N TRP o 203 " --> pdb=" O ASN o 199 " (cutoff:3.500A) Processing helix chain 'o' and resid 235 through 244 removed outlier: 3.632A pdb=" N LEU o 239 " --> pdb=" O PHE o 235 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 69 removed outlier: 4.222A pdb=" N LYS p 63 " --> pdb=" O GLN p 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE p 67 " --> pdb=" O LYS p 63 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 80 removed outlier: 4.846A pdb=" N ALA p 76 " --> pdb=" O PRO p 72 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE p 78 " --> pdb=" O THR p 74 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR p 80 " --> pdb=" O ALA p 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 98 removed outlier: 4.002A pdb=" N LYS p 96 " --> pdb=" O LYS p 92 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR p 97 " --> pdb=" O LEU p 93 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG p 98 " --> pdb=" O PHE p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 119 Processing helix chain 'p' and resid 135 through 146 Processing helix chain 'p' and resid 159 through 174 removed outlier: 4.604A pdb=" N VAL p 163 " --> pdb=" O PRO p 159 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE p 165 " --> pdb=" O GLU p 161 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU p 166 " --> pdb=" O LEU p 162 " (cutoff:3.500A) Proline residue: p 167 - end of helix Processing helix chain 'p' and resid 182 through 191 Processing helix chain 'p' and resid 204 through 222 removed outlier: 3.674A pdb=" N GLU p 208 " --> pdb=" O ARG p 204 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA p 209 " --> pdb=" O ALA p 205 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA p 210 " --> pdb=" O GLU p 206 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR p 217 " --> pdb=" O LYS p 213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 225 through 233 removed outlier: 4.682A pdb=" N LYS p 231 " --> pdb=" O ASP p 227 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS p 232 " --> pdb=" O GLU p 228 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TRP p 233 " --> pdb=" O VAL p 229 " (cutoff:3.500A) Processing helix chain 'p' and resid 239 through 255 removed outlier: 4.216A pdb=" N SER p 255 " --> pdb=" O LYS p 251 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 84 removed outlier: 3.640A pdb=" N ARG q 69 " --> pdb=" O VAL q 65 " (cutoff:3.500A) Processing helix chain 'q' and resid 150 through 166 removed outlier: 4.143A pdb=" N CYS q 165 " --> pdb=" O LEU q 161 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG q 166 " --> pdb=" O GLN q 162 " (cutoff:3.500A) Processing helix chain 'q' and resid 171 through 176 removed outlier: 4.109A pdb=" N LEU q 176 " --> pdb=" O ILE q 172 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 10 removed outlier: 4.429A pdb=" N TYR r 9 " --> pdb=" O PRO r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 47 removed outlier: 4.412A pdb=" N PHE r 46 " --> pdb=" O THR r 42 " (cutoff:3.500A) Proline residue: r 47 - end of helix No H-bonds generated for 'chain 'r' and resid 42 through 47' Processing helix chain 'r' and resid 61 through 80 Processing helix chain 'r' and resid 107 through 112 removed outlier: 4.663A pdb=" N LEU r 111 " --> pdb=" O GLY r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 144 through 160 removed outlier: 3.558A pdb=" N GLU r 150 " --> pdb=" O ASP r 146 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR r 157 " --> pdb=" O ARG r 153 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS r 158 " --> pdb=" O ARG r 154 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE r 159 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 160 - end of helix Processing helix chain 'r' and resid 177 through 188 removed outlier: 4.306A pdb=" N ALA r 187 " --> pdb=" O LYS r 183 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY r 188 " --> pdb=" O LYS r 184 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 213 removed outlier: 4.577A pdb=" N PHE r 213 " --> pdb=" O ASN r 209 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 219 removed outlier: 4.578A pdb=" N ALA r 219 " --> pdb=" O GLU r 215 " (cutoff:3.500A) Processing helix chain 's' and resid 27 through 42 Processing helix chain 's' and resid 73 through 88 Processing helix chain 's' and resid 108 through 113 removed outlier: 4.450A pdb=" N LEU s 112 " --> pdb=" O GLU s 108 " (cutoff:3.500A) Processing helix chain 's' and resid 136 through 141 removed outlier: 3.837A pdb=" N ARG s 140 " --> pdb=" O ALA s 136 " (cutoff:3.500A) Processing helix chain 's' and resid 155 through 167 removed outlier: 4.922A pdb=" N TYR s 167 " --> pdb=" O PHE s 163 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 22 removed outlier: 4.153A pdb=" N ARG t 21 " --> pdb=" O HIS t 17 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL t 22 " --> pdb=" O TRP t 18 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 17 through 22' Processing helix chain 't' and resid 27 through 47 Processing helix chain 't' and resid 76 through 84 Processing helix chain 't' and resid 86 through 94 Processing helix chain 't' and resid 105 through 123 Processing helix chain 't' and resid 140 through 146 Proline residue: t 146 - end of helix Processing helix chain 't' and resid 165 through 180 removed outlier: 6.292A pdb=" N THR t 169 " --> pdb=" O SER t 165 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU t 170 " --> pdb=" O ALA t 166 " (cutoff:3.500A) Processing helix chain 't' and resid 181 through 193 Processing helix chain 'u' and resid 59 through 64 removed outlier: 4.075A pdb=" N VAL u 63 " --> pdb=" O ASN u 59 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL u 64 " --> pdb=" O LEU u 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 59 through 64' Processing helix chain 'u' and resid 77 through 89 Processing helix chain 'u' and resid 90 through 98 removed outlier: 3.837A pdb=" N SER u 97 " --> pdb=" O LYS u 93 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER u 98 " --> pdb=" O TRP u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 99 through 112 Processing helix chain 'u' and resid 113 through 138 removed outlier: 4.238A pdb=" N ALA u 136 " --> pdb=" O LYS u 132 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS u 137 " --> pdb=" O LYS u 133 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA u 138 " --> pdb=" O ALA u 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 21 removed outlier: 3.807A pdb=" N GLU a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 84 Processing helix chain 'a' and resid 153 through 160 removed outlier: 4.345A pdb=" N PHE a 157 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 175 removed outlier: 5.475A pdb=" N GLU a 175 " --> pdb=" O ASN a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 206 removed outlier: 3.944A pdb=" N GLY a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 228 Processing helix chain 'a' and resid 232 through 244 Processing helix chain 'a' and resid 250 through 258 Processing helix chain 'a' and resid 259 through 278 Processing helix chain 'a' and resid 299 through 305 removed outlier: 4.250A pdb=" N ILE a 305 " --> pdb=" O ASP a 301 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 324 removed outlier: 4.108A pdb=" N ASP a 322 " --> pdb=" O GLY a 318 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER a 323 " --> pdb=" O GLY a 319 " (cutoff:3.500A) Processing helix chain 'a' and resid 332 through 396 removed outlier: 6.631A pdb=" N THR a 336 " --> pdb=" O PRO a 332 " (cutoff:3.500A) Processing helix chain 'a' and resid 397 through 413 removed outlier: 3.570A pdb=" N GLN a 412 " --> pdb=" O GLY a 408 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Processing helix chain 'a' and resid 415 through 430 Processing helix chain 'a' and resid 431 through 438 removed outlier: 4.139A pdb=" N LEU a 437 " --> pdb=" O ILE a 433 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASN a 438 " --> pdb=" O ALA a 434 " (cutoff:3.500A) Processing helix chain 'a' and resid 513 through 562 removed outlier: 3.592A pdb=" N GLN a 530 " --> pdb=" O LYS a 526 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS a 531 " --> pdb=" O THR a 527 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLY a 540 " --> pdb=" O GLU a 536 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS a 541 " --> pdb=" O LYS a 537 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP a 551 " --> pdb=" O GLU a 547 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS a 556 " --> pdb=" O GLN a 552 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS a 562 " --> pdb=" O LEU a 558 " (cutoff:3.500A) Processing helix chain 'a' and resid 593 through 604 Processing helix chain 'a' and resid 631 through 647 removed outlier: 4.240A pdb=" N GLU a 647 " --> pdb=" O MET a 643 " (cutoff:3.500A) Processing helix chain 'a' and resid 661 through 666 removed outlier: 3.585A pdb=" N VAL a 665 " --> pdb=" O PHE a 661 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER a 666 " --> pdb=" O ALA a 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 661 through 666' Processing helix chain 'a' and resid 839 through 850 removed outlier: 4.554A pdb=" N LYS a 843 " --> pdb=" O GLY a 839 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS a 846 " --> pdb=" O GLY a 842 " (cutoff:3.500A) Processing helix chain 'a' and resid 855 through 867 Processing helix chain 'a' and resid 868 through 910 removed outlier: 3.921A pdb=" N ARG a 886 " --> pdb=" O GLU a 882 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS a 906 " --> pdb=" O LEU a 902 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE a 907 " --> pdb=" O GLN a 903 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR a 908 " --> pdb=" O ALA a 904 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS a 909 " --> pdb=" O LEU a 905 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS a 910 " --> pdb=" O LYS a 906 " (cutoff:3.500A) Processing helix chain 'a' and resid 916 through 924 removed outlier: 4.222A pdb=" N HIS a 920 " --> pdb=" O ASN a 916 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS a 921 " --> pdb=" O TYR a 917 " (cutoff:3.500A) Processing helix chain 'a' and resid 943 through 951 removed outlier: 4.690A pdb=" N LYS a 949 " --> pdb=" O PRO a 945 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR a 950 " --> pdb=" O ALA a 946 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS a 951 " --> pdb=" O LEU a 947 " (cutoff:3.500A) Processing helix chain 'a' and resid 962 through 977 removed outlier: 4.406A pdb=" N ARG a 977 " --> pdb=" O TYR a 973 " (cutoff:3.500A) Processing helix chain 'a' and resid 990 through 1001 removed outlier: 5.519A pdb=" N LYS a1001 " --> pdb=" O ILE a 997 " (cutoff:3.500A) Processing helix chain 'a' and resid 1002 through 1010 removed outlier: 3.884A pdb=" N LEU a1007 " --> pdb=" O GLN a1003 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU a1008 " --> pdb=" O ASP a1004 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N CYS a1010 " --> pdb=" O VAL a1006 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.617A pdb=" N GLN e 11 " --> pdb=" O ASN e 7 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR e 12 " --> pdb=" O THR e 8 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN e 13 " --> pdb=" O PHE e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 42 removed outlier: 3.621A pdb=" N LEU e 42 " --> pdb=" O LEU e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 removed outlier: 5.486A pdb=" N ARG e 57 " --> pdb=" O SER e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 76 removed outlier: 3.952A pdb=" N PHE e 76 " --> pdb=" O LEU e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 84 removed outlier: 3.630A pdb=" N PHE e 83 " --> pdb=" O ASN e 79 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASN e 84 " --> pdb=" O GLU e 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 79 through 84' Processing helix chain 'e' and resid 85 through 99 removed outlier: 3.519A pdb=" N ALA e 96 " --> pdb=" O SER e 92 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS e 97 " --> pdb=" O GLN e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 Processing helix chain 'e' and resid 123 through 130 removed outlier: 6.216A pdb=" N LYS e 127 " --> pdb=" O LYS e 123 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N PHE e 128 " --> pdb=" O LYS e 124 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS e 130 " --> pdb=" O SER e 126 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 142 removed outlier: 4.221A pdb=" N LEU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU e 142 " --> pdb=" O LEU e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 144 through 160 Proline residue: e 150 - end of helix Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 186 Processing helix chain 'e' and resid 189 through 195 removed outlier: 4.480A pdb=" N ASP e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 227 removed outlier: 3.717A pdb=" N SER e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS e 227 " --> pdb=" O PHE e 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 228 through 234 Processing helix chain 'e' and resid 235 through 243 Processing helix chain 'e' and resid 244 through 251 removed outlier: 3.751A pdb=" N LEU e 249 " --> pdb=" O SER e 245 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU e 250 " --> pdb=" O ILE e 246 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASN e 251 " --> pdb=" O TRP e 247 " (cutoff:3.500A) Processing helix chain 'e' and resid 257 through 275 removed outlier: 4.620A pdb=" N TYR e 261 " --> pdb=" O ASN e 257 " (cutoff:3.500A) Processing helix chain 'e' and resid 276 through 281 removed outlier: 4.148A pdb=" N LYS e 281 " --> pdb=" O MET e 277 " (cutoff:3.500A) Processing helix chain 'e' and resid 282 through 298 removed outlier: 3.628A pdb=" N THR e 296 " --> pdb=" O LEU e 292 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE e 298 " --> pdb=" O SER e 294 " (cutoff:3.500A) Processing helix chain 'e' and resid 302 through 311 Proline residue: e 308 - end of helix Proline residue: e 311 - end of helix Processing helix chain 'e' and resid 312 through 325 removed outlier: 3.646A pdb=" N TYR e 323 " --> pdb=" O THR e 319 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU e 324 " --> pdb=" O LEU e 320 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP e 325 " --> pdb=" O ASP e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 326 through 333 removed outlier: 3.567A pdb=" N SER e 330 " --> pdb=" O GLY e 326 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP e 332 " --> pdb=" O ILE e 328 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS e 333 " --> pdb=" O TRP e 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 350 removed outlier: 3.973A pdb=" N THR e 348 " --> pdb=" O SER e 344 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER e 349 " --> pdb=" O VAL e 345 " (cutoff:3.500A) Proline residue: e 350 - end of helix Processing helix chain 'e' and resid 353 through 369 removed outlier: 4.496A pdb=" N ARG e 367 " --> pdb=" O SER e 363 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS e 368 " --> pdb=" O SER e 364 " (cutoff:3.500A) Processing helix chain 'e' and resid 375 through 392 Proline residue: e 379 - end of helix removed outlier: 3.608A pdb=" N GLY e 392 " --> pdb=" O LEU e 388 " (cutoff:3.500A) Processing helix chain 'e' and resid 397 through 417 removed outlier: 3.631A pdb=" N ASP e 415 " --> pdb=" O LYS e 411 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER e 416 " --> pdb=" O PHE e 412 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER e 417 " --> pdb=" O ALA e 413 " (cutoff:3.500A) Processing helix chain 'e' and resid 418 through 436 Processing helix chain 'e' and resid 438 through 443 removed outlier: 4.876A pdb=" N THR e 443 " --> pdb=" O LEU e 439 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 450 removed outlier: 3.571A pdb=" N SER e 450 " --> pdb=" O ASN e 446 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 468 removed outlier: 3.608A pdb=" N TRP e 458 " --> pdb=" O PRO e 454 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 477 removed outlier: 5.139A pdb=" N VAL e 477 " --> pdb=" O ARG e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 478 through 490 Processing helix chain 'e' and resid 493 through 512 Proline residue: e 512 - end of helix Processing helix chain 'e' and resid 514 through 520 removed outlier: 3.676A pdb=" N TYR e 519 " --> pdb=" O VAL e 515 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP e 520 " --> pdb=" O PHE e 516 " (cutoff:3.500A) Processing helix chain 'e' and resid 521 through 533 removed outlier: 4.834A pdb=" N ASP e 533 " --> pdb=" O PHE e 529 " (cutoff:3.500A) Processing helix chain 'e' and resid 534 through 552 removed outlier: 4.502A pdb=" N GLY e 539 " --> pdb=" O ILE e 535 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS e 540 " --> pdb=" O PHE e 536 " (cutoff:3.500A) Proline residue: e 549 - end of helix Processing helix chain 'e' and resid 556 through 571 removed outlier: 3.717A pdb=" N ILE e 563 " --> pdb=" O ASN e 559 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS e 571 " --> pdb=" O TYR e 567 " (cutoff:3.500A) Processing helix chain 'e' and resid 572 through 577 removed outlier: 5.366A pdb=" N THR e 577 " --> pdb=" O PHE e 573 " (cutoff:3.500A) Processing helix chain 'e' and resid 578 through 594 removed outlier: 4.978A pdb=" N ASN e 594 " --> pdb=" O ALA e 590 " (cutoff:3.500A) Processing helix chain 'e' and resid 596 through 608 removed outlier: 5.284A pdb=" N ASP e 608 " --> pdb=" O MET e 604 " (cutoff:3.500A) Processing helix chain 'e' and resid 609 through 619 removed outlier: 5.366A pdb=" N ASP e 619 " --> pdb=" O LEU e 615 " (cutoff:3.500A) Processing helix chain 'e' and resid 622 through 634 Processing helix chain 'e' and resid 640 through 646 removed outlier: 4.438A pdb=" N ASN e 646 " --> pdb=" O ILE e 642 " (cutoff:3.500A) Processing helix chain 'e' and resid 651 through 666 Processing helix chain 'e' and resid 667 through 679 removed outlier: 4.834A pdb=" N ASP e 679 " --> pdb=" O LEU e 675 " (cutoff:3.500A) Processing helix chain 'e' and resid 680 through 690 Processing helix chain 'e' and resid 691 through 698 removed outlier: 5.335A pdb=" N TYR e 698 " --> pdb=" O SER e 694 " (cutoff:3.500A) Processing helix chain 'e' and resid 701 through 720 removed outlier: 4.386A pdb=" N SER e 720 " --> pdb=" O ALA e 716 " (cutoff:3.500A) Processing helix chain 'e' and resid 721 through 737 Processing helix chain 'e' and resid 742 through 758 removed outlier: 4.317A pdb=" N TYR e 746 " --> pdb=" O ALA e 742 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU e 752 " --> pdb=" O THR e 748 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU e 753 " --> pdb=" O HIS e 749 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN e 758 " --> pdb=" O ILE e 754 " (cutoff:3.500A) Processing helix chain 'e' and resid 759 through 765 removed outlier: 3.906A pdb=" N ILE e 763 " --> pdb=" O ASP e 759 " (cutoff:3.500A) Processing helix chain 'e' and resid 768 through 777 removed outlier: 3.982A pdb=" N VAL e 772 " --> pdb=" O ASN e 768 " (cutoff:3.500A) Processing helix chain 'e' and resid 781 through 788 removed outlier: 4.185A pdb=" N SER e 785 " --> pdb=" O ASP e 781 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU e 786 " --> pdb=" O TYR e 782 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL e 787 " --> pdb=" O ARG e 783 " (cutoff:3.500A) Processing helix chain 'e' and resid 792 through 798 removed outlier: 4.581A pdb=" N LEU e 796 " --> pdb=" O THR e 792 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU e 797 " --> pdb=" O ASN e 793 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU e 798 " --> pdb=" O THR e 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 792 through 798' Processing helix chain 'e' and resid 805 through 827 Proline residue: e 827 - end of helix Processing helix chain 'e' and resid 831 through 852 Processing helix chain 'e' and resid 856 through 861 removed outlier: 4.284A pdb=" N TYR e 860 " --> pdb=" O ASN e 856 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP e 861 " --> pdb=" O ASP e 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 856 through 861' Processing helix chain 'e' and resid 875 through 886 Proline residue: e 886 - end of helix Processing helix chain 'e' and resid 895 through 903 removed outlier: 3.558A pdb=" N SER e 901 " --> pdb=" O ASP e 897 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN e 902 " --> pdb=" O ILE e 898 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER e 903 " --> pdb=" O ALA e 899 " (cutoff:3.500A) Processing helix chain 'e' and resid 904 through 921 Processing helix chain 'e' and resid 927 through 947 removed outlier: 3.638A pdb=" N SER e 935 " --> pdb=" O GLY e 931 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLN e 947 " --> pdb=" O THR e 943 " (cutoff:3.500A) Processing helix chain 'e' and resid 950 through 965 Processing helix chain 'e' and resid 970 through 986 removed outlier: 3.834A pdb=" N THR e 974 " --> pdb=" O LYS e 970 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY e 986 " --> pdb=" O SER e 982 " (cutoff:3.500A) Processing helix chain 'e' and resid 988 through 995 Processing helix chain 'e' and resid 996 through 1008 Processing helix chain 'e' and resid 1020 through 1037 Processing helix chain 'e' and resid 1044 through 1063 removed outlier: 4.388A pdb=" N VAL e1048 " --> pdb=" O SER e1044 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE e1062 " --> pdb=" O LYS e1058 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU e1063 " --> pdb=" O LEU e1059 " (cutoff:3.500A) Processing helix chain 'e' and resid 1064 through 1069 removed outlier: 3.791A pdb=" N GLY e1069 " --> pdb=" O VAL e1065 " (cutoff:3.500A) Processing helix chain 'e' and resid 1070 through 1090 removed outlier: 3.515A pdb=" N LEU e1075 " --> pdb=" O THR e1071 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP e1090 " --> pdb=" O MET e1086 " (cutoff:3.500A) Processing helix chain 'e' and resid 1094 through 1111 Processing helix chain 'e' and resid 1123 through 1137 removed outlier: 3.703A pdb=" N MET e1135 " --> pdb=" O LEU e1131 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE e1136 " --> pdb=" O ILE e1132 " (cutoff:3.500A) Processing helix chain 'e' and resid 1145 through 1163 removed outlier: 3.652A pdb=" N THR e1149 " --> pdb=" O ASN e1145 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLU e1163 " --> pdb=" O ILE e1159 " (cutoff:3.500A) Processing helix chain 'e' and resid 1164 through 1172 removed outlier: 3.587A pdb=" N SER e1169 " --> pdb=" O LYS e1165 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN e1170 " --> pdb=" O LYS e1166 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS e1172 " --> pdb=" O GLU e1168 " (cutoff:3.500A) Processing helix chain 'e' and resid 1173 through 1181 removed outlier: 4.571A pdb=" N ASP e1181 " --> pdb=" O VAL e1177 " (cutoff:3.500A) Processing helix chain 'e' and resid 1182 through 1188 removed outlier: 4.688A pdb=" N ASN e1187 " --> pdb=" O ASP e1183 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE e1188 " --> pdb=" O ILE e1184 " (cutoff:3.500A) Processing helix chain 'e' and resid 1189 through 1217 removed outlier: 3.628A pdb=" N ASP e1208 " --> pdb=" O LYS e1204 " (cutoff:3.500A) Processing helix chain 'e' and resid 1235 through 1240 removed outlier: 3.727A pdb=" N LYS e1239 " --> pdb=" O ASN e1235 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU e1240 " --> pdb=" O SER e1236 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1235 through 1240' Processing helix chain 'e' and resid 1241 through 1251 Processing helix chain 'e' and resid 1261 through 1281 removed outlier: 3.543A pdb=" N TYR e1278 " --> pdb=" O LEU e1274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE e1279 " --> pdb=" O ILE e1275 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP e1281 " --> pdb=" O MET e1277 " (cutoff:3.500A) Processing helix chain 'e' and resid 1283 through 1298 removed outlier: 3.505A pdb=" N ILE e1289 " --> pdb=" O ASN e1285 " (cutoff:3.500A) Processing helix chain 'e' and resid 1299 through 1312 removed outlier: 5.363A pdb=" N ASP e1312 " --> pdb=" O THR e1308 " (cutoff:3.500A) Processing helix chain 'e' and resid 1315 through 1323 removed outlier: 3.984A pdb=" N TRP e1319 " --> pdb=" O ASP e1315 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASP e1323 " --> pdb=" O TRP e1319 " (cutoff:3.500A) Processing helix chain 'e' and resid 1324 through 1329 Processing helix chain 'e' and resid 1341 through 1363 Processing helix chain 'e' and resid 1364 through 1374 removed outlier: 4.948A pdb=" N SER e1368 " --> pdb=" O GLY e1364 " (cutoff:3.500A) Processing helix chain 'e' and resid 1376 through 1390 Processing helix chain 'e' and resid 1391 through 1411 removed outlier: 4.599A pdb=" N ASP e1408 " --> pdb=" O ASN e1404 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG e1409 " --> pdb=" O SER e1405 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU e1410 " --> pdb=" O LYS e1406 " (cutoff:3.500A) Processing helix chain 'e' and resid 1465 through 1481 Processing helix chain 'e' and resid 1486 through 1503 Processing helix chain 'e' and resid 1535 through 1547 removed outlier: 4.303A pdb=" N GLY e1547 " --> pdb=" O PHE e1543 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 17 removed outlier: 4.234A pdb=" N PHE g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 42 removed outlier: 3.829A pdb=" N PHE g 38 " --> pdb=" O PHE g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 63 removed outlier: 4.797A pdb=" N MET g 62 " --> pdb=" O ILE g 58 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 88 Processing helix chain 'g' and resid 103 through 108 Processing helix chain 'g' and resid 122 through 133 Processing helix chain 'g' and resid 147 through 152 Processing helix chain 'g' and resid 166 through 178 Processing helix chain 'g' and resid 192 through 197 Processing helix chain 'g' and resid 211 through 223 Processing helix chain 'z' and resid 28 through 37 Proline residue: z 34 - end of helix Processing helix chain 'z' and resid 39 through 52 Processing helix chain 'z' and resid 77 through 87 removed outlier: 5.035A pdb=" N GLU z 87 " --> pdb=" O THR z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 106 through 118 Processing helix chain 'z' and resid 125 through 138 removed outlier: 4.664A pdb=" N SER z 138 " --> pdb=" O GLY z 134 " (cutoff:3.500A) Processing helix chain 'z' and resid 151 through 156 removed outlier: 5.015A pdb=" N ASN z 156 " --> pdb=" O ILE z 152 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 163 Proline residue: z 163 - end of helix Processing helix chain '0' and resid 3 through 23 removed outlier: 4.981A pdb=" N LYS 0 23 " --> pdb=" O LEU 0 19 " (cutoff:3.500A) Processing helix chain '0' and resid 34 through 46 Processing helix chain '0' and resid 55 through 71 removed outlier: 4.923A pdb=" N SER 0 68 " --> pdb=" O ARG 0 64 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP 0 69 " --> pdb=" O GLY 0 65 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU 0 70 " --> pdb=" O PHE 0 66 " (cutoff:3.500A) Proline residue: 0 71 - end of helix Processing helix chain '0' and resid 72 through 81 removed outlier: 4.428A pdb=" N LEU 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU 0 77 " --> pdb=" O PHE 0 73 " (cutoff:3.500A) Proline residue: 0 78 - end of helix removed outlier: 4.205A pdb=" N LYS 0 81 " --> pdb=" O LEU 0 77 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 72 through 81' Processing helix chain '0' and resid 93 through 103 Processing helix chain 'w' and resid 5 through 21 Processing helix chain 'w' and resid 70 through 81 removed outlier: 3.728A pdb=" N SER w 79 " --> pdb=" O ASP w 75 " (cutoff:3.500A) Processing helix chain 'w' and resid 86 through 94 removed outlier: 3.659A pdb=" N ASN w 94 " --> pdb=" O LEU w 90 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 108 removed outlier: 4.877A pdb=" N ASN w 108 " --> pdb=" O SER w 104 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 124 removed outlier: 4.556A pdb=" N LYS w 118 " --> pdb=" O GLU w 114 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN w 119 " --> pdb=" O VAL w 115 " (cutoff:3.500A) Proline residue: w 121 - end of helix Processing helix chain 'w' and resid 126 through 132 Processing helix chain 'w' and resid 143 through 154 Processing helix chain 'w' and resid 175 through 195 removed outlier: 5.072A pdb=" N LYS w 195 " --> pdb=" O VAL w 191 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.466A pdb=" N VAL A 35 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 61 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 58 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 133 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 117 through 121 removed outlier: 3.634A pdb=" N ASN A 117 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A 129 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 6 through 10 Processing sheet with id= 4, first strand: chain 'C' and resid 16 through 20 Processing sheet with id= 5, first strand: chain 'C' and resid 57 through 60 removed outlier: 5.435A pdb=" N LYS C 80 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 124 through 131 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'D' and resid 119 through 122 removed outlier: 4.878A pdb=" N THR D 100 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 24 through 31 removed outlier: 6.706A pdb=" N ILE F 10 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 87 through 96 removed outlier: 5.101A pdb=" N ASN F 74 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 6 through 10 removed outlier: 4.566A pdb=" N GLU F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 38 through 43 removed outlier: 4.577A pdb=" N ASP G 38 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS G 60 " --> pdb=" O ILE G 42 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.171A pdb=" N ASN H 101 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 79 through 82 removed outlier: 3.921A pdb=" N ALA I 82 " --> pdb=" O ASP I 97 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP I 97 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN I 98 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA I 21 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET I 59 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP I 56 " --> pdb=" O VAL I 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 84 through 87 removed outlier: 4.506A pdb=" N VAL I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'I' and resid 75 through 78 Processing sheet with id= 16, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.440A pdb=" N GLU J 4 " --> pdb=" O LYS J 12 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS J 12 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP J 6 " --> pdb=" O GLY J 10 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 18 through 22 Processing sheet with id= 18, first strand: chain 'K' and resid 81 through 86 removed outlier: 3.734A pdb=" N LYS K 120 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR K 119 " --> pdb=" O ARG K 115 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 56 through 59 removed outlier: 4.092A pdb=" N GLN L 66 " --> pdb=" O VAL L 58 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 72 through 75 Processing sheet with id= 21, first strand: chain 'L' and resid 86 through 89 removed outlier: 4.344A pdb=" N ALA L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 8 through 13 removed outlier: 4.145A pdb=" N LYS M 9 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS M 21 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 27 through 30 removed outlier: 4.644A pdb=" N LYS M 27 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 99 through 102 Processing sheet with id= 25, first strand: chain 'P' and resid 22 through 25 removed outlier: 6.372A pdb=" N LYS P 22 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU P 41 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS P 66 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 48 through 51 removed outlier: 4.934A pdb=" N ASP Q 48 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL Q 8 " --> pdb=" O ARG Q 77 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR Q 9 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 71 through 77 Processing sheet with id= 28, first strand: chain 'S' and resid 11 through 15 removed outlier: 6.754A pdb=" N LEU S 29 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG S 82 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS S 63 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS S 47 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG S 48 " --> pdb=" O PHE S 101 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 8 through 14 removed outlier: 4.046A pdb=" N ALA S 96 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 19 through 24 removed outlier: 4.587A pdb=" N LYS T 19 " --> pdb=" O VAL T 35 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'X' and resid 2 through 5 removed outlier: 4.535A pdb=" N VAL X 55 " --> pdb=" O ILE X 5 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR X 22 " --> pdb=" O ARG X 46 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Z' and resid 100 through 103 removed outlier: 4.137A pdb=" N ALA Z 101 " --> pdb=" O CYS Z 96 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS Z 93 " --> pdb=" O LYS Z 124 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLN Z 120 " --> pdb=" O ARG Z 97 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'b' and resid 7 through 10 removed outlier: 4.478A pdb=" N VAL b 68 " --> pdb=" O LEU b 85 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR b 79 " --> pdb=" O CYS b 74 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'c' and resid 47 through 50 removed outlier: 6.881A pdb=" N ILE c 54 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY c 53 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS c 62 " --> pdb=" O CYS c 57 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'j' and resid 47 through 50 removed outlier: 3.921A pdb=" N GLN j 47 " --> pdb=" O LYS j 60 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS j 60 " --> pdb=" O LYS j 46 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN j 86 " --> pdb=" O VAL j 45 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'j' and resid 111 through 114 removed outlier: 4.418A pdb=" N THR j 111 " --> pdb=" O ILE j 136 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG j 147 " --> pdb=" O ILE j 137 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'j' and resid 58 through 64 Processing sheet with id= 38, first strand: chain 'j' and resid 145 through 150 removed outlier: 4.406A pdb=" N ALA j 154 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'k' and resid 41 through 44 removed outlier: 4.889A pdb=" N ALA k 42 " --> pdb=" O ASN k 184 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN k 182 " --> pdb=" O THR k 44 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS k 177 " --> pdb=" O THR k 164 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU k 161 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS k 201 " --> pdb=" O VAL k 86 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'k' and resid 53 through 59 removed outlier: 6.661A pdb=" N VAL k 78 " --> pdb=" O ALA k 51 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG k 334 " --> pdb=" O LYS k 50 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE k 335 " --> pdb=" O VAL k 220 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL k 220 " --> pdb=" O ILE k 335 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS k 273 " --> pdb=" O THR k 221 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'k' and resid 98 through 101 Processing sheet with id= 42, first strand: chain 'k' and resid 284 through 288 removed outlier: 3.741A pdb=" N GLY k 288 " --> pdb=" O ASN k 319 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN k 319 " --> pdb=" O GLY k 288 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'k' and resid 76 through 80 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'k' and resid 88 through 93 removed outlier: 3.744A pdb=" N GLY k 88 " --> pdb=" O LEU k 161 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'k' and resid 213 through 216 removed outlier: 4.189A pdb=" N GLU k 213 " --> pdb=" O ILE k 282 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 75 through 78 removed outlier: 4.384A pdb=" N GLN l 87 " --> pdb=" O VAL l 77 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 205 through 208 Processing sheet with id= 48, first strand: chain 'm' and resid 72 through 75 removed outlier: 6.834A pdb=" N ILE m 64 " --> pdb=" O LEU m 75 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'n' and resid 37 through 42 removed outlier: 3.955A pdb=" N THR n 38 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS n 50 " --> pdb=" O LEU n 42 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 133 through 138 removed outlier: 7.863A pdb=" N TYR o 133 " --> pdb=" O ILE o 89 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS o 82 " --> pdb=" O VAL o 119 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER o 113 " --> pdb=" O ARG o 88 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN o 112 " --> pdb=" O LEU o 207 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 152 through 155 removed outlier: 8.623A pdb=" N GLY o 152 " --> pdb=" O LEU o 163 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'p' and resid 176 through 181 Processing sheet with id= 53, first strand: chain 'q' and resid 5 through 12 removed outlier: 4.944A pdb=" N GLN q 51 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU q 52 " --> pdb=" O VAL q 48 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 17 through 20 removed outlier: 5.995A pdb=" N ARG q 23 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 132 through 137 removed outlier: 4.964A pdb=" N GLU q 143 " --> pdb=" O SER q 137 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP q 142 " --> pdb=" O TYR q 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 86 through 90 Processing sheet with id= 57, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.337A pdb=" N TYR r 34 " --> pdb=" O VAL r 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU r 52 " --> pdb=" O ILE r 135 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN r 133 " --> pdb=" O SER r 54 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'r' and resid 56 through 59 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'r' and resid 189 through 193 removed outlier: 7.658A pdb=" N GLU r 189 " --> pdb=" O LEU r 200 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE r 196 " --> pdb=" O ASP r 193 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'r' and resid 49 through 55 removed outlier: 5.069A pdb=" N CYS r 49 " --> pdb=" O SER r 168 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLN r 162 " --> pdb=" O ASN r 55 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 's' and resid 45 through 49 removed outlier: 5.683A pdb=" N SER s 22 " --> pdb=" O GLY s 124 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY s 124 " --> pdb=" O SER s 22 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 's' and resid 52 through 55 removed outlier: 7.191A pdb=" N TYR s 52 " --> pdb=" O ARG s 61 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG s 61 " --> pdb=" O TYR s 52 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 's' and resid 89 through 92 removed outlier: 3.628A pdb=" N ASP s 170 " --> pdb=" O TYR s 89 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU s 91 " --> pdb=" O ASP s 170 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 't' and resid 56 through 59 Processing sheet with id= 65, first strand: chain 'u' and resid 19 through 24 removed outlier: 4.471A pdb=" N ARG u 19 " --> pdb=" O ILE u 35 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS u 31 " --> pdb=" O ILE u 23 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 36 through 39 removed outlier: 6.764A pdb=" N LYS u 43 " --> pdb=" O ILE u 39 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'a' and resid 24 through 27 removed outlier: 4.390A pdb=" N TYR a 24 " --> pdb=" O LEU a 89 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS a 87 " --> pdb=" O LEU a 26 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 28 through 32 removed outlier: 3.592A pdb=" N ASN a 28 " --> pdb=" O LYS a 42 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN a 38 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 91 through 94 removed outlier: 6.886A pdb=" N ARG a 99 " --> pdb=" O PHE a 116 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN a 121 " --> pdb=" O GLU a 115 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 306 through 310 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 'a' and resid 446 through 454 removed outlier: 8.826A pdb=" N ASN a 446 " --> pdb=" O LEU a 510 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU a 502 " --> pdb=" O LEU a 454 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'a' and resid 577 through 581 removed outlier: 4.044A pdb=" N LEU a 587 " --> pdb=" O LYS a 623 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY a 591 " --> pdb=" O HIS a 619 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N HIS a 619 " --> pdb=" O GLY a 591 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'a' and resid 656 through 660 Processing sheet with id= 74, first strand: chain 'a' and resid 939 through 942 removed outlier: 4.719A pdb=" N TYR a 952 " --> pdb=" O PHE a 703 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY a 959 " --> pdb=" O LYS a1013 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS a1013 " --> pdb=" O GLY a 959 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'e' and resid 1417 through 1423 removed outlier: 5.632A pdb=" N ASN e1426 " --> pdb=" O LEU e1445 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU e1440 " --> pdb=" O VAL e1459 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'g' and resid 23 through 27 Processing sheet with id= 77, first strand: chain 'g' and resid 69 through 73 Processing sheet with id= 78, first strand: chain 'g' and resid 114 through 117 Processing sheet with id= 79, first strand: chain 'g' and resid 158 through 161 Processing sheet with id= 80, first strand: chain 'z' and resid 11 through 17 removed outlier: 3.527A pdb=" N LYS z 11 " --> pdb=" O GLN z 65 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL z 60 " --> pdb=" O PRO z 75 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '0' and resid 49 through 53 removed outlier: 3.837A pdb=" N SER 0 24 " --> pdb=" O THR 0 89 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL 0 27 " --> pdb=" O VAL 0 188 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'w' and resid 49 through 53 removed outlier: 7.221A pdb=" N PHE w 49 " --> pdb=" O LEU w 159 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'w' and resid 65 through 68 Processing sheet with id= 84, first strand: chain 'w' and resid 163 through 169 removed outlier: 6.357A pdb=" N LEU w 163 " --> pdb=" O LEU w 38 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL w 32 " --> pdb=" O VAL w 169 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU w 204 " --> pdb=" O LEU w 216 " (cutoff:3.500A) 3309 hydrogen bonds defined for protein. 9840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2924 hydrogen bonds 4658 hydrogen bond angles 0 basepair planarities 1188 basepair parallelities 2007 stacking parallelities Total time for adding SS restraints: 254.82 Time building geometry restraints manager: 62.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 19500 1.32 - 1.45: 62810 1.45 - 1.57: 70923 1.57 - 1.69: 7273 1.69 - 1.82: 263 Bond restraints: 160769 Sorted by residual: bond pdb=" CA SER e 44 " pdb=" C SER e 44 " ideal model delta sigma weight residual 1.522 1.472 0.050 1.23e-02 6.61e+03 1.63e+01 bond pdb=" O3' G f2874 " pdb=" P B U f2875 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.50e+01 bond pdb=" CA PHE e 405 " pdb=" C PHE e 405 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.27e-02 6.20e+03 1.47e+01 bond pdb=" CA LEU e1445 " pdb=" C LEU e1445 " ideal model delta sigma weight residual 1.522 1.482 0.041 1.14e-02 7.69e+03 1.27e+01 bond pdb=" O3' U f2868 " pdb=" P U f2869 " ideal model delta sigma weight residual 1.607 1.554 0.053 1.50e-02 4.44e+03 1.27e+01 ... (remaining 160764 not shown) Histogram of bond angle deviations from ideal: 94.25 - 102.72: 6135 102.72 - 111.18: 83331 111.18 - 119.65: 73072 119.65 - 128.12: 66414 128.12 - 136.58: 6020 Bond angle restraints: 234972 Sorted by residual: angle pdb=" N GLY e1364 " pdb=" CA GLY e1364 " pdb=" C GLY e1364 " ideal model delta sigma weight residual 112.49 127.34 -14.85 1.21e+00 6.83e-01 1.51e+02 angle pdb=" N SER e1460 " pdb=" CA SER e1460 " pdb=" C SER e1460 " ideal model delta sigma weight residual 111.36 122.34 -10.98 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N ASP e1181 " pdb=" CA ASP e1181 " pdb=" C ASP e1181 " ideal model delta sigma weight residual 111.28 120.88 -9.60 1.09e+00 8.42e-01 7.75e+01 angle pdb=" N GLN e1141 " pdb=" CA GLN e1141 " pdb=" C GLN e1141 " ideal model delta sigma weight residual 111.28 120.83 -9.55 1.09e+00 8.42e-01 7.67e+01 angle pdb=" N ASN e 793 " pdb=" CA ASN e 793 " pdb=" C ASN e 793 " ideal model delta sigma weight residual 113.28 102.65 10.63 1.22e+00 6.72e-01 7.60e+01 ... (remaining 234967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 92343 35.99 - 71.99: 8386 71.99 - 107.98: 868 107.98 - 143.98: 19 143.98 - 179.97: 56 Dihedral angle restraints: 101672 sinusoidal: 74627 harmonic: 27045 Sorted by residual: dihedral pdb=" CA GLY e 392 " pdb=" C GLY e 392 " pdb=" N PHE e 393 " pdb=" CA PHE e 393 " ideal model delta harmonic sigma weight residual -180.00 -47.07 -132.93 0 5.00e+00 4.00e-02 7.07e+02 dihedral pdb=" CA THR p 30 " pdb=" C THR p 30 " pdb=" N PRO p 31 " pdb=" CA PRO p 31 " ideal model delta harmonic sigma weight residual -180.00 -124.92 -55.08 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA GLY O 20 " pdb=" C GLY O 20 " pdb=" N ILE O 21 " pdb=" CA ILE O 21 " ideal model delta harmonic sigma weight residual -180.00 -132.47 -47.53 0 5.00e+00 4.00e-02 9.03e+01 ... (remaining 101669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 28498 0.149 - 0.298: 805 0.298 - 0.448: 51 0.448 - 0.597: 2 0.597 - 0.746: 1 Chirality restraints: 29357 Sorted by residual: chirality pdb=" CB ILE U 118 " pdb=" CA ILE U 118 " pdb=" CG1 ILE U 118 " pdb=" CG2 ILE U 118 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA ASP p 158 " pdb=" N ASP p 158 " pdb=" C ASP p 158 " pdb=" CB ASP p 158 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" C3' G f 282 " pdb=" C4' G f 282 " pdb=" O3' G f 282 " pdb=" C2' G f 282 " both_signs ideal model delta sigma weight residual False -2.48 -2.01 -0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 29354 not shown) Planarity restraints: 16287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP m 95 " -0.035 2.00e-02 2.50e+03 3.47e-02 3.01e+01 pdb=" CG TRP m 95 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP m 95 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP m 95 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP m 95 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP m 95 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP m 95 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 95 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 95 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP m 95 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 5 " -0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C ARG d 5 " 0.082 2.00e-02 2.50e+03 pdb=" O ARG d 5 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA d 6 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 60 " 0.014 2.00e-02 2.50e+03 3.10e-02 1.93e+01 pdb=" CG TYR N 60 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR N 60 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR N 60 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR N 60 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR N 60 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR N 60 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 60 " -0.006 2.00e-02 2.50e+03 ... (remaining 16284 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 19 2.08 - 2.78: 32601 2.78 - 3.49: 192942 3.49 - 4.19: 470866 4.19 - 4.90: 653800 Nonbonded interactions: 1350228 Sorted by model distance: nonbonded pdb=" ND2 ASN V 91 " pdb=" NE2 GLN w 199 " model vdw 1.371 3.200 nonbonded pdb=" OP1 U f1258 " pdb=" NH1 ARG 0 46 " model vdw 1.522 2.520 nonbonded pdb=" CB GLU e 324 " pdb=" OG1 THR e 327 " model vdw 1.548 3.440 nonbonded pdb=" O3' A y 76 " pdb=" C UNK 1 57 " model vdw 1.636 3.270 nonbonded pdb=" O ASN e 882 " pdb=" O GLN e 885 " model vdw 1.687 3.040 ... (remaining 1350223 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 'x' and (resid 1 through 17 or resid 21 through 76)) selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 22.450 Check model and map are aligned: 1.580 Set scattering table: 1.020 Process input model: 617.180 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.480 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 664.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 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 0.096 160769 Z= 0.381 Angle : 0.903 16.551 234972 Z= 0.511 Chirality : 0.057 0.746 29357 Planarity : 0.007 0.103 16287 Dihedral : 21.716 179.971 84174 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.10 % Rotamer: Outliers : 0.98 % Allowed : 1.53 % Favored : 97.49 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.08), residues: 9175 helix: 0.72 (0.08), residues: 3853 sheet: -0.05 (0.15), residues: 1152 loop : -1.19 (0.09), residues: 4170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP m 95 HIS 0.017 0.002 HIS r 123 PHE 0.046 0.002 PHE o 229 TYR 0.067 0.002 TYR N 60 ARG 0.026 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1037 time to evaluate : 8.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 148 ASP cc_start: 0.8315 (t70) cc_final: 0.8046 (t0) REVERT: H 25 ASN cc_start: 0.8767 (m-40) cc_final: 0.8233 (m-40) REVERT: P 20 SER cc_start: 0.8928 (t) cc_final: 0.7850 (t) REVERT: U 30 GLU cc_start: 0.6995 (tp30) cc_final: 0.6700 (tp30) REVERT: U 34 GLN cc_start: 0.8108 (mt0) cc_final: 0.7332 (mt0) REVERT: V 64 SER cc_start: 0.8937 (m) cc_final: 0.8440 (t) REVERT: V 92 ASN cc_start: 0.8844 (m-40) cc_final: 0.8489 (m-40) REVERT: c 85 ARG cc_start: 0.8413 (tmm-80) cc_final: 0.8165 (ttp-110) REVERT: d 17 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7987 (ttmt) REVERT: k 308 MET cc_start: 0.8706 (mmm) cc_final: 0.8475 (mtp) REVERT: n 132 THR cc_start: 0.8731 (p) cc_final: 0.8265 (t) REVERT: n 137 ASP cc_start: 0.8241 (m-30) cc_final: 0.7431 (m-30) REVERT: p 243 GLN cc_start: 0.8565 (tp40) cc_final: 0.8311 (mm-40) REVERT: q 136 PHE cc_start: 0.8127 (m-80) cc_final: 0.7674 (m-80) REVERT: s 79 ILE cc_start: 0.9545 (mt) cc_final: 0.9342 (mt) REVERT: s 107 ASP cc_start: 0.8232 (m-30) cc_final: 0.7561 (m-30) REVERT: a 21 LEU cc_start: 0.8847 (mm) cc_final: 0.8572 (mm) REVERT: a 411 ASP cc_start: 0.8999 (m-30) cc_final: 0.8527 (t0) REVERT: e 67 MET cc_start: 0.8853 (tpp) cc_final: 0.8642 (tpp) REVERT: e 780 ILE cc_start: -0.3825 (OUTLIER) cc_final: -0.5755 (mm) REVERT: e 1142 GLU cc_start: 0.4285 (OUTLIER) cc_final: 0.2562 (tp30) REVERT: e 1464 ILE cc_start: 0.2904 (OUTLIER) cc_final: 0.2414 (pp) REVERT: e 1553 LEU cc_start: 0.0376 (OUTLIER) cc_final: -0.0025 (tp) REVERT: g 6 GLN cc_start: 0.8463 (mt0) cc_final: 0.8152 (mt0) REVERT: g 67 ARG cc_start: 0.8956 (ptm-80) cc_final: 0.8732 (ptm-80) REVERT: g 68 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8468 (mtm-85) REVERT: g 97 VAL cc_start: 0.9443 (t) cc_final: 0.9148 (m) REVERT: g 221 ILE cc_start: 0.8703 (tp) cc_final: 0.8397 (tp) REVERT: 0 38 MET cc_start: 0.9604 (mmm) cc_final: 0.9017 (tmm) REVERT: 0 52 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8112 (tp) REVERT: 0 69 ASP cc_start: 0.9080 (p0) cc_final: 0.8019 (p0) REVERT: 0 189 GLN cc_start: 0.6167 (OUTLIER) cc_final: 0.5597 (tm130) REVERT: 0 191 TYR cc_start: 0.9038 (t80) cc_final: 0.8120 (t80) REVERT: w 210 MET cc_start: -0.0125 (mmp) cc_final: -0.0734 (mpm) outliers start: 73 outliers final: 12 residues processed: 1106 average time/residue: 2.1554 time to fit residues: 3452.8175 Evaluate side-chains 742 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 724 time to evaluate : 7.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain c residue 88 GLU Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain e residue 230 SER Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 400 GLU Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 780 ILE Chi-restraints excluded: chain e residue 904 VAL Chi-restraints excluded: chain e residue 1142 GLU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain e residue 1553 LEU Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 189 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1071 optimal weight: 7.9990 chunk 961 optimal weight: 8.9990 chunk 533 optimal weight: 20.0000 chunk 328 optimal weight: 8.9990 chunk 648 optimal weight: 10.0000 chunk 513 optimal weight: 10.0000 chunk 994 optimal weight: 5.9990 chunk 384 optimal weight: 8.9990 chunk 604 optimal weight: 10.0000 chunk 740 optimal weight: 5.9990 chunk 1152 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN A B 122 GLN A C 137 ASN F 157 GLN G 127 GLN L 42 GLN M 78 ASN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 ASN S 42 GLN U 16 GLN U 62 GLN ** V 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN X 40 GLN X 57 ASN X 76 ASN Y 32 ASN j 132 ASN ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 116 ASN l 361 HIS m 39 GLN ** o 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 146 GLN o 225 GLN p 38 GLN s 6 GLN s 47 GLN a 599 GLN ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 189 ASN e 233 ASN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 397 ASN ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 805 ASN e 833 HIS ** e 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1141 GLN e1235 ASN e1288 GLN ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1457 ASN e1477 GLN ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 225 GLN 0 37 GLN ** w 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 160769 Z= 0.496 Angle : 0.693 12.198 234972 Z= 0.365 Chirality : 0.045 0.342 29357 Planarity : 0.006 0.107 16287 Dihedral : 22.653 179.886 66710 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 2.10 % Allowed : 8.91 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.08 % 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: 0.11 (0.08), residues: 9175 helix: 1.19 (0.08), residues: 3894 sheet: -0.14 (0.15), residues: 1152 loop : -0.93 (0.09), residues: 4129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP u 12 HIS 0.013 0.002 HIS e 733 PHE 0.030 0.002 PHE o 229 TYR 0.035 0.002 TYR N 60 ARG 0.015 0.001 ARG e1049 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 733 time to evaluate : 8.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7552 (tt0) cc_final: 0.7262 (tt0) REVERT: C 53 ASP cc_start: 0.7814 (t0) cc_final: 0.7508 (t0) REVERT: E 144 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8345 (tm-30) REVERT: H 24 GLU cc_start: 0.8416 (pp20) cc_final: 0.8105 (OUTLIER) REVERT: H 25 ASN cc_start: 0.8965 (m-40) cc_final: 0.8591 (m-40) REVERT: L 74 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: P 27 TYR cc_start: 0.8874 (t80) cc_final: 0.8595 (t80) REVERT: X 10 GLN cc_start: 0.8804 (tt0) cc_final: 0.8507 (tt0) REVERT: X 14 LEU cc_start: 0.9504 (tm) cc_final: 0.9155 (tt) REVERT: X 77 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7773 (mmm-85) REVERT: Y 36 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7197 (mmp-170) REVERT: d 17 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8009 (ttmt) REVERT: j 143 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: k 137 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6531 (t80) REVERT: k 318 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8228 (mmmm) REVERT: n 133 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7289 (tm-30) REVERT: n 137 ASP cc_start: 0.8363 (m-30) cc_final: 0.7772 (m-30) REVERT: s 35 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9069 (tmmm) REVERT: s 38 GLU cc_start: 0.8565 (tp30) cc_final: 0.8297 (tp30) REVERT: s 79 ILE cc_start: 0.9626 (mt) cc_final: 0.9416 (mm) REVERT: a 411 ASP cc_start: 0.9088 (m-30) cc_final: 0.8719 (t0) REVERT: e 67 MET cc_start: 0.8753 (tpp) cc_final: 0.8406 (tpp) REVERT: e 1068 MET cc_start: -0.0106 (mtt) cc_final: -0.0415 (mtt) REVERT: e 1086 MET cc_start: 0.6551 (pp-130) cc_final: 0.6334 (ppp) REVERT: e 1162 MET cc_start: 0.6040 (tmt) cc_final: 0.5706 (tmt) REVERT: e 1384 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8756 (pp20) REVERT: e 1464 ILE cc_start: 0.2968 (OUTLIER) cc_final: 0.2394 (pp) REVERT: g 6 GLN cc_start: 0.8308 (mt0) cc_final: 0.7869 (mt0) REVERT: g 67 ARG cc_start: 0.9058 (ptm-80) cc_final: 0.8705 (ptm-80) REVERT: g 139 ARG cc_start: 0.7809 (mtp85) cc_final: 0.7557 (mtt-85) REVERT: 0 6 GLU cc_start: 0.9598 (tm-30) cc_final: 0.9231 (pp20) REVERT: 0 16 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8751 (tpp80) REVERT: 0 22 TYR cc_start: 0.9044 (m-80) cc_final: 0.8724 (m-80) REVERT: 0 26 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8169 (t80) REVERT: 0 37 GLN cc_start: 0.9112 (tt0) cc_final: 0.8892 (mm-40) REVERT: 0 40 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8957 (pt0) REVERT: 0 52 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8290 (tp) REVERT: 0 57 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7824 (t) REVERT: 0 60 ARG cc_start: 0.8977 (mtt180) cc_final: 0.8665 (mtt-85) REVERT: 0 98 ASN cc_start: 0.9541 (m110) cc_final: 0.9202 (p0) REVERT: 0 191 TYR cc_start: 0.8791 (t80) cc_final: 0.8335 (t80) REVERT: w 210 MET cc_start: 0.0202 (mmp) cc_final: -0.0141 (mpm) outliers start: 156 outliers final: 64 residues processed: 819 average time/residue: 2.1586 time to fit residues: 2573.4311 Evaluate side-chains 762 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 686 time to evaluate : 7.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain j residue 143 GLU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 318 LYS Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 149 ILE Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 34 SER Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 904 VAL Chi-restraints excluded: chain e residue 990 VAL Chi-restraints excluded: chain e residue 1091 ASP Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1384 GLU Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 31 ASP Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain w residue 217 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 640 optimal weight: 8.9990 chunk 357 optimal weight: 7.9990 chunk 959 optimal weight: 40.0000 chunk 784 optimal weight: 7.9990 chunk 317 optimal weight: 4.9990 chunk 1154 optimal weight: 30.0000 chunk 1247 optimal weight: 40.0000 chunk 1028 optimal weight: 20.0000 chunk 1144 optimal weight: 50.0000 chunk 393 optimal weight: 10.0000 chunk 926 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN N 67 HIS T 108 GLN W 13 ASN X 57 ASN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 GLN j 47 GLN k 293 ASN k 319 ASN n 5 GLN o 225 GLN p 77 GLN r 123 HIS ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN t 114 GLN t 160 GLN t 162 ASN u 27 GLN u 105 GLN ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 894 ASN ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 21 ASN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 810 GLN ** e 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 225 GLN 0 36 GLN w 96 ASN ** w 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 160769 Z= 0.503 Angle : 0.674 10.226 234972 Z= 0.355 Chirality : 0.044 0.339 29357 Planarity : 0.005 0.104 16287 Dihedral : 22.629 179.892 66686 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 2.61 % Allowed : 10.85 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.10 % 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: 0.28 (0.09), residues: 9175 helix: 1.39 (0.08), residues: 3919 sheet: -0.18 (0.14), residues: 1163 loop : -0.88 (0.09), residues: 4093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP u 85 HIS 0.008 0.001 HIS k 13 PHE 0.045 0.002 PHE 0 66 TYR 0.046 0.002 TYR w 217 ARG 0.011 0.001 ARG g 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 725 time to evaluate : 8.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7698 (tt0) cc_final: 0.7375 (tt0) REVERT: C 53 ASP cc_start: 0.7882 (t0) cc_final: 0.7544 (t0) REVERT: C 120 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8690 (p0) REVERT: E 92 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: E 144 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8195 (tm-30) REVERT: H 24 GLU cc_start: 0.8556 (pp20) cc_final: 0.8350 (pp20) REVERT: H 25 ASN cc_start: 0.9029 (m-40) cc_final: 0.8616 (m-40) REVERT: H 92 TRP cc_start: 0.7859 (m-90) cc_final: 0.7410 (m-90) REVERT: J 4 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6787 (mm-30) REVERT: J 58 HIS cc_start: 0.7809 (t70) cc_final: 0.7539 (t70) REVERT: S 33 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: V 66 GLU cc_start: 0.7104 (pp20) cc_final: 0.6527 (tm-30) REVERT: X 10 GLN cc_start: 0.8713 (tt0) cc_final: 0.8216 (tt0) REVERT: X 14 LEU cc_start: 0.9470 (tm) cc_final: 0.9268 (tt) REVERT: X 77 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7772 (mmm160) REVERT: Y 36 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7211 (mmp-170) REVERT: d 17 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8184 (ttmm) REVERT: j 143 GLU cc_start: 0.8274 (pp20) cc_final: 0.7952 (pp20) REVERT: k 137 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6778 (t80) REVERT: k 323 MET cc_start: 0.8355 (ttm) cc_final: 0.8136 (ttm) REVERT: l 285 ASP cc_start: 0.8182 (t0) cc_final: 0.7812 (t0) REVERT: m 95 TRP cc_start: 0.9620 (OUTLIER) cc_final: 0.7756 (t60) REVERT: n 133 GLU cc_start: 0.7267 (tm-30) cc_final: 0.7014 (tm-30) REVERT: n 137 ASP cc_start: 0.8259 (m-30) cc_final: 0.7811 (m-30) REVERT: s 22 SER cc_start: 0.9235 (m) cc_final: 0.8827 (t) REVERT: s 35 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9112 (tmmm) REVERT: s 38 GLU cc_start: 0.8551 (tp30) cc_final: 0.8224 (tp30) REVERT: a 411 ASP cc_start: 0.9099 (m-30) cc_final: 0.8752 (t0) REVERT: a 697 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7044 (pp) REVERT: e 67 MET cc_start: 0.8746 (tpp) cc_final: 0.8281 (tmm) REVERT: e 963 MET cc_start: 0.2527 (OUTLIER) cc_final: 0.0668 (mpp) REVERT: e 1068 MET cc_start: 0.0244 (mtt) cc_final: -0.0233 (mtt) REVERT: e 1086 MET cc_start: 0.7230 (pp-130) cc_final: 0.7005 (ppp) REVERT: e 1162 MET cc_start: 0.5972 (tmt) cc_final: 0.5441 (tmt) REVERT: e 1379 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9115 (tm) REVERT: e 1464 ILE cc_start: 0.3128 (OUTLIER) cc_final: 0.2438 (pp) REVERT: g 6 GLN cc_start: 0.8214 (mt0) cc_final: 0.7777 (mt0) REVERT: g 67 ARG cc_start: 0.9077 (ptm-80) cc_final: 0.8840 (ptm-80) REVERT: g 139 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7185 (mtt-85) REVERT: g 157 GLN cc_start: 0.9225 (mm-40) cc_final: 0.9008 (mm-40) REVERT: 0 7 LYS cc_start: 0.9701 (tttt) cc_final: 0.9427 (tmmt) REVERT: 0 16 ARG cc_start: 0.9255 (tpp80) cc_final: 0.8781 (tpp80) REVERT: 0 22 TYR cc_start: 0.8994 (m-80) cc_final: 0.8701 (m-80) REVERT: 0 38 MET cc_start: 0.9510 (mmm) cc_final: 0.8727 (tmm) REVERT: 0 52 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8184 (tp) REVERT: 0 55 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8627 (mtpp) REVERT: 0 60 ARG cc_start: 0.8980 (mtt180) cc_final: 0.8631 (mpt-90) REVERT: 0 64 ARG cc_start: 0.9027 (mtm110) cc_final: 0.8149 (mtm-85) REVERT: 0 98 ASN cc_start: 0.9534 (m110) cc_final: 0.9133 (p0) REVERT: 0 191 TYR cc_start: 0.8878 (t80) cc_final: 0.8436 (t80) outliers start: 194 outliers final: 91 residues processed: 843 average time/residue: 2.1454 time to fit residues: 2642.1011 Evaluate side-chains 789 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 685 time to evaluate : 7.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain l residue 323 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 246 MET Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 113 GLU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 34 SER Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 904 VAL Chi-restraints excluded: chain e residue 963 MET Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1379 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain e residue 1516 HIS Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1140 optimal weight: 50.0000 chunk 867 optimal weight: 5.9990 chunk 599 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 550 optimal weight: 10.0000 chunk 775 optimal weight: 4.9990 chunk 1158 optimal weight: 40.0000 chunk 1226 optimal weight: 7.9990 chunk 605 optimal weight: 5.9990 chunk 1098 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN E 34 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN J 58 HIS L 42 GLN M 123 GLN S 106 ASN T 108 GLN X 57 ASN b 102 GLN j 47 GLN j 97 ASN k 293 ASN p 77 GLN r 123 HIS ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN t 162 ASN u 27 GLN ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 894 ASN a 957 GLN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 810 GLN e 832 ASN ** e 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 225 GLN ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 GLN ** 0 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 160769 Z= 0.406 Angle : 0.628 10.072 234972 Z= 0.331 Chirality : 0.041 0.306 29357 Planarity : 0.005 0.101 16287 Dihedral : 22.614 179.898 66686 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.28 % Favored : 95.66 % Rotamer: Outliers : 2.71 % Allowed : 12.41 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.09 % 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: 0.40 (0.09), residues: 9175 helix: 1.52 (0.08), residues: 3916 sheet: -0.13 (0.15), residues: 1158 loop : -0.84 (0.09), residues: 4101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP u 85 HIS 0.011 0.001 HIS r 123 PHE 0.047 0.002 PHE 0 66 TYR 0.022 0.002 TYR g 151 ARG 0.009 0.001 ARG g 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 712 time to evaluate : 7.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.7948 (t0) cc_final: 0.7642 (t0) REVERT: C 120 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8623 (p0) REVERT: H 25 ASN cc_start: 0.9045 (m-40) cc_final: 0.8664 (m-40) REVERT: H 91 ASP cc_start: 0.8019 (t0) cc_final: 0.7679 (t0) REVERT: H 92 TRP cc_start: 0.7787 (m-90) cc_final: 0.7350 (m-90) REVERT: R 19 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.9099 (ttt-90) REVERT: S 33 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: V 66 GLU cc_start: 0.7084 (pp20) cc_final: 0.6523 (tm-30) REVERT: X 77 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7743 (mmm-85) REVERT: Y 36 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7201 (mmp-170) REVERT: d 17 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8181 (ttmm) REVERT: j 143 GLU cc_start: 0.8413 (pp20) cc_final: 0.8105 (pp20) REVERT: k 137 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7064 (t80) REVERT: k 323 MET cc_start: 0.8341 (ttm) cc_final: 0.8115 (ttm) REVERT: m 95 TRP cc_start: 0.9629 (OUTLIER) cc_final: 0.7783 (t60) REVERT: m 158 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7917 (ptt-90) REVERT: n 137 ASP cc_start: 0.8284 (m-30) cc_final: 0.7853 (m-30) REVERT: s 22 SER cc_start: 0.9252 (m) cc_final: 0.8940 (t) REVERT: s 35 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9097 (tmmm) REVERT: s 38 GLU cc_start: 0.8584 (tp30) cc_final: 0.8215 (tp30) REVERT: a 411 ASP cc_start: 0.9071 (m-30) cc_final: 0.8746 (t0) REVERT: a 697 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7161 (pp) REVERT: a 887 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8898 (tm-30) REVERT: a 918 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8875 (p0) REVERT: e 67 MET cc_start: 0.8747 (tpp) cc_final: 0.8457 (tpp) REVERT: e 809 MET cc_start: 0.8443 (ppp) cc_final: 0.8054 (ppp) REVERT: e 1068 MET cc_start: 0.0395 (mtt) cc_final: -0.0185 (mtt) REVERT: e 1162 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5428 (tmt) REVERT: e 1379 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9144 (tm) REVERT: e 1464 ILE cc_start: 0.3445 (OUTLIER) cc_final: 0.2748 (pp) REVERT: g 1 MET cc_start: 0.5717 (ttt) cc_final: 0.4160 (mtp) REVERT: g 6 GLN cc_start: 0.8222 (mt0) cc_final: 0.7854 (mt0) REVERT: g 67 ARG cc_start: 0.9115 (ptm-80) cc_final: 0.8865 (ptm-80) REVERT: g 139 ARG cc_start: 0.7504 (mtp85) cc_final: 0.7085 (mtp85) REVERT: 0 7 LYS cc_start: 0.9715 (tttt) cc_final: 0.9150 (tmmt) REVERT: 0 14 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8710 (tptp) REVERT: 0 26 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8264 (t80) REVERT: 0 38 MET cc_start: 0.9538 (mmm) cc_final: 0.8753 (tmm) REVERT: 0 52 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8248 (tm) REVERT: 0 53 MET cc_start: 0.6995 (mmm) cc_final: 0.6757 (mmm) REVERT: 0 60 ARG cc_start: 0.8890 (mtt180) cc_final: 0.8519 (mtt-85) REVERT: 0 64 ARG cc_start: 0.8880 (mtm110) cc_final: 0.8264 (mtm-85) REVERT: 0 191 TYR cc_start: 0.8899 (t80) cc_final: 0.8545 (t80) REVERT: w 210 MET cc_start: 0.0731 (mpm) cc_final: 0.0393 (mpm) outliers start: 202 outliers final: 112 residues processed: 838 average time/residue: 2.1206 time to fit residues: 2601.8955 Evaluate side-chains 813 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 685 time to evaluate : 8.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 34 SER Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 116 TYR Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 894 ASN Chi-restraints excluded: chain a residue 918 ASP Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 1091 ASP Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1379 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain e residue 1516 HIS Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain 0 residue 24 SER Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1021 optimal weight: 8.9990 chunk 696 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 913 optimal weight: 10.0000 chunk 506 optimal weight: 7.9990 chunk 1046 optimal weight: 5.9990 chunk 847 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 626 optimal weight: 10.0000 chunk 1100 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN E 118 HIS ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN L 26 GLN L 42 GLN M 123 GLN S 106 ASN T 108 GLN X 57 ASN ** b 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 GLN k 293 ASN p 77 GLN r 123 HIS ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN t 114 GLN t 160 GLN t 162 ASN ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 831 ASN e 885 GLN ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1422 ASN e1455 GLN ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 157 GLN g 225 GLN 0 36 GLN ** 0 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 160769 Z= 0.384 Angle : 0.616 10.103 234972 Z= 0.325 Chirality : 0.041 0.306 29357 Planarity : 0.005 0.099 16287 Dihedral : 22.591 179.563 66683 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 3.12 % Allowed : 13.22 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.08 % 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: 0.47 (0.09), residues: 9175 helix: 1.59 (0.08), residues: 3906 sheet: -0.05 (0.15), residues: 1166 loop : -0.81 (0.09), residues: 4103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP n 9 HIS 0.006 0.001 HIS F 114 PHE 0.038 0.002 PHE 0 66 TYR 0.041 0.002 TYR s 116 ARG 0.009 0.001 ARG g 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 710 time to evaluate : 8.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7914 (tp30) cc_final: 0.7683 (tp30) REVERT: B 84 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9076 (tt) REVERT: C 53 ASP cc_start: 0.7984 (t0) cc_final: 0.7701 (t0) REVERT: C 120 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8597 (p0) REVERT: E 144 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8122 (tm-30) REVERT: H 24 GLU cc_start: 0.8670 (pp20) cc_final: 0.8423 (OUTLIER) REVERT: H 25 ASN cc_start: 0.9007 (m-40) cc_final: 0.8715 (m-40) REVERT: H 91 ASP cc_start: 0.7978 (t0) cc_final: 0.7564 (t0) REVERT: H 92 TRP cc_start: 0.7572 (m-90) cc_final: 0.6640 (m-90) REVERT: J 2 LYS cc_start: 0.8302 (tptm) cc_final: 0.8083 (tptm) REVERT: R 19 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.9082 (ttt-90) REVERT: S 33 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7468 (pp20) REVERT: V 66 GLU cc_start: 0.7101 (pp20) cc_final: 0.6571 (tm-30) REVERT: X 77 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7727 (mmm-85) REVERT: Y 36 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7198 (mmp-170) REVERT: j 143 GLU cc_start: 0.8541 (pp20) cc_final: 0.8267 (pp20) REVERT: k 137 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7093 (t80) REVERT: k 323 MET cc_start: 0.8335 (ttm) cc_final: 0.8129 (ttm) REVERT: m 95 TRP cc_start: 0.9632 (OUTLIER) cc_final: 0.7818 (t60) REVERT: m 158 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7916 (ptt-90) REVERT: n 137 ASP cc_start: 0.8310 (m-30) cc_final: 0.7786 (m-30) REVERT: q 11 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: s 22 SER cc_start: 0.9207 (m) cc_final: 0.8932 (t) REVERT: s 35 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9103 (tmmm) REVERT: s 38 GLU cc_start: 0.8587 (tp30) cc_final: 0.8194 (tp30) REVERT: s 108 GLU cc_start: 0.8037 (pp20) cc_final: 0.7824 (pp20) REVERT: s 117 ASP cc_start: 0.8251 (t0) cc_final: 0.7965 (t0) REVERT: a 411 ASP cc_start: 0.9055 (m-30) cc_final: 0.8836 (t0) REVERT: a 589 MET cc_start: 0.8215 (pmm) cc_final: 0.7808 (ppp) REVERT: a 621 TRP cc_start: 0.6183 (m-10) cc_final: 0.5664 (m-10) REVERT: a 697 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7165 (pp) REVERT: a 699 MET cc_start: 0.3550 (mmm) cc_final: 0.2862 (mmm) REVERT: e 67 MET cc_start: 0.8733 (tpp) cc_final: 0.8396 (tpp) REVERT: e 809 MET cc_start: 0.8491 (ppp) cc_final: 0.8163 (ppp) REVERT: e 1033 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7836 (mttt) REVERT: e 1060 MET cc_start: 0.0507 (OUTLIER) cc_final: 0.0161 (mpt) REVERT: e 1068 MET cc_start: 0.0206 (mtt) cc_final: -0.0356 (mtt) REVERT: e 1162 MET cc_start: 0.5981 (OUTLIER) cc_final: 0.5442 (tmt) REVERT: e 1464 ILE cc_start: 0.3501 (OUTLIER) cc_final: 0.2817 (pp) REVERT: g 6 GLN cc_start: 0.8123 (mt0) cc_final: 0.7764 (mt0) REVERT: g 67 ARG cc_start: 0.9100 (ptm-80) cc_final: 0.8779 (ptm-80) REVERT: 0 7 LYS cc_start: 0.9499 (tttt) cc_final: 0.9186 (tmmt) REVERT: 0 10 GLU cc_start: 0.9496 (pp20) cc_final: 0.9213 (pp20) REVERT: 0 14 LYS cc_start: 0.8976 (ttpp) cc_final: 0.8673 (tptp) REVERT: 0 26 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8279 (t80) REVERT: 0 38 MET cc_start: 0.9561 (mmm) cc_final: 0.8703 (tmm) REVERT: 0 52 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8205 (tp) REVERT: 0 55 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8593 (mtmt) REVERT: 0 60 ARG cc_start: 0.8902 (mtt180) cc_final: 0.8647 (mtt180) REVERT: 0 98 ASN cc_start: 0.9611 (m110) cc_final: 0.9234 (p0) REVERT: 0 191 TYR cc_start: 0.8911 (t80) cc_final: 0.8578 (t80) outliers start: 232 outliers final: 129 residues processed: 856 average time/residue: 2.0743 time to fit residues: 2614.1599 Evaluate side-chains 830 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 684 time to evaluate : 7.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 58 GLU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 323 VAL Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 125 VAL Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 11 GLU Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 113 GLU Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 48 SER Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain e residue 230 SER Chi-restraints excluded: chain e residue 713 LEU Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1060 MET Chi-restraints excluded: chain e residue 1091 ASP Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 157 GLN Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain 0 residue 18 TYR Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain w residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 412 optimal weight: 7.9990 chunk 1104 optimal weight: 20.0000 chunk 242 optimal weight: 1.9990 chunk 720 optimal weight: 0.6980 chunk 302 optimal weight: 5.9990 chunk 1227 optimal weight: 10.0000 chunk 1019 optimal weight: 20.0000 chunk 568 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 406 optimal weight: 10.0000 chunk 644 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN M 123 GLN S 106 ASN T 108 GLN Y 32 ASN ** b 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 GLN k 293 ASN m 296 GLN p 59 GLN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN t 162 ASN ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 438 ASN ** e 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 930 ASN ** e1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 225 GLN ** 0 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 160769 Z= 0.308 Angle : 0.589 11.705 234972 Z= 0.312 Chirality : 0.039 0.316 29357 Planarity : 0.005 0.097 16287 Dihedral : 22.580 179.822 66683 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 2.86 % Allowed : 14.48 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.07 % 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: 0.55 (0.09), residues: 9175 helix: 1.65 (0.08), residues: 3918 sheet: -0.03 (0.15), residues: 1155 loop : -0.77 (0.09), residues: 4102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP n 9 HIS 0.005 0.001 HIS F 114 PHE 0.035 0.001 PHE 0 66 TYR 0.033 0.001 TYR 0 22 ARG 0.010 0.000 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 712 time to evaluate : 8.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8111 (ttt90) REVERT: A 193 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7786 (ttm-80) REVERT: B 84 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9044 (tt) REVERT: C 53 ASP cc_start: 0.7983 (t0) cc_final: 0.7719 (t0) REVERT: E 144 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8165 (tm-30) REVERT: H 24 GLU cc_start: 0.8612 (pp20) cc_final: 0.8405 (OUTLIER) REVERT: H 25 ASN cc_start: 0.9017 (m-40) cc_final: 0.8716 (m-40) REVERT: H 92 TRP cc_start: 0.7404 (m-90) cc_final: 0.6818 (m-90) REVERT: J 2 LYS cc_start: 0.8344 (tptm) cc_final: 0.8028 (tptm) REVERT: P 74 ASN cc_start: 0.9443 (OUTLIER) cc_final: 0.9044 (p0) REVERT: R 19 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.9078 (ttt180) REVERT: S 33 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7413 (pp20) REVERT: T 97 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: V 66 GLU cc_start: 0.7146 (pp20) cc_final: 0.6899 (tm-30) REVERT: X 77 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7677 (mmm-85) REVERT: Y 36 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7183 (mmp-170) REVERT: d 17 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7812 (ttmt) REVERT: j 143 GLU cc_start: 0.8587 (pp20) cc_final: 0.8313 (pp20) REVERT: k 137 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7066 (t80) REVERT: l 285 ASP cc_start: 0.8168 (t0) cc_final: 0.7613 (t0) REVERT: m 95 TRP cc_start: 0.9611 (OUTLIER) cc_final: 0.7732 (t60) REVERT: m 158 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7922 (ptt-90) REVERT: n 137 ASP cc_start: 0.8205 (m-30) cc_final: 0.7927 (m-30) REVERT: q 11 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: s 15 GLU cc_start: 0.7961 (tt0) cc_final: 0.7546 (tt0) REVERT: s 22 SER cc_start: 0.9156 (m) cc_final: 0.8924 (t) REVERT: s 35 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9086 (tmmm) REVERT: s 38 GLU cc_start: 0.8588 (tp30) cc_final: 0.8192 (tp30) REVERT: a 411 ASP cc_start: 0.9031 (m-30) cc_final: 0.8826 (t0) REVERT: a 589 MET cc_start: 0.8226 (pmm) cc_final: 0.7839 (ppp) REVERT: a 621 TRP cc_start: 0.6386 (m-10) cc_final: 0.5942 (m-10) REVERT: a 697 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7246 (pp) REVERT: a 918 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8860 (p0) REVERT: e 67 MET cc_start: 0.8708 (tpp) cc_final: 0.8364 (tpp) REVERT: e 125 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8631 (mt) REVERT: e 277 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.5148 (ppp) REVERT: e 809 MET cc_start: 0.8527 (ppp) cc_final: 0.8142 (ppp) REVERT: e 1033 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7958 (mttt) REVERT: e 1068 MET cc_start: 0.0218 (mtt) cc_final: -0.0363 (mtt) REVERT: e 1162 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5478 (tmt) REVERT: e 1464 ILE cc_start: 0.3569 (OUTLIER) cc_final: 0.2918 (pp) REVERT: g 6 GLN cc_start: 0.8078 (mt0) cc_final: 0.7728 (mt0) REVERT: g 67 ARG cc_start: 0.9107 (ptm-80) cc_final: 0.8750 (ptm-80) REVERT: 0 7 LYS cc_start: 0.9525 (tttt) cc_final: 0.9141 (tmmt) REVERT: 0 8 LYS cc_start: 0.8911 (mttt) cc_final: 0.8280 (mttm) REVERT: 0 10 GLU cc_start: 0.9556 (pp20) cc_final: 0.9319 (pp20) REVERT: 0 14 LYS cc_start: 0.8971 (ttpp) cc_final: 0.8609 (tptp) REVERT: 0 16 ARG cc_start: 0.9372 (ptm-80) cc_final: 0.8596 (ttp80) REVERT: 0 26 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8424 (t80) REVERT: 0 38 MET cc_start: 0.9553 (mmm) cc_final: 0.8674 (tmm) REVERT: 0 40 GLU cc_start: 0.8994 (pt0) cc_final: 0.8639 (pp20) REVERT: 0 44 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8695 (mm-30) REVERT: 0 52 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8321 (tm) REVERT: 0 53 MET cc_start: 0.6998 (mmm) cc_final: 0.6735 (mmm) REVERT: 0 60 ARG cc_start: 0.8943 (mtt180) cc_final: 0.8697 (mtt180) REVERT: 0 98 ASN cc_start: 0.9546 (m110) cc_final: 0.9155 (p0) REVERT: 0 191 TYR cc_start: 0.8957 (t80) cc_final: 0.8544 (t80) REVERT: w 33 GLU cc_start: -0.0894 (OUTLIER) cc_final: -0.2632 (mt-10) REVERT: w 210 MET cc_start: 0.0915 (mpm) cc_final: 0.0375 (mmp) outliers start: 213 outliers final: 135 residues processed: 851 average time/residue: 2.1181 time to fit residues: 2655.7852 Evaluate side-chains 843 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 685 time to evaluate : 8.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 58 MET Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 74 ASN Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 20 MET Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 177 ASP Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 125 VAL Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 11 GLU Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain a residue 918 ASP Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 320 LEU Chi-restraints excluded: chain e residue 713 LEU Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1091 ASP Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain e residue 1516 HIS Chi-restraints excluded: chain g residue 5 THR Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain w residue 33 GLU Chi-restraints excluded: chain w residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1183 optimal weight: 30.0000 chunk 138 optimal weight: 3.9990 chunk 699 optimal weight: 5.9990 chunk 896 optimal weight: 3.9990 chunk 694 optimal weight: 10.0000 chunk 1033 optimal weight: 50.0000 chunk 685 optimal weight: 8.9990 chunk 1223 optimal weight: 50.0000 chunk 765 optimal weight: 3.9990 chunk 745 optimal weight: 0.2980 chunk 564 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN H 52 ASN L 42 GLN M 123 GLN S 106 ASN T 108 GLN X 10 GLN Y 32 ASN ** b 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 GLN k 293 ASN p 59 GLN r 175 ASN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN t 114 GLN t 160 GLN t 162 ASN ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 849 ASN ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 157 GLN g 225 GLN ** 0 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 160769 Z= 0.258 Angle : 0.572 10.087 234972 Z= 0.303 Chirality : 0.037 0.349 29357 Planarity : 0.004 0.095 16287 Dihedral : 22.556 179.608 66683 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 2.61 % Allowed : 15.23 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.07 % 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: 0.61 (0.09), residues: 9175 helix: 1.70 (0.08), residues: 3929 sheet: -0.06 (0.15), residues: 1140 loop : -0.72 (0.09), residues: 4106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP n 9 HIS 0.004 0.001 HIS l 311 PHE 0.029 0.001 PHE 0 88 TYR 0.026 0.001 TYR 0 22 ARG 0.011 0.000 ARG g 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 705 time to evaluate : 8.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8113 (ttt90) REVERT: A 193 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8645 (ttp-110) REVERT: B 84 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9030 (tt) REVERT: C 53 ASP cc_start: 0.7825 (t0) cc_final: 0.7557 (t0) REVERT: E 144 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8173 (tm-30) REVERT: H 25 ASN cc_start: 0.9006 (m-40) cc_final: 0.8727 (m-40) REVERT: H 91 ASP cc_start: 0.7908 (t0) cc_final: 0.7564 (t0) REVERT: J 2 LYS cc_start: 0.8318 (tptm) cc_final: 0.7984 (tptm) REVERT: L 74 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: R 19 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.9082 (ttt180) REVERT: S 33 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7374 (pp20) REVERT: V 66 GLU cc_start: 0.7191 (pp20) cc_final: 0.6963 (tm-30) REVERT: X 77 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7661 (mmm-85) REVERT: d 17 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7837 (ttmt) REVERT: j 143 GLU cc_start: 0.8598 (pp20) cc_final: 0.8375 (pp20) REVERT: k 137 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7058 (t80) REVERT: m 95 TRP cc_start: 0.9583 (OUTLIER) cc_final: 0.7773 (t60) REVERT: m 158 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7910 (ptt-90) REVERT: q 11 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: s 22 SER cc_start: 0.9136 (m) cc_final: 0.8879 (t) REVERT: s 35 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9078 (tmmm) REVERT: s 38 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: a 589 MET cc_start: 0.8172 (pmm) cc_final: 0.7665 (pp-130) REVERT: a 697 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7212 (pp) REVERT: a 699 MET cc_start: 0.3408 (mmm) cc_final: 0.2515 (mmm) REVERT: a 918 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8826 (p0) REVERT: e 67 MET cc_start: 0.8701 (tpp) cc_final: 0.8380 (tpp) REVERT: e 125 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.8641 (mt) REVERT: e 277 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.4398 (ppp) REVERT: e 809 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8138 (ppp) REVERT: e 893 MET cc_start: -0.0405 (tmt) cc_final: -0.1718 (tmt) REVERT: e 963 MET cc_start: 0.2626 (mpt) cc_final: -0.0069 (ptt) REVERT: e 1033 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7942 (mttt) REVERT: e 1060 MET cc_start: 0.0193 (OUTLIER) cc_final: -0.0184 (mpt) REVERT: e 1068 MET cc_start: 0.0133 (mtt) cc_final: -0.0432 (mtt) REVERT: e 1162 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5517 (tmt) REVERT: e 1464 ILE cc_start: 0.3533 (OUTLIER) cc_final: 0.2898 (pp) REVERT: g 1 MET cc_start: 0.5478 (ttt) cc_final: 0.4107 (tpt) REVERT: g 6 GLN cc_start: 0.8011 (mt0) cc_final: 0.7696 (mt0) REVERT: g 67 ARG cc_start: 0.9117 (ptm-80) cc_final: 0.8745 (ptm-80) REVERT: 0 7 LYS cc_start: 0.9530 (tttt) cc_final: 0.9219 (tmmt) REVERT: 0 10 GLU cc_start: 0.9606 (pp20) cc_final: 0.9308 (pp20) REVERT: 0 14 LYS cc_start: 0.9003 (ttpp) cc_final: 0.8595 (tptp) REVERT: 0 26 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8621 (t80) REVERT: 0 38 MET cc_start: 0.9549 (mmm) cc_final: 0.8675 (tmm) REVERT: 0 40 GLU cc_start: 0.9025 (pt0) cc_final: 0.8731 (pp20) REVERT: 0 44 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8954 (mm-30) REVERT: 0 52 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8243 (tm) REVERT: 0 53 MET cc_start: 0.7087 (mmm) cc_final: 0.6797 (mmm) REVERT: 0 55 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8377 (mtmt) REVERT: 0 60 ARG cc_start: 0.8994 (mtt180) cc_final: 0.8779 (mtt180) REVERT: 0 191 TYR cc_start: 0.8919 (t80) cc_final: 0.8560 (t80) REVERT: w 33 GLU cc_start: -0.0945 (OUTLIER) cc_final: -0.2861 (mt-10) REVERT: w 210 MET cc_start: 0.0739 (mpm) cc_final: 0.0297 (mpm) outliers start: 194 outliers final: 131 residues processed: 836 average time/residue: 2.1782 time to fit residues: 2687.2108 Evaluate side-chains 838 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 682 time to evaluate : 8.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 20 MET Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 177 ASP Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 125 VAL Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 11 GLU Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 38 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain a residue 918 ASP Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 320 LEU Chi-restraints excluded: chain e residue 713 LEU Chi-restraints excluded: chain e residue 809 MET Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1060 MET Chi-restraints excluded: chain e residue 1091 ASP Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain g residue 5 THR Chi-restraints excluded: chain g residue 62 MET Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain w residue 33 GLU Chi-restraints excluded: chain w residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 756 optimal weight: 4.9990 chunk 488 optimal weight: 10.0000 chunk 730 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 777 optimal weight: 8.9990 chunk 833 optimal weight: 4.9990 chunk 604 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 961 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN S 106 ASN T 108 GLN X 10 GLN Y 32 ASN ** b 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 GLN k 293 ASN n 5 GLN p 59 GLN r 175 ASN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN t 162 ASN ** e 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 170 GLN g 225 GLN ** 0 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 160769 Z= 0.302 Angle : 0.590 14.218 234972 Z= 0.311 Chirality : 0.038 0.363 29357 Planarity : 0.004 0.096 16287 Dihedral : 22.519 179.610 66683 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 2.58 % Allowed : 15.65 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.09), residues: 9175 helix: 1.72 (0.08), residues: 3928 sheet: -0.09 (0.15), residues: 1150 loop : -0.71 (0.09), residues: 4097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP n 9 HIS 0.005 0.001 HIS l 311 PHE 0.024 0.001 PHE o 229 TYR 0.030 0.001 TYR P 23 ARG 0.011 0.000 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 690 time to evaluate : 8.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8136 (ttt90) REVERT: A 193 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8659 (ttp-110) REVERT: B 84 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9051 (tt) REVERT: C 53 ASP cc_start: 0.7900 (t0) cc_final: 0.7631 (t0) REVERT: E 144 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8162 (tm-30) REVERT: E 151 ARG cc_start: 0.8284 (ttp80) cc_final: 0.8041 (ttp80) REVERT: H 24 GLU cc_start: 0.8664 (pp20) cc_final: 0.8377 (OUTLIER) REVERT: H 25 ASN cc_start: 0.8974 (m-40) cc_final: 0.8711 (m-40) REVERT: H 87 ASN cc_start: 0.9244 (m110) cc_final: 0.9023 (m110) REVERT: L 74 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: P 74 ASN cc_start: 0.9408 (OUTLIER) cc_final: 0.9029 (p0) REVERT: R 19 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.9075 (ttt180) REVERT: S 33 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7380 (pp20) REVERT: V 66 GLU cc_start: 0.7208 (pp20) cc_final: 0.6985 (tm-30) REVERT: X 77 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7672 (mmm-85) REVERT: d 17 LYS cc_start: 0.8360 (ttmm) cc_final: 0.7854 (ttmt) REVERT: k 137 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7162 (t80) REVERT: m 95 TRP cc_start: 0.9594 (OUTLIER) cc_final: 0.7790 (t60) REVERT: m 158 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7919 (ptt-90) REVERT: n 137 ASP cc_start: 0.7991 (m-30) cc_final: 0.7680 (m-30) REVERT: s 22 SER cc_start: 0.9121 (m) cc_final: 0.8891 (t) REVERT: s 35 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9079 (tmmm) REVERT: s 38 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: a 589 MET cc_start: 0.8160 (pmm) cc_final: 0.7773 (ppp) REVERT: a 621 TRP cc_start: 0.6258 (m-10) cc_final: 0.5884 (m-10) REVERT: a 697 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7254 (pp) REVERT: a 699 MET cc_start: 0.3491 (mmm) cc_final: 0.2910 (mmm) REVERT: a 918 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8865 (p0) REVERT: e 67 MET cc_start: 0.8716 (tpp) cc_final: 0.8405 (tpp) REVERT: e 277 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.5626 (ppp) REVERT: e 809 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8132 (ppp) REVERT: e 893 MET cc_start: -0.0449 (tmt) cc_final: -0.1939 (tmt) REVERT: e 963 MET cc_start: 0.2604 (mpt) cc_final: -0.0089 (ptt) REVERT: e 1033 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8081 (mttt) REVERT: e 1060 MET cc_start: 0.0163 (OUTLIER) cc_final: -0.0211 (mpt) REVERT: e 1068 MET cc_start: 0.0152 (mtt) cc_final: -0.0439 (mtt) REVERT: e 1162 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5507 (tmt) REVERT: e 1464 ILE cc_start: 0.3537 (OUTLIER) cc_final: 0.2890 (pp) REVERT: g 6 GLN cc_start: 0.8022 (mt0) cc_final: 0.7740 (mt0) REVERT: g 67 ARG cc_start: 0.9184 (ptm-80) cc_final: 0.8804 (ptm-80) REVERT: 0 7 LYS cc_start: 0.9535 (tttt) cc_final: 0.9111 (tmmt) REVERT: 0 10 GLU cc_start: 0.9634 (pp20) cc_final: 0.9393 (pp20) REVERT: 0 26 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8663 (t80) REVERT: 0 38 MET cc_start: 0.9549 (mmm) cc_final: 0.8719 (tmm) REVERT: 0 40 GLU cc_start: 0.9059 (pt0) cc_final: 0.8736 (pp20) REVERT: 0 44 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8982 (mm-30) REVERT: 0 52 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8309 (tm) REVERT: 0 53 MET cc_start: 0.7129 (mmm) cc_final: 0.6913 (mmm) REVERT: 0 60 ARG cc_start: 0.9010 (mtt180) cc_final: 0.8806 (mtt180) REVERT: 0 191 TYR cc_start: 0.8881 (t80) cc_final: 0.8398 (t80) REVERT: w 33 GLU cc_start: -0.0833 (OUTLIER) cc_final: -0.2719 (mt-10) REVERT: w 210 MET cc_start: 0.0841 (mpm) cc_final: 0.0368 (mpm) outliers start: 192 outliers final: 145 residues processed: 821 average time/residue: 2.0769 time to fit residues: 2504.1649 Evaluate side-chains 841 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 673 time to evaluate : 8.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 74 ASN Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 20 MET Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 177 ASP Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 125 VAL Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 38 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 918 ASP Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 320 LEU Chi-restraints excluded: chain e residue 713 LEU Chi-restraints excluded: chain e residue 809 MET Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1060 MET Chi-restraints excluded: chain e residue 1091 ASP Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain g residue 5 THR Chi-restraints excluded: chain g residue 62 MET Chi-restraints excluded: chain g residue 225 GLN Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain w residue 33 GLU Chi-restraints excluded: chain w residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1112 optimal weight: 50.0000 chunk 1171 optimal weight: 50.0000 chunk 1069 optimal weight: 50.0000 chunk 1139 optimal weight: 7.9990 chunk 686 optimal weight: 8.9990 chunk 496 optimal weight: 10.0000 chunk 895 optimal weight: 6.9990 chunk 349 optimal weight: 30.0000 chunk 1029 optimal weight: 0.7980 chunk 1077 optimal weight: 3.9990 chunk 1135 optimal weight: 20.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN S 106 ASN T 108 GLN X 10 GLN Y 32 ASN ** b 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN p 59 GLN r 175 ASN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN t 114 GLN t 160 GLN t 162 ASN ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 995 GLN ** e1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 170 GLN ** 0 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 160769 Z= 0.381 Angle : 0.621 13.789 234972 Z= 0.327 Chirality : 0.040 0.342 29357 Planarity : 0.005 0.097 16287 Dihedral : 22.503 179.992 66681 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 2.55 % Allowed : 16.12 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.07 % 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: 0.58 (0.09), residues: 9175 helix: 1.68 (0.08), residues: 3940 sheet: -0.11 (0.15), residues: 1161 loop : -0.74 (0.09), residues: 4074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP n 9 HIS 0.006 0.001 HIS j 38 PHE 0.027 0.001 PHE o 229 TYR 0.035 0.002 TYR P 23 ARG 0.012 0.000 ARG J 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 680 time to evaluate : 7.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8155 (ttt90) REVERT: A 193 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7842 (ttm-80) REVERT: B 84 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9073 (tt) REVERT: C 53 ASP cc_start: 0.7927 (t0) cc_final: 0.7658 (t0) REVERT: E 144 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8199 (tm-30) REVERT: H 24 GLU cc_start: 0.8670 (pp20) cc_final: 0.8411 (OUTLIER) REVERT: H 25 ASN cc_start: 0.8990 (m-40) cc_final: 0.8731 (m-40) REVERT: P 74 ASN cc_start: 0.9408 (OUTLIER) cc_final: 0.9026 (p0) REVERT: R 19 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.9089 (ttt-90) REVERT: S 33 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: X 77 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7700 (mmm-85) REVERT: k 137 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7201 (t80) REVERT: m 95 TRP cc_start: 0.9621 (OUTLIER) cc_final: 0.7735 (t60) REVERT: m 158 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7928 (ptt-90) REVERT: s 35 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9103 (tmmm) REVERT: s 38 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8168 (tp30) REVERT: a 589 MET cc_start: 0.8145 (pmm) cc_final: 0.7759 (ppp) REVERT: a 621 TRP cc_start: 0.6251 (m-10) cc_final: 0.5879 (m-10) REVERT: a 697 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7461 (pp) REVERT: a 918 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8871 (p0) REVERT: a 996 MET cc_start: 0.8407 (pp-130) cc_final: 0.8085 (pp-130) REVERT: e 67 MET cc_start: 0.8721 (tpp) cc_final: 0.8412 (tpp) REVERT: e 277 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5449 (pmt) REVERT: e 809 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8125 (ppp) REVERT: e 893 MET cc_start: -0.0376 (tmt) cc_final: -0.1886 (tmt) REVERT: e 963 MET cc_start: 0.2625 (mpt) cc_final: -0.0066 (ptt) REVERT: e 1033 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7971 (mttp) REVERT: e 1060 MET cc_start: 0.0156 (OUTLIER) cc_final: -0.0209 (mpt) REVERT: e 1068 MET cc_start: 0.0063 (mtt) cc_final: -0.0519 (mtt) REVERT: e 1162 MET cc_start: 0.6043 (OUTLIER) cc_final: 0.5515 (tmt) REVERT: e 1464 ILE cc_start: 0.3593 (OUTLIER) cc_final: 0.2953 (pp) REVERT: g 1 MET cc_start: 0.5452 (ttt) cc_final: 0.3949 (tpt) REVERT: g 6 GLN cc_start: 0.8061 (mt0) cc_final: 0.7784 (mt0) REVERT: g 67 ARG cc_start: 0.9214 (ptm-80) cc_final: 0.8843 (ptm-80) REVERT: 0 7 LYS cc_start: 0.9548 (tttt) cc_final: 0.9162 (tmmt) REVERT: 0 8 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8633 (mttm) REVERT: 0 10 GLU cc_start: 0.9667 (pp20) cc_final: 0.9417 (pp20) REVERT: 0 14 LYS cc_start: 0.9133 (tmmm) cc_final: 0.8903 (tptp) REVERT: 0 22 TYR cc_start: 0.8522 (m-80) cc_final: 0.8316 (m-80) REVERT: 0 26 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8645 (t80) REVERT: 0 38 MET cc_start: 0.9539 (mmm) cc_final: 0.8739 (tmm) REVERT: 0 40 GLU cc_start: 0.9053 (pt0) cc_final: 0.8727 (pp20) REVERT: 0 44 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8976 (mm-30) REVERT: 0 52 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8123 (tp) REVERT: 0 55 LYS cc_start: 0.8947 (mtmt) cc_final: 0.8655 (mtmt) REVERT: 0 60 ARG cc_start: 0.9019 (mtt180) cc_final: 0.8811 (mtt180) REVERT: 0 191 TYR cc_start: 0.8876 (t80) cc_final: 0.8450 (t80) REVERT: w 33 GLU cc_start: -0.0488 (OUTLIER) cc_final: -0.2766 (mt-10) REVERT: w 210 MET cc_start: 0.0850 (mpm) cc_final: 0.0395 (mpm) outliers start: 190 outliers final: 143 residues processed: 808 average time/residue: 2.1740 time to fit residues: 2573.9340 Evaluate side-chains 831 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 666 time to evaluate : 8.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 74 ASN Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 20 MET Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 177 ASP Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 323 VAL Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 125 VAL Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 38 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 918 ASP Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 320 LEU Chi-restraints excluded: chain e residue 713 LEU Chi-restraints excluded: chain e residue 809 MET Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1060 MET Chi-restraints excluded: chain e residue 1091 ASP Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain g residue 5 THR Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 88 PHE Chi-restraints excluded: chain w residue 33 GLU Chi-restraints excluded: chain w residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 748 optimal weight: 3.9990 chunk 1205 optimal weight: 9.9990 chunk 735 optimal weight: 10.0000 chunk 571 optimal weight: 10.0000 chunk 837 optimal weight: 0.9990 chunk 1264 optimal weight: 6.9990 chunk 1163 optimal weight: 50.0000 chunk 1006 optimal weight: 20.0000 chunk 104 optimal weight: 0.0980 chunk 777 optimal weight: 6.9990 chunk 617 optimal weight: 10.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN H 52 ASN M 123 GLN S 106 ASN T 108 GLN X 10 GLN Y 32 ASN ** b 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN p 59 GLN q 157 ASN r 175 ASN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN t 162 ASN e 233 ASN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 170 GLN g 225 GLN ** 0 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 160769 Z= 0.268 Angle : 0.591 13.688 234972 Z= 0.311 Chirality : 0.038 0.339 29357 Planarity : 0.004 0.095 16287 Dihedral : 22.522 179.557 66679 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 2.39 % Allowed : 16.43 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.09), residues: 9175 helix: 1.72 (0.08), residues: 3932 sheet: -0.09 (0.15), residues: 1161 loop : -0.71 (0.09), residues: 4082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP n 9 HIS 0.005 0.001 HIS e1273 PHE 0.026 0.001 PHE 0 88 TYR 0.034 0.001 TYR P 23 ARG 0.012 0.000 ARG J 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 691 time to evaluate : 8.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8134 (ttt90) REVERT: A 193 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8650 (ttp-110) REVERT: B 84 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9038 (tt) REVERT: C 53 ASP cc_start: 0.7911 (t0) cc_final: 0.7644 (t0) REVERT: H 24 GLU cc_start: 0.8667 (pp20) cc_final: 0.8420 (OUTLIER) REVERT: H 25 ASN cc_start: 0.8973 (m-40) cc_final: 0.8730 (m-40) REVERT: L 74 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: P 74 ASN cc_start: 0.9398 (OUTLIER) cc_final: 0.9013 (p0) REVERT: R 19 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.9077 (ttt180) REVERT: S 33 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: X 16 ARG cc_start: 0.8498 (ptp90) cc_final: 0.8246 (mtt-85) REVERT: X 77 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7662 (mmm-85) REVERT: d 17 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7819 (ttmt) REVERT: k 137 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7136 (t80) REVERT: m 95 TRP cc_start: 0.9584 (OUTLIER) cc_final: 0.7772 (t60) REVERT: m 158 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7893 (ptt-90) REVERT: s 38 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8176 (tp30) REVERT: a 589 MET cc_start: 0.8107 (pmm) cc_final: 0.7594 (pp-130) REVERT: a 697 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7387 (pp) REVERT: a 699 MET cc_start: 0.3366 (mmm) cc_final: 0.2572 (mmm) REVERT: a 918 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8933 (p0) REVERT: a 996 MET cc_start: 0.8430 (pp-130) cc_final: 0.8138 (pp-130) REVERT: e 67 MET cc_start: 0.8715 (tpp) cc_final: 0.8432 (tpp) REVERT: e 223 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7799 (t80) REVERT: e 809 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8114 (ppp) REVERT: e 893 MET cc_start: -0.0413 (tmt) cc_final: -0.1973 (tmt) REVERT: e 963 MET cc_start: 0.2685 (mpt) cc_final: -0.0043 (ptt) REVERT: e 1033 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7963 (mttp) REVERT: e 1060 MET cc_start: 0.0070 (OUTLIER) cc_final: -0.0307 (mpt) REVERT: e 1068 MET cc_start: -0.0108 (mtt) cc_final: -0.0667 (mtt) REVERT: e 1162 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5436 (tmt) REVERT: e 1464 ILE cc_start: 0.3580 (OUTLIER) cc_final: 0.2939 (pp) REVERT: g 1 MET cc_start: 0.5174 (ttt) cc_final: 0.4030 (tpt) REVERT: g 6 GLN cc_start: 0.7975 (mt0) cc_final: 0.7707 (mt0) REVERT: g 67 ARG cc_start: 0.9194 (ptm-80) cc_final: 0.8814 (ptm-80) REVERT: 0 7 LYS cc_start: 0.9546 (tttt) cc_final: 0.9153 (tmmt) REVERT: 0 8 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8504 (mttm) REVERT: 0 10 GLU cc_start: 0.9672 (pp20) cc_final: 0.9416 (pp20) REVERT: 0 16 ARG cc_start: 0.9386 (ptm-80) cc_final: 0.9174 (ptm-80) REVERT: 0 26 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8675 (t80) REVERT: 0 38 MET cc_start: 0.9557 (mmm) cc_final: 0.8696 (tmm) REVERT: 0 40 GLU cc_start: 0.9061 (pt0) cc_final: 0.8697 (pp20) REVERT: 0 44 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8954 (mm-30) REVERT: 0 52 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8097 (tm) REVERT: 0 191 TYR cc_start: 0.8845 (t80) cc_final: 0.8412 (t80) REVERT: w 33 GLU cc_start: -0.0402 (OUTLIER) cc_final: -0.2974 (mt-10) REVERT: w 210 MET cc_start: 0.0877 (mpm) cc_final: 0.0422 (mpm) outliers start: 178 outliers final: 138 residues processed: 813 average time/residue: 2.1282 time to fit residues: 2547.9987 Evaluate side-chains 836 residues out of total 7993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 676 time to evaluate : 8.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 74 ASN Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 20 MET Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 177 ASP Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 125 VAL Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 38 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 918 ASP Chi-restraints excluded: chain e residue 158 CYS Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 320 LEU Chi-restraints excluded: chain e residue 713 LEU Chi-restraints excluded: chain e residue 809 MET Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1060 MET Chi-restraints excluded: chain e residue 1091 ASP Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1464 ILE Chi-restraints excluded: chain g residue 5 THR Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain w residue 33 GLU Chi-restraints excluded: chain w residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 799 optimal weight: 5.9990 chunk 1072 optimal weight: 50.0000 chunk 308 optimal weight: 6.9990 chunk 928 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 279 optimal weight: 5.9990 chunk 1008 optimal weight: 50.0000 chunk 421 optimal weight: 10.0000 chunk 1035 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN J 58 HIS T 108 GLN U 34 GLN Y 32 ASN ** b 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN p 59 GLN q 157 ASN r 175 ASN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN t 114 GLN t 160 GLN t 162 ASN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 170 GLN g 225 GLN ** 0 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.070568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.042316 restraints weight = 522198.328| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 1.94 r_work: 0.2557 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2445 r_free = 0.2445 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 160769 Z= 0.277 Angle : 0.591 13.517 234972 Z= 0.312 Chirality : 0.038 0.323 29357 Planarity : 0.004 0.095 16287 Dihedral : 22.500 179.693 66679 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 2.34 % Allowed : 16.59 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: 0.62 (0.09), residues: 9175 helix: 1.72 (0.08), residues: 3921 sheet: -0.11 (0.15), residues: 1171 loop : -0.70 (0.09), residues: 4083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP n 9 HIS 0.005 0.001 HIS e 111 PHE 0.055 0.001 PHE 0 88 TYR 0.032 0.001 TYR P 23 ARG 0.009 0.000 ARG g 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47625.35 seconds wall clock time: 829 minutes 53.76 seconds (49793.76 seconds total)