Starting phenix.real_space_refine on Mon Sep 30 11:57:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6n_0691/09_2024/6j6n_0691.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6n_0691/09_2024/6j6n_0691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6n_0691/09_2024/6j6n_0691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6n_0691/09_2024/6j6n_0691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6n_0691/09_2024/6j6n_0691.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6n_0691/09_2024/6j6n_0691.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 553 5.49 5 Mg 6 5.21 5 S 241 5.16 5 C 47913 2.51 5 N 13797 2.21 5 O 16421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 78937 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 15793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1913, 15793 Classifications: {'peptide': 1913} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 99, 'TRANS': 1811} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 7348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 920, 7348 Classifications: {'peptide': 920} Link IDs: {'PTRANS': 51, 'TRANS': 868} Chain breaks: 2 Chain: "J" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 190 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "O" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2810 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 343} Chain: "P" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1608 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2301 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2089 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1291 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "Z" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3651 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 7, 'TRANS': 439} Chain breaks: 1 Chain: "c" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 2978 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 8 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 621 Unresolved non-hydrogen angles: 800 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 13, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 367 Chain: "d" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 3881 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 11, 'TRANS': 554} Chain breaks: 15 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1000 Unresolved non-hydrogen angles: 1272 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 3, 'TYR:plan': 13, 'ASN:plan1': 6, 'TRP:plan': 6, 'ASP:plan': 19, 'PHE:plan': 13, 'GLU:plan': 35, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 592 Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 822 Classifications: {'peptide': 102} Link IDs: {'TRANS': 101} Chain breaks: 1 Chain: "n" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1894 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 281} Chain breaks: 9 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 10, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 338 Chain: "H" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 629 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "B" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1206 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 7, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna2p': 21, 'rna3p': 35} Chain breaks: 1 Chain: "D" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 3795 Classifications: {'RNA': 179} Modifications used: {'5*END': 1, 'rna2p_pur': 18, 'rna2p_pyr': 12, 'rna3p_pur': 70, 'rna3p_pyr': 79} Link IDs: {'rna2p': 30, 'rna3p': 148} Chain breaks: 1 Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2192 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 13, 'rna3p_pur': 46, 'rna3p_pyr': 35} Link IDs: {'rna2p': 22, 'rna3p': 80} Chain: "L" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 4325 Classifications: {'RNA': 205} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 19, 'rna3p_pur': 82, 'rna3p_pyr': 95} Link IDs: {'rna2p': 28, 'rna3p': 176} Chain breaks: 10 Chain: "v" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 4625 Classifications: {'peptide': 722} Incomplete info: {'truncation_to_alanine': 368} Link IDs: {'PTRANS': 22, 'TRANS': 699} Chain breaks: 27 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1437 Unresolved non-hydrogen angles: 1831 Unresolved non-hydrogen dihedrals: 1236 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 5, 'TYR:plan': 18, 'ASN:plan1': 15, 'TRP:plan': 11, 'ASP:plan': 24, 'PHE:plan': 22, 'GLU:plan': 39, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 852 Chain: "a" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 416 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 1, 'PHE:plan': 8, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 145 Chain: "b" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 841 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 561 Unresolved non-hydrogen angles: 718 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 15, 'TYR:plan': 4, 'ASN:plan1': 14, 'HIS:plan': 7, 'PHE:plan': 5, 'GLU:plan': 8, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 305 Chain: "t" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 926 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 258 Chain: "u" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 552 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "h" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "g" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 785 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "k" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 809 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "e" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 785 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "s" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 749 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "i" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 541 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "w" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "x" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 552 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "y" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 616 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "z" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "r" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 823 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "p" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 843 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "q" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 850 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "o" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 830 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" 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} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27834 SG CYS Q 13 66.433 141.825 113.876 1.00 38.65 S ATOM 27858 SG CYS Q 16 65.306 145.398 114.840 1.00 34.76 S ATOM 28292 SG CYS Q 71 68.535 143.811 116.135 1.00 28.88 S ATOM 28313 SG CYS Q 74 65.211 142.708 117.293 1.00 31.72 S ATOM 27992 SG CYS Q 34 78.337 146.371 122.863 1.00 27.70 S ATOM 28015 SG CYS Q 37 81.985 146.308 123.123 1.00 25.14 S ATOM 28214 SG CYS Q 61 80.501 145.955 119.739 1.00 30.93 S ATOM 28238 SG CYS Q 64 80.213 143.139 122.052 1.00 32.29 S ATOM 30632 SG CYS R 73 53.856 159.836 133.095 1.00 29.81 S ATOM 30694 SG CYS R 81 52.297 163.066 133.998 1.00 26.72 S ATOM 30734 SG CYS R 87 52.903 162.278 130.372 1.00 35.29 S ATOM 33594 SG CYS T 104 54.856 179.962 115.039 1.00 34.38 S ATOM 33600 SG CYS T 105 58.275 181.539 115.970 1.00 32.61 S ATOM 33625 SG CYS T 108 58.151 178.568 113.519 1.00 27.14 S ATOM 33939 SG CYS T 148 56.867 178.156 116.836 1.00 28.55 S ATOM 33594 SG CYS T 104 54.856 179.962 115.039 1.00 34.38 S ATOM 33728 SG CYS T 122 55.019 176.479 113.129 1.00 37.55 S ATOM 33949 SG CYS T 150 51.774 177.882 114.381 1.00 32.53 S ATOM 33970 SG CYS T 153 53.392 179.251 111.603 1.00 16.09 S ATOM 33625 SG CYS T 108 58.151 178.568 113.519 1.00 27.14 S ATOM 33714 SG CYS T 120 58.096 175.513 111.715 1.00 35.62 S ATOM 33728 SG CYS T 122 55.019 176.479 113.129 1.00 37.55 S ATOM 33916 SG CYS T 145 57.677 175.044 115.392 1.00 29.87 S Time building chain proxies: 33.04, per 1000 atoms: 0.42 Number of scatterers: 78937 At special positions: 0 Unit cell: (246.05, 304.57, 305.9, 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 6 29.99 S 241 16.00 P 553 15.00 Mg 6 11.99 O 16421 8.00 N 13797 7.00 C 47913 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 - 3.00 Amino acid : True - 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: 14.60 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 400 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 74 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 71 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 13 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 16 " pdb=" ZN Q 401 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 37 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 61 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 64 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 34 " pdb=" ZN R 400 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 81 " pdb="ZN ZN R 400 " - pdb=" NE2 HIS R 91 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 73 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 87 " pdb=" ZN T1000 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 148 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 104 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 105 " pdb=" ZN T1001 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 153 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 150 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 104 " pdb=" ZN T1002 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 120 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 145 " Number of angles added : 33 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17190 Finding SS restraints... Secondary structure from input PDB file: 323 helices and 55 sheets defined 49.5% alpha, 13.0% beta 138 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 22.95 Creating SS restraints... Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.831A pdb=" N LEU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.675A pdb=" N LEU A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 209 through 231 removed outlier: 3.692A pdb=" N ARG A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 304 through 315 removed outlier: 3.592A pdb=" N MET A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.609A pdb=" N TYR A 327 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 329 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.528A pdb=" N ASN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 removed outlier: 4.023A pdb=" N HIS A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.750A pdb=" N ASN A 487 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.901A pdb=" N PHE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 535 removed outlier: 3.982A pdb=" N SER A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 553 removed outlier: 3.503A pdb=" N SER A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 553 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 586 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 616 through 641 removed outlier: 3.706A pdb=" N THR A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 659 removed outlier: 3.586A pdb=" N ASN A 658 " --> pdb=" O HIS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 673 through 692 removed outlier: 3.544A pdb=" N LYS A 684 " --> pdb=" O CYS A 680 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 689 " --> pdb=" O HIS A 685 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 718 removed outlier: 3.540A pdb=" N TRP A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 736 Processing helix chain 'A' and resid 749 through 768 removed outlier: 3.538A pdb=" N VAL A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 795 removed outlier: 4.213A pdb=" N ARG A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 837 Processing helix chain 'A' and resid 841 through 871 removed outlier: 3.520A pdb=" N VAL A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 893 Processing helix chain 'A' and resid 907 through 921 Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 985 through 1006 removed outlier: 3.546A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1035 removed outlier: 3.758A pdb=" N LEU A1035 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1061 removed outlier: 3.873A pdb=" N ILE A1061 " --> pdb=" O ALA A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1074 removed outlier: 3.563A pdb=" N LEU A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1087 removed outlier: 3.706A pdb=" N ASN A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1136 removed outlier: 3.634A pdb=" N ILE A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1124 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1125 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLU A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A1130 " --> pdb=" O LEU A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1155 removed outlier: 3.723A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1190 removed outlier: 3.685A pdb=" N TYR A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1201 removed outlier: 3.987A pdb=" N GLY A1200 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A1201 " --> pdb=" O ASN A1197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1196 through 1201' Processing helix chain 'A' and resid 1216 through 1234 removed outlier: 3.690A pdb=" N SER A1232 " --> pdb=" O TRP A1228 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A1233 " --> pdb=" O GLU A1229 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A1234 " --> pdb=" O ILE A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1323 Processing helix chain 'A' and resid 1327 through 1346 removed outlier: 3.597A pdb=" N VAL A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A1345 " --> pdb=" O SER A1341 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1351 removed outlier: 3.626A pdb=" N ILE A1350 " --> pdb=" O ARG A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1375 removed outlier: 3.803A pdb=" N LEU A1357 " --> pdb=" O THR A1353 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1375 " --> pdb=" O VAL A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1390 removed outlier: 3.993A pdb=" N PHE A1388 " --> pdb=" O PRO A1384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1471 removed outlier: 3.724A pdb=" N ARG A1456 " --> pdb=" O LEU A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1484 removed outlier: 4.004A pdb=" N GLY A1482 " --> pdb=" O GLU A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1496 Processing helix chain 'A' and resid 1498 through 1503 Processing helix chain 'A' and resid 1507 through 1514 removed outlier: 3.525A pdb=" N ARG A1511 " --> pdb=" O GLY A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1519 removed outlier: 3.756A pdb=" N SER A1518 " --> pdb=" O PHE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1534 Processing helix chain 'A' and resid 1539 through 1550 removed outlier: 3.998A pdb=" N ARG A1543 " --> pdb=" O LEU A1539 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1558 Processing helix chain 'A' and resid 1561 through 1566 removed outlier: 4.021A pdb=" N GLY A1566 " --> pdb=" O PHE A1562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1610 Processing helix chain 'A' and resid 1610 through 1615 Processing helix chain 'A' and resid 1638 through 1649 removed outlier: 3.565A pdb=" N ILE A1643 " --> pdb=" O PRO A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1652 through 1670 Processing helix chain 'A' and resid 1689 through 1693 removed outlier: 3.528A pdb=" N TYR A1692 " --> pdb=" O ARG A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1762 Processing helix chain 'A' and resid 1794 through 1809 removed outlier: 3.700A pdb=" N ASN A1800 " --> pdb=" O PRO A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1824 Processing helix chain 'A' and resid 1840 through 1844 removed outlier: 3.717A pdb=" N LEU A1843 " --> pdb=" O TYR A1840 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A1844 " --> pdb=" O ALA A1841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1840 through 1844' Processing helix chain 'A' and resid 1897 through 1901 removed outlier: 3.515A pdb=" N ALA A1900 " --> pdb=" O SER A1897 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A1901 " --> pdb=" O VAL A1898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1897 through 1901' Processing helix chain 'A' and resid 1904 through 1924 removed outlier: 3.943A pdb=" N LYS A1910 " --> pdb=" O SER A1906 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP A1911 " --> pdb=" O GLN A1907 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1924 " --> pdb=" O LEU A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1940 through 1948 Processing helix chain 'A' and resid 1966 through 1971 Processing helix chain 'A' and resid 1971 through 1980 Processing helix chain 'A' and resid 1992 through 1999 removed outlier: 4.066A pdb=" N LEU A1996 " --> pdb=" O TYR A1992 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A1997 " --> pdb=" O ASP A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2018 removed outlier: 3.523A pdb=" N ALA A2014 " --> pdb=" O LEU A2010 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A2016 " --> pdb=" O LEU A2012 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A2017 " --> pdb=" O ARG A2013 " (cutoff:3.500A) Processing helix chain 'A' and resid 2020 through 2027 Processing helix chain 'A' and resid 2045 through 2068 removed outlier: 3.614A pdb=" N LYS A2066 " --> pdb=" O GLU A2062 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A2067 " --> pdb=" O TYR A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2084 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 145 through 158 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 231 removed outlier: 3.635A pdb=" N THR C 225 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.793A pdb=" N LEU C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 removed outlier: 3.550A pdb=" N SER C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 340 through 349 removed outlier: 3.669A pdb=" N THR C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 348 " --> pdb=" O PHE C 344 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 377 Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 392 through 404 Processing helix chain 'C' and resid 410 through 415 removed outlier: 3.585A pdb=" N LEU C 413 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 414 " --> pdb=" O GLU C 411 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 415 " --> pdb=" O ALA C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 410 through 415' Processing helix chain 'C' and resid 416 through 429 Processing helix chain 'C' and resid 432 through 443 Processing helix chain 'C' and resid 444 through 457 removed outlier: 3.680A pdb=" N LEU C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASP C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 513 removed outlier: 3.589A pdb=" N GLN C 511 " --> pdb=" O SER C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 589 removed outlier: 3.717A pdb=" N MET C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 587 " --> pdb=" O LYS C 583 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 613 No H-bonds generated for 'chain 'C' and resid 611 through 613' Processing helix chain 'C' and resid 614 through 629 Processing helix chain 'C' and resid 648 through 662 Processing helix chain 'C' and resid 716 through 725 Processing helix chain 'C' and resid 743 through 754 Processing helix chain 'C' and resid 758 through 764 Processing helix chain 'C' and resid 778 through 784 removed outlier: 3.664A pdb=" N GLU C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 790 removed outlier: 3.502A pdb=" N LEU C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 804 removed outlier: 3.508A pdb=" N LYS C 804 " --> pdb=" O TYR C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 853 removed outlier: 3.618A pdb=" N SER C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) Proline residue: C 840 - end of helix removed outlier: 3.516A pdb=" N LYS C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 847 " --> pdb=" O LYS C 843 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 849 " --> pdb=" O ALA C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 883 removed outlier: 3.859A pdb=" N ARG C 883 " --> pdb=" O LEU C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 922 removed outlier: 3.680A pdb=" N ARG C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 920 " --> pdb=" O THR C 916 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 921 " --> pdb=" O ASP C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 960 No H-bonds generated for 'chain 'C' and resid 958 through 960' Processing helix chain 'C' and resid 961 through 974 removed outlier: 3.566A pdb=" N VAL C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1004 removed outlier: 3.569A pdb=" N GLN C1000 " --> pdb=" O GLU C 996 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN C1004 " --> pdb=" O GLN C1000 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 102 Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'P' and resid 59 through 85 removed outlier: 3.521A pdb=" N GLN P 64 " --> pdb=" O LYS P 60 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 186 removed outlier: 3.564A pdb=" N ARG P 185 " --> pdb=" O ALA P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 245 removed outlier: 3.651A pdb=" N MET P 202 " --> pdb=" O ASN P 198 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU P 224 " --> pdb=" O ARG P 220 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS P 226 " --> pdb=" O LYS P 222 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 18 removed outlier: 3.591A pdb=" N LEU Q 17 " --> pdb=" O CYS Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 69 Processing helix chain 'Q' and resid 83 through 96 removed outlier: 3.565A pdb=" N SER Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL Q 94 " --> pdb=" O LEU Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 115 removed outlier: 3.754A pdb=" N SER Q 114 " --> pdb=" O LYS Q 110 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 124 removed outlier: 4.300A pdb=" N GLN Q 124 " --> pdb=" O GLY Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 146 removed outlier: 3.621A pdb=" N ASN Q 134 " --> pdb=" O SER Q 130 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE Q 135 " --> pdb=" O GLU Q 131 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN Q 141 " --> pdb=" O ASP Q 137 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE Q 142 " --> pdb=" O LYS Q 138 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG Q 145 " --> pdb=" O ASN Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 188 removed outlier: 3.856A pdb=" N LYS Q 188 " --> pdb=" O SER Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 228 removed outlier: 3.593A pdb=" N ILE Q 219 " --> pdb=" O PRO Q 215 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR Q 220 " --> pdb=" O GLU Q 216 " (cutoff:3.500A) Processing helix chain 'Q' and resid 231 through 236 removed outlier: 4.287A pdb=" N GLY Q 235 " --> pdb=" O LYS Q 231 " (cutoff:3.500A) Processing helix chain 'Q' and resid 256 through 265 removed outlier: 3.840A pdb=" N GLU Q 260 " --> pdb=" O SER Q 256 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG Q 261 " --> pdb=" O GLU Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 305 through 325 removed outlier: 3.971A pdb=" N LYS Q 311 " --> pdb=" O ALA Q 307 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU Q 312 " --> pdb=" O GLU Q 308 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS Q 318 " --> pdb=" O LEU Q 314 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU Q 319 " --> pdb=" O SER Q 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 59 Processing helix chain 'R' and resid 62 through 68 removed outlier: 4.200A pdb=" N ASN R 66 " --> pdb=" O THR R 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP R 67 " --> pdb=" O ARG R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 78 Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'R' and resid 95 through 102 Processing helix chain 'R' and resid 141 through 146 Processing helix chain 'R' and resid 154 through 165 removed outlier: 3.546A pdb=" N SER R 165 " --> pdb=" O ARG R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 199 removed outlier: 3.617A pdb=" N ALA R 192 " --> pdb=" O TYR R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 215 removed outlier: 3.548A pdb=" N TRP R 212 " --> pdb=" O ASP R 209 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP R 213 " --> pdb=" O LYS R 210 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG R 215 " --> pdb=" O TRP R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 261 removed outlier: 4.187A pdb=" N ARG R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS R 252 " --> pdb=" O ASN R 248 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN R 255 " --> pdb=" O VAL R 251 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN R 256 " --> pdb=" O HIS R 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 19 removed outlier: 4.329A pdb=" N ALA S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA S 19 " --> pdb=" O ALA S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 31 removed outlier: 3.517A pdb=" N LEU S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 27 through 31' Processing helix chain 'S' and resid 163 through 173 removed outlier: 3.554A pdb=" N LYS S 172 " --> pdb=" O GLU S 168 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 17 removed outlier: 3.574A pdb=" N PHE T 16 " --> pdb=" O PRO T 13 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU T 17 " --> pdb=" O ASP T 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 13 through 17' Processing helix chain 'T' and resid 19 through 34 removed outlier: 3.550A pdb=" N GLN T 34 " --> pdb=" O LEU T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 68 removed outlier: 3.625A pdb=" N GLU T 47 " --> pdb=" O ALA T 43 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE T 52 " --> pdb=" O GLN T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 84 Processing helix chain 'T' and resid 88 through 97 removed outlier: 3.632A pdb=" N LYS T 97 " --> pdb=" O ALA T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 110 removed outlier: 4.156A pdb=" N ILE T 109 " --> pdb=" O CYS T 105 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 105 through 110' Processing helix chain 'T' and resid 120 through 124 Processing helix chain 'T' and resid 125 through 137 Processing helix chain 'Z' and resid 9 through 31 removed outlier: 3.556A pdb=" N SER Z 26 " --> pdb=" O ARG Z 22 " (cutoff:3.500A) Proline residue: Z 27 - end of helix Processing helix chain 'Z' and resid 36 through 47 removed outlier: 3.578A pdb=" N VAL Z 47 " --> pdb=" O ASP Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 66 removed outlier: 3.549A pdb=" N VAL Z 60 " --> pdb=" O ILE Z 56 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE Z 63 " --> pdb=" O ASN Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 87 removed outlier: 3.565A pdb=" N LEU Z 79 " --> pdb=" O ALA Z 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 109 removed outlier: 3.931A pdb=" N GLY Z 91 " --> pdb=" O ILE Z 87 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU Z 98 " --> pdb=" O LEU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 110 through 127 removed outlier: 3.634A pdb=" N GLY Z 115 " --> pdb=" O TYR Z 111 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN Z 116 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS Z 120 " --> pdb=" O ASN Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 4.009A pdb=" N ILE Z 135 " --> pdb=" O HIS Z 131 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE Z 138 " --> pdb=" O VAL Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 166 removed outlier: 4.068A pdb=" N ALA Z 153 " --> pdb=" O ARG Z 149 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE Z 157 " --> pdb=" O ALA Z 153 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP Z 160 " --> pdb=" O LYS Z 156 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS Z 161 " --> pdb=" O ILE Z 157 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Z 164 " --> pdb=" O TRP Z 160 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 184 removed outlier: 3.553A pdb=" N MET Z 172 " --> pdb=" O LYS Z 168 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU Z 181 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN Z 182 " --> pdb=" O ARG Z 178 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 203 removed outlier: 3.648A pdb=" N GLU Z 192 " --> pdb=" O SER Z 188 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER Z 193 " --> pdb=" O THR Z 189 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU Z 194 " --> pdb=" O LEU Z 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN Z 202 " --> pdb=" O PHE Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 237 through 241 Processing helix chain 'Z' and resid 285 through 301 Processing helix chain 'Z' and resid 304 through 315 removed outlier: 3.536A pdb=" N LEU Z 315 " --> pdb=" O LYS Z 311 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 335 removed outlier: 3.914A pdb=" N VAL Z 326 " --> pdb=" O LYS Z 322 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP Z 327 " --> pdb=" O LYS Z 323 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 352 removed outlier: 3.618A pdb=" N ARG Z 349 " --> pdb=" O ILE Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 354 through 371 removed outlier: 3.629A pdb=" N GLN Z 358 " --> pdb=" O HIS Z 354 " (cutoff:3.500A) Processing helix chain 'Z' and resid 372 through 376 Processing helix chain 'Z' and resid 377 through 394 removed outlier: 3.740A pdb=" N ARG Z 382 " --> pdb=" O THR Z 378 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE Z 383 " --> pdb=" O ASP Z 379 " (cutoff:3.500A) Processing helix chain 'Z' and resid 398 through 405 removed outlier: 3.723A pdb=" N ILE Z 404 " --> pdb=" O CYS Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 432 removed outlier: 3.521A pdb=" N ILE Z 418 " --> pdb=" O PRO Z 414 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU Z 426 " --> pdb=" O PHE Z 422 " (cutoff:3.500A) Processing helix chain 'Z' and resid 432 through 444 removed outlier: 4.201A pdb=" N LYS Z 444 " --> pdb=" O LEU Z 440 " (cutoff:3.500A) Processing helix chain 'Z' and resid 454 through 469 removed outlier: 3.532A pdb=" N ILE Z 458 " --> pdb=" O ASP Z 454 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA Z 467 " --> pdb=" O ASN Z 463 " (cutoff:3.500A) Processing helix chain 'Z' and resid 474 through 485 removed outlier: 3.540A pdb=" N ARG Z 478 " --> pdb=" O THR Z 474 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER Z 479 " --> pdb=" O GLU Z 475 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE Z 483 " --> pdb=" O SER Z 479 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE Z 484 " --> pdb=" O ARG Z 480 " (cutoff:3.500A) Processing helix chain 'c' and resid 14 through 29 Processing helix chain 'c' and resid 32 through 40 removed outlier: 3.934A pdb=" N LEU c 39 " --> pdb=" O LYS c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 66 through 80 removed outlier: 3.539A pdb=" N ARG c 78 " --> pdb=" O LEU c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 92 Processing helix chain 'c' and resid 94 through 107 Processing helix chain 'c' and resid 147 through 160 removed outlier: 3.643A pdb=" N LEU c 160 " --> pdb=" O ARG c 156 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 194 removed outlier: 3.540A pdb=" N THR c 168 " --> pdb=" O GLY c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 231 through 251 removed outlier: 3.693A pdb=" N ARG c 235 " --> pdb=" O SER c 231 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN c 249 " --> pdb=" O GLU c 245 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG c 250 " --> pdb=" O ARG c 246 " (cutoff:3.500A) Processing helix chain 'c' and resid 337 through 356 Processing helix chain 'c' and resid 358 through 364 removed outlier: 3.686A pdb=" N ARG c 363 " --> pdb=" O LYS c 359 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS c 364 " --> pdb=" O SER c 360 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 380 removed outlier: 3.576A pdb=" N LYS c 377 " --> pdb=" O LEU c 373 " (cutoff:3.500A) Processing helix chain 'c' and resid 387 through 401 removed outlier: 3.539A pdb=" N GLU c 391 " --> pdb=" O ASP c 387 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU c 401 " --> pdb=" O GLU c 397 " (cutoff:3.500A) Processing helix chain 'c' and resid 425 through 438 Proline residue: c 432 - end of helix removed outlier: 3.543A pdb=" N THR c 437 " --> pdb=" O LEU c 433 " (cutoff:3.500A) Processing helix chain 'c' and resid 445 through 469 removed outlier: 3.554A pdb=" N LYS c 465 " --> pdb=" O ASN c 461 " (cutoff:3.500A) Proline residue: c 467 - end of helix Processing helix chain 'c' and resid 483 through 511 removed outlier: 3.687A pdb=" N HIS c 487 " --> pdb=" O SER c 483 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE c 488 " --> pdb=" O ARG c 484 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR c 489 " --> pdb=" O MET c 485 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE c 499 " --> pdb=" O MET c 495 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS c 500 " --> pdb=" O LYS c 496 " (cutoff:3.500A) Proline residue: c 504 - end of helix Processing helix chain 'c' and resid 512 through 582 removed outlier: 3.834A pdb=" N LYS c 516 " --> pdb=" O SER c 512 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU c 523 " --> pdb=" O SER c 519 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU c 527 " --> pdb=" O LEU c 523 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN c 528 " --> pdb=" O GLN c 524 " (cutoff:3.500A) Proline residue: c 532 - end of helix removed outlier: 3.706A pdb=" N GLN c 536 " --> pdb=" O PRO c 532 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU c 549 " --> pdb=" O CYS c 545 " (cutoff:3.500A) Proline residue: c 550 - end of helix removed outlier: 3.822A pdb=" N ILE c 553 " --> pdb=" O LEU c 549 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN c 556 " --> pdb=" O LEU c 552 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG c 557 " --> pdb=" O ILE c 553 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER c 572 " --> pdb=" O GLN c 568 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG c 577 " --> pdb=" O LEU c 573 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS c 578 " --> pdb=" O GLU c 574 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG c 579 " --> pdb=" O GLY c 575 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU c 580 " --> pdb=" O ARG c 576 " (cutoff:3.500A) Processing helix chain 'c' and resid 582 through 587 removed outlier: 3.642A pdb=" N SER c 586 " --> pdb=" O ALA c 582 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER c 587 " --> pdb=" O MET c 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 582 through 587' Processing helix chain 'd' and resid 39 through 61 removed outlier: 3.540A pdb=" N ARG d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 78 removed outlier: 3.559A pdb=" N ILE d 76 " --> pdb=" O ALA d 72 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 95 removed outlier: 3.609A pdb=" N SER d 86 " --> pdb=" O ARG d 82 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE d 88 " --> pdb=" O ALA d 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL d 94 " --> pdb=" O ARG d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 112 removed outlier: 3.710A pdb=" N VAL d 112 " --> pdb=" O ALA d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 129 Processing helix chain 'd' and resid 132 through 146 removed outlier: 3.686A pdb=" N TRP d 136 " --> pdb=" O VAL d 132 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR d 139 " --> pdb=" O LEU d 135 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL d 142 " --> pdb=" O LYS d 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 160 removed outlier: 3.584A pdb=" N VAL d 152 " --> pdb=" O ASN d 148 " (cutoff:3.500A) Processing helix chain 'd' and resid 161 through 163 No H-bonds generated for 'chain 'd' and resid 161 through 163' Processing helix chain 'd' and resid 165 through 180 removed outlier: 3.826A pdb=" N TRP d 169 " --> pdb=" O GLY d 165 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 193 removed outlier: 3.507A pdb=" N GLU d 187 " --> pdb=" O ASN d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 213 removed outlier: 3.657A pdb=" N HIS d 212 " --> pdb=" O PHE d 208 " (cutoff:3.500A) Processing helix chain 'd' and resid 214 through 232 removed outlier: 3.825A pdb=" N SER d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 233 through 236 Processing helix chain 'd' and resid 239 through 257 removed outlier: 3.746A pdb=" N LYS d 245 " --> pdb=" O MET d 241 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU d 246 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP d 253 " --> pdb=" O SER d 249 " (cutoff:3.500A) Processing helix chain 'd' and resid 259 through 274 removed outlier: 4.005A pdb=" N TYR d 267 " --> pdb=" O SER d 263 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN d 268 " --> pdb=" O SER d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 277 through 283 removed outlier: 3.823A pdb=" N LYS d 281 " --> pdb=" O ASN d 277 " (cutoff:3.500A) Processing helix chain 'd' and resid 284 through 292 removed outlier: 3.945A pdb=" N GLU d 288 " --> pdb=" O LEU d 284 " (cutoff:3.500A) Processing helix chain 'd' and resid 293 through 316 removed outlier: 3.525A pdb=" N SER d 302 " --> pdb=" O GLU d 298 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR d 303 " --> pdb=" O GLU d 299 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS d 304 " --> pdb=" O THR d 300 " (cutoff:3.500A) Processing helix chain 'd' and resid 319 through 334 removed outlier: 3.553A pdb=" N TRP d 323 " --> pdb=" O ASP d 319 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU d 325 " --> pdb=" O ASP d 321 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP d 328 " --> pdb=" O TRP d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 336 through 350 removed outlier: 3.626A pdb=" N GLN d 340 " --> pdb=" O LYS d 336 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU d 343 " --> pdb=" O MET d 339 " (cutoff:3.500A) Processing helix chain 'd' and resid 353 through 370 removed outlier: 3.980A pdb=" N VAL d 358 " --> pdb=" O LEU d 354 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN d 359 " --> pdb=" O SER d 355 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP d 360 " --> pdb=" O LYS d 356 " (cutoff:3.500A) Processing helix chain 'd' and resid 375 through 383 Processing helix chain 'd' and resid 384 through 386 No H-bonds generated for 'chain 'd' and resid 384 through 386' Processing helix chain 'd' and resid 389 through 396 Processing helix chain 'd' and resid 406 through 418 removed outlier: 3.631A pdb=" N LYS d 412 " --> pdb=" O LEU d 408 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE d 413 " --> pdb=" O MET d 409 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS d 417 " --> pdb=" O PHE d 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 424 through 439 removed outlier: 3.518A pdb=" N LEU d 433 " --> pdb=" O LYS d 429 " (cutoff:3.500A) Proline residue: d 435 - end of helix Processing helix chain 'd' and resid 446 through 460 removed outlier: 3.874A pdb=" N GLU d 452 " --> pdb=" O VAL d 448 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE d 453 " --> pdb=" O LYS d 449 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS d 458 " --> pdb=" O ASP d 454 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE d 459 " --> pdb=" O ARG d 455 " (cutoff:3.500A) Processing helix chain 'd' and resid 463 through 475 Proline residue: d 468 - end of helix Processing helix chain 'd' and resid 481 through 494 removed outlier: 3.818A pdb=" N GLY d 485 " --> pdb=" O GLU d 481 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG d 489 " --> pdb=" O GLY d 485 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE d 493 " --> pdb=" O ARG d 489 " (cutoff:3.500A) Processing helix chain 'd' and resid 498 through 512 removed outlier: 4.056A pdb=" N ASP d 503 " --> pdb=" O ASP d 499 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE d 504 " --> pdb=" O GLU d 500 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL d 512 " --> pdb=" O GLU d 508 " (cutoff:3.500A) Processing helix chain 'd' and resid 515 through 523 Processing helix chain 'd' and resid 532 through 548 removed outlier: 4.016A pdb=" N LEU d 538 " --> pdb=" O TYR d 534 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU d 540 " --> pdb=" O ARG d 536 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN d 541 " --> pdb=" O TYR d 537 " (cutoff:3.500A) Proline residue: d 545 - end of helix Processing helix chain 'd' and resid 556 through 571 removed outlier: 3.515A pdb=" N GLN d 562 " --> pdb=" O THR d 558 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU d 570 " --> pdb=" O ASP d 566 " (cutoff:3.500A) Processing helix chain 'd' and resid 576 through 590 removed outlier: 4.011A pdb=" N ASN d 587 " --> pdb=" O ILE d 583 " (cutoff:3.500A) Processing helix chain 'd' and resid 596 through 615 Processing helix chain 'd' and resid 621 through 636 Processing helix chain 'I' and resid 98 through 122 Processing helix chain 'I' and resid 160 through 190 removed outlier: 4.641A pdb=" N TYR I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 211 removed outlier: 3.546A pdb=" N LYS I 201 " --> pdb=" O ASN I 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 61 removed outlier: 3.637A pdb=" N LYS n 61 " --> pdb=" O LYS n 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 64 removed outlier: 4.550A pdb=" N GLU H 49 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU H 57 " --> pdb=" O GLN H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 96 Processing helix chain 'v' and resid 48 through 52 Processing helix chain 'v' and resid 57 through 68 removed outlier: 3.656A pdb=" N GLN v 67 " --> pdb=" O ARG v 63 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE v 68 " --> pdb=" O PHE v 64 " (cutoff:3.500A) Processing helix chain 'v' and resid 72 through 84 Processing helix chain 'v' and resid 88 through 101 removed outlier: 3.537A pdb=" N ARG v 92 " --> pdb=" O VAL v 88 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU v 101 " --> pdb=" O PHE v 97 " (cutoff:3.500A) Processing helix chain 'v' and resid 106 through 118 Processing helix chain 'v' and resid 121 through 132 Processing helix chain 'v' and resid 137 through 149 removed outlier: 3.738A pdb=" N TRP v 148 " --> pdb=" O HIS v 144 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP v 149 " --> pdb=" O ARG v 145 " (cutoff:3.500A) Processing helix chain 'v' and resid 153 through 164 removed outlier: 3.702A pdb=" N LYS v 158 " --> pdb=" O PHE v 154 " (cutoff:3.500A) Proline residue: v 161 - end of helix Processing helix chain 'v' and resid 168 through 183 Processing helix chain 'v' and resid 186 through 199 Processing helix chain 'v' and resid 202 through 215 removed outlier: 3.671A pdb=" N ILE v 214 " --> pdb=" O TRP v 210 " (cutoff:3.500A) Processing helix chain 'v' and resid 220 through 231 removed outlier: 3.771A pdb=" N LEU v 231 " --> pdb=" O ARG v 227 " (cutoff:3.500A) Processing helix chain 'v' and resid 236 through 248 Processing helix chain 'v' and resid 251 through 261 Processing helix chain 'v' and resid 262 through 264 No H-bonds generated for 'chain 'v' and resid 262 through 264' Processing helix chain 'v' and resid 267 through 280 removed outlier: 3.645A pdb=" N LYS v 280 " --> pdb=" O ALA v 276 " (cutoff:3.500A) Processing helix chain 'v' and resid 283 through 295 Processing helix chain 'v' and resid 303 through 316 Processing helix chain 'v' and resid 319 through 332 Processing helix chain 'v' and resid 336 through 347 removed outlier: 3.664A pdb=" N ILE v 342 " --> pdb=" O ASP v 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN v 344 " --> pdb=" O ASP v 340 " (cutoff:3.500A) Processing helix chain 'v' and resid 350 through 364 Processing helix chain 'v' and resid 369 through 382 removed outlier: 3.614A pdb=" N TRP v 374 " --> pdb=" O ASN v 370 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET v 382 " --> pdb=" O LEU v 378 " (cutoff:3.500A) Processing helix chain 'v' and resid 386 through 399 removed outlier: 3.551A pdb=" N ASP v 393 " --> pdb=" O ILE v 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN v 397 " --> pdb=" O ASP v 393 " (cutoff:3.500A) Processing helix chain 'v' and resid 404 through 414 removed outlier: 3.936A pdb=" N VAL v 408 " --> pdb=" O ASP v 404 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG v 414 " --> pdb=" O THR v 410 " (cutoff:3.500A) Processing helix chain 'v' and resid 420 through 435 removed outlier: 3.828A pdb=" N CYS v 425 " --> pdb=" O ALA v 421 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER v 429 " --> pdb=" O CYS v 425 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU v 430 " --> pdb=" O ASN v 426 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU v 433 " --> pdb=" O SER v 429 " (cutoff:3.500A) Processing helix chain 'v' and resid 444 through 459 removed outlier: 3.528A pdb=" N ARG v 448 " --> pdb=" O GLY v 444 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP v 450 " --> pdb=" O PHE v 446 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR v 457 " --> pdb=" O TYR v 453 " (cutoff:3.500A) Processing helix chain 'v' and resid 465 through 475 removed outlier: 3.778A pdb=" N LEU v 469 " --> pdb=" O THR v 465 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER v 473 " --> pdb=" O LEU v 469 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU v 474 " --> pdb=" O TRP v 470 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS v 475 " --> pdb=" O THR v 471 " (cutoff:3.500A) Processing helix chain 'v' and resid 481 through 499 removed outlier: 3.602A pdb=" N GLU v 486 " --> pdb=" O GLU v 482 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE v 487 " --> pdb=" O ASP v 483 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR v 488 " --> pdb=" O LEU v 484 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU v 495 " --> pdb=" O TRP v 491 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP v 497 " --> pdb=" O ASP v 493 " (cutoff:3.500A) Processing helix chain 'v' and resid 500 through 510 removed outlier: 3.536A pdb=" N LEU v 508 " --> pdb=" O ALA v 504 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP v 510 " --> pdb=" O SER v 506 " (cutoff:3.500A) Processing helix chain 'v' and resid 517 through 528 removed outlier: 3.684A pdb=" N LEU v 521 " --> pdb=" O ASN v 517 " (cutoff:3.500A) Processing helix chain 'v' and resid 537 through 540 removed outlier: 3.607A pdb=" N ASN v 540 " --> pdb=" O VAL v 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 537 through 540' Processing helix chain 'v' and resid 541 through 556 Processing helix chain 'v' and resid 564 through 581 removed outlier: 3.533A pdb=" N VAL v 577 " --> pdb=" O ALA v 573 " (cutoff:3.500A) Processing helix chain 'v' and resid 584 through 598 removed outlier: 3.634A pdb=" N HIS v 598 " --> pdb=" O PHE v 594 " (cutoff:3.500A) Processing helix chain 'v' and resid 600 through 612 removed outlier: 4.302A pdb=" N GLN v 606 " --> pdb=" O MET v 602 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR v 611 " --> pdb=" O VAL v 607 " (cutoff:3.500A) Processing helix chain 'v' and resid 613 through 615 No H-bonds generated for 'chain 'v' and resid 613 through 615' Processing helix chain 'v' and resid 619 through 634 removed outlier: 3.704A pdb=" N GLU v 626 " --> pdb=" O GLU v 622 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL v 630 " --> pdb=" O GLU v 626 " (cutoff:3.500A) Processing helix chain 'v' and resid 640 through 659 removed outlier: 3.927A pdb=" N LYS v 653 " --> pdb=" O GLU v 649 " (cutoff:3.500A) Processing helix chain 'v' and resid 662 through 677 removed outlier: 3.605A pdb=" N PHE v 666 " --> pdb=" O CYS v 662 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE v 667 " --> pdb=" O LYS v 663 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU v 673 " --> pdb=" O TYR v 669 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU v 674 " --> pdb=" O SER v 670 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG v 675 " --> pdb=" O VAL v 671 " (cutoff:3.500A) Processing helix chain 'v' and resid 681 through 691 removed outlier: 3.826A pdb=" N ARG v 688 " --> pdb=" O ILE v 684 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG v 689 " --> pdb=" O GLU v 685 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY v 690 " --> pdb=" O ILE v 686 " (cutoff:3.500A) Processing helix chain 'v' and resid 706 through 715 removed outlier: 4.333A pdb=" N CYS v 712 " --> pdb=" O LEU v 708 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE v 713 " --> pdb=" O TRP v 709 " (cutoff:3.500A) Processing helix chain 'v' and resid 715 through 721 removed outlier: 3.693A pdb=" N THR v 719 " --> pdb=" O LYS v 715 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU v 720 " --> pdb=" O ALA v 716 " (cutoff:3.500A) Processing helix chain 'v' and resid 724 through 733 removed outlier: 4.098A pdb=" N LEU v 728 " --> pdb=" O VAL v 724 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE v 733 " --> pdb=" O TYR v 729 " (cutoff:3.500A) Processing helix chain 'v' and resid 741 through 756 Processing helix chain 'v' and resid 762 through 772 Processing helix chain 'v' and resid 779 through 792 Processing helix chain 'v' and resid 799 through 819 Processing helix chain 'a' and resid 40 through 53 Processing helix chain 'a' and resid 78 through 89 Processing helix chain 'b' and resid 4 through 11 Processing helix chain 'b' and resid 42 through 46 removed outlier: 3.598A pdb=" N SER b 45 " --> pdb=" O SER b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 109 through 118 removed outlier: 3.686A pdb=" N LEU b 117 " --> pdb=" O ASP b 113 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG b 118 " --> pdb=" O LEU b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 137 removed outlier: 4.309A pdb=" N HIS b 136 " --> pdb=" O ASN b 132 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU b 137 " --> pdb=" O GLN b 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 132 through 137' Processing helix chain 'b' and resid 139 through 148 Processing helix chain 'b' and resid 160 through 170 Processing helix chain 't' and resid 13 through 32 Processing helix chain 't' and resid 52 through 65 removed outlier: 4.265A pdb=" N THR t 56 " --> pdb=" O ASN t 52 " (cutoff:3.500A) Processing helix chain 't' and resid 82 through 110 Proline residue: t 96 - end of helix Proline residue: t 105 - end of helix Processing helix chain 't' and resid 111 through 175 removed outlier: 3.630A pdb=" N VAL t 117 " --> pdb=" O LEU t 113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU t 128 " --> pdb=" O GLN t 124 " (cutoff:3.500A) Proline residue: t 133 - end of helix removed outlier: 3.610A pdb=" N ARG t 148 " --> pdb=" O ASN t 144 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN t 149 " --> pdb=" O ASP t 145 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG t 172 " --> pdb=" O LEU t 168 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 23 Processing helix chain 'm' and resid 3 through 9 removed outlier: 3.908A pdb=" N LEU m 7 " --> pdb=" O LEU m 3 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS m 9 " --> pdb=" O ASN m 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 67 removed outlier: 3.625A pdb=" N ALA m 63 " --> pdb=" O GLY m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 107 removed outlier: 3.781A pdb=" N LEU m 106 " --> pdb=" O ASN m 102 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 119 Processing helix chain 'h' and resid 14 through 22 Processing helix chain 'g' and resid 14 through 28 removed outlier: 3.641A pdb=" N GLU g 19 " --> pdb=" O ARG g 15 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 41 Processing helix chain 'k' and resid 54 through 59 removed outlier: 4.471A pdb=" N ASP k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) Processing helix chain 'k' and resid 104 through 109 removed outlier: 4.161A pdb=" N LEU k 109 " --> pdb=" O LYS k 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 14 through 28 removed outlier: 3.642A pdb=" N GLU e 19 " --> pdb=" O ARG e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 40 Processing helix chain 's' and resid 54 through 62 Processing helix chain 'l' and resid 6 through 15 Processing helix chain 'l' and resid 75 through 85 Proline residue: l 82 - end of helix removed outlier: 3.529A pdb=" N LYS l 85 " --> pdb=" O PRO l 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 12 through 23 Processing helix chain 'w' and resid 14 through 22 Processing helix chain 'y' and resid 6 through 14 Processing helix chain 'y' and resid 75 through 85 removed outlier: 3.971A pdb=" N ASN y 80 " --> pdb=" O LEU y 77 " (cutoff:3.500A) Proline residue: y 82 - end of helix Processing helix chain 'z' and resid 3 through 8 removed outlier: 3.909A pdb=" N LEU z 7 " --> pdb=" O LEU z 3 " (cutoff:3.500A) Processing helix chain 'z' and resid 9 through 11 No H-bonds generated for 'chain 'z' and resid 9 through 11' Processing helix chain 'z' and resid 58 through 67 removed outlier: 3.625A pdb=" N ALA z 63 " --> pdb=" O GLY z 59 " (cutoff:3.500A) Processing helix chain 'z' and resid 102 through 107 removed outlier: 3.781A pdb=" N LEU z 106 " --> pdb=" O ASN z 102 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 35 Processing helix chain 'r' and resid 78 through 137 removed outlier: 3.663A pdb=" N THR r 82 " --> pdb=" O PRO r 78 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU r 98 " --> pdb=" O GLU r 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU r 102 " --> pdb=" O LEU r 98 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU r 121 " --> pdb=" O ASP r 117 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA r 124 " --> pdb=" O LYS r 120 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN r 125 " --> pdb=" O LEU r 121 " (cutoff:3.500A) Processing helix chain 'p' and resid 25 through 35 Processing helix chain 'p' and resid 81 through 142 removed outlier: 3.503A pdb=" N SER p 104 " --> pdb=" O SER p 100 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR p 106 " --> pdb=" O LEU p 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU p 115 " --> pdb=" O THR p 111 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET p 128 " --> pdb=" O ALA p 124 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN p 131 " --> pdb=" O LEU p 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU p 132 " --> pdb=" O MET p 128 " (cutoff:3.500A) Proline residue: p 138 - end of helix removed outlier: 3.769A pdb=" N SER p 141 " --> pdb=" O LEU p 137 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN p 142 " --> pdb=" O PRO p 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 35 Processing helix chain 'q' and resid 77 through 143 removed outlier: 4.024A pdb=" N LEU q 81 " --> pdb=" O ILE q 77 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA q 90 " --> pdb=" O ASN q 86 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU q 105 " --> pdb=" O THR q 101 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL q 122 " --> pdb=" O ALA q 118 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA q 123 " --> pdb=" O ALA q 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET q 128 " --> pdb=" O ALA q 124 " (cutoff:3.500A) Proline residue: q 138 - end of helix removed outlier: 3.728A pdb=" N GLN q 143 " --> pdb=" O LYS q 139 " (cutoff:3.500A) Processing helix chain 'o' and resid 25 through 35 removed outlier: 3.707A pdb=" N GLN o 30 " --> pdb=" O SER o 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 78 through 140 removed outlier: 3.512A pdb=" N LEU o 93 " --> pdb=" O ASP o 89 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU o 98 " --> pdb=" O GLU o 94 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR o 101 " --> pdb=" O LYS o 97 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER o 104 " --> pdb=" O SER o 100 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS o 107 " --> pdb=" O ASP o 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU o 121 " --> pdb=" O ASP o 117 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL o 122 " --> pdb=" O ALA o 118 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET o 128 " --> pdb=" O ALA o 124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN o 131 " --> pdb=" O LEU o 127 " (cutoff:3.500A) Proline residue: o 138 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 593 Processing sheet with id=AA5, first strand: chain 'A' and resid 978 through 983 removed outlier: 3.575A pdb=" N ILE A 969 " --> pdb=" O ASN A1091 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1013 through 1014 removed outlier: 6.520A pdb=" N LEU A1171 " --> pdb=" O ARG A1159 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A1161 " --> pdb=" O TYR A1169 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A1169 " --> pdb=" O TYR A1161 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG A1163 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A1167 " --> pdb=" O ARG A1163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1258 through 1260 removed outlier: 3.590A pdb=" N ALA A1298 " --> pdb=" O LEU A1288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1406 through 1408 Processing sheet with id=AA9, first strand: chain 'A' and resid 1624 through 1625 Processing sheet with id=AB1, first strand: chain 'A' and resid 1678 through 1683 removed outlier: 7.031A pdb=" N GLU A1704 " --> pdb=" O GLU A1679 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N VAL A1681 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR A1702 " --> pdb=" O VAL A1681 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP A1733 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE A1775 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP A1735 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE A1777 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A1737 " --> pdb=" O ILE A1777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1709 through 1711 removed outlier: 3.788A pdb=" N LEU A1727 " --> pdb=" O VAL A1711 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1849 through 1852 removed outlier: 5.750A pdb=" N LEU A1850 " --> pdb=" O ILE A1934 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1877 through 1882 removed outlier: 3.629A pdb=" N PHE A1989 " --> pdb=" O LEU A1889 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2033 through 2034 removed outlier: 4.408A pdb=" N THR A2033 " --> pdb=" O SER A2042 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 77 removed outlier: 6.203A pdb=" N GLU C 75 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASN O 136 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU C 77 " --> pdb=" O ASN O 136 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU O 131 " --> pdb=" O LYS O 427 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS O 427 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG O 133 " --> pdb=" O ILE O 425 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER O 422 " --> pdb=" O GLU O 418 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 194 through 201 removed outlier: 3.733A pdb=" N ASN C 194 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 353 through 355 Processing sheet with id=AB9, first strand: chain 'C' and resid 536 through 538 removed outlier: 6.693A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU C 473 " --> pdb=" O VAL C 486 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL C 486 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 475 " --> pdb=" O SER C 484 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER C 484 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N ILE C 561 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU C 545 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 541 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 542 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AC2, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC3, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC4, first strand: chain 'C' and resid 678 through 681 removed outlier: 6.935A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 678 through 681 removed outlier: 10.360A pdb=" N LYS C 939 " --> pdb=" O PRO C 855 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N LEU C 857 " --> pdb=" O TRP C 937 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N TRP C 937 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N GLU C 859 " --> pdb=" O LYS C 935 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N LYS C 935 " --> pdb=" O GLU C 859 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N ILE C 861 " --> pdb=" O TRP C 933 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP C 933 " --> pdb=" O ILE C 861 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 714 removed outlier: 6.582A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL C 773 " --> pdb=" O TYR C 818 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU C 820 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE C 775 " --> pdb=" O LEU C 820 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N SER C 822 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER C 767 " --> pdb=" O LEU C 774 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 776 " --> pdb=" O VAL C 765 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL C 765 " --> pdb=" O ASN C 776 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 727 through 729 Processing sheet with id=AC8, first strand: chain 'O' and resid 142 through 147 removed outlier: 3.726A pdb=" N LYS O 165 " --> pdb=" O THR O 157 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR O 176 " --> pdb=" O VAL O 166 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP O 168 " --> pdb=" O LEU O 174 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU O 174 " --> pdb=" O ASP O 168 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 185 through 190 removed outlier: 6.686A pdb=" N VAL O 206 " --> pdb=" O ASP O 219 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP O 219 " --> pdb=" O VAL O 206 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS O 208 " --> pdb=" O ILE O 217 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 227 through 232 removed outlier: 3.571A pdb=" N ALA O 242 " --> pdb=" O THR O 229 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY O 243 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL O 247 " --> pdb=" O GLY O 243 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP O 252 " --> pdb=" O PRO O 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 269 through 274 removed outlier: 4.774A pdb=" N VAL O 281 " --> pdb=" O TRP O 293 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL O 290 " --> pdb=" O VAL O 303 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL O 303 " --> pdb=" O VAL O 290 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU O 292 " --> pdb=" O MET O 301 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 313 through 316 removed outlier: 3.549A pdb=" N ALA O 313 " --> pdb=" O ALA O 326 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE O 331 " --> pdb=" O ASN O 344 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN O 344 " --> pdb=" O ILE O 331 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER O 333 " --> pdb=" O LEU O 342 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 353 through 358 removed outlier: 3.746A pdb=" N THR O 355 " --> pdb=" O GLY O 367 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL O 372 " --> pdb=" O GLY O 368 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN O 385 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP O 377 " --> pdb=" O LYS O 383 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS O 383 " --> pdb=" O ASP O 377 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 111 through 116 removed outlier: 6.695A pdb=" N HIS P 111 " --> pdb=" O ILE Q 23 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N MET Q 25 " --> pdb=" O HIS P 111 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU P 113 " --> pdb=" O MET Q 25 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS Q 27 " --> pdb=" O GLU P 113 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL P 115 " --> pdb=" O LYS Q 27 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 207 through 208 Processing sheet with id=AD7, first strand: chain 'Q' and resid 269 through 272 removed outlier: 4.295A pdb=" N THR Q 272 " --> pdb=" O LEU Q 276 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU Q 276 " --> pdb=" O THR Q 272 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY Q 279 " --> pdb=" O ILE Q 290 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 30 through 31 removed outlier: 3.654A pdb=" N LYS R 36 " --> pdb=" O ASN R 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 170 through 176 Processing sheet with id=AE1, first strand: chain 'I' and resid 144 through 145 Processing sheet with id=AE2, first strand: chain 'n' and resid 153 through 159 removed outlier: 4.973A pdb=" N VAL n 154 " --> pdb=" O ASP n 455 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP n 455 " --> pdb=" O VAL n 154 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS n 450 " --> pdb=" O GLY n 446 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'n' and resid 168 through 170 Processing sheet with id=AE4, first strand: chain 'n' and resid 187 through 190 removed outlier: 3.637A pdb=" N ARG n 200 " --> pdb=" O ILE n 189 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'n' and resid 211 through 214 removed outlier: 3.774A pdb=" N VAL n 230 " --> pdb=" O LEU n 244 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR n 242 " --> pdb=" O ILE n 232 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP n 234 " --> pdb=" O VAL n 240 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL n 240 " --> pdb=" O ASP n 234 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'n' and resid 251 through 255 removed outlier: 4.075A pdb=" N LEU n 267 " --> pdb=" O LYS n 271 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS n 271 " --> pdb=" O LEU n 267 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE n 272 " --> pdb=" O TYR n 289 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'n' and resid 296 through 301 removed outlier: 3.914A pdb=" N PHE n 308 " --> pdb=" O TRP n 320 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU n 321 " --> pdb=" O PRO n 327 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'n' and resid 342 through 344 Processing sheet with id=AE9, first strand: chain 'n' and resid 381 through 383 removed outlier: 3.518A pdb=" N SER n 382 " --> pdb=" O ALA n 390 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP n 410 " --> pdb=" O SER n 400 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP n 402 " --> pdb=" O PHE n 408 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE n 408 " --> pdb=" O ASP n 402 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'a' and resid 30 through 32 removed outlier: 3.846A pdb=" N ALA a 72 " --> pdb=" O VAL a 32 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR a 75 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 55 through 58 removed outlier: 6.272A pdb=" N HIS b 55 " --> pdb=" O HIS b 77 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU b 79 " --> pdb=" O HIS b 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU b 57 " --> pdb=" O LEU b 79 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N HIS b 77 " --> pdb=" O ASN b 100 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N THR b 102 " --> pdb=" O HIS b 77 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU b 79 " --> pdb=" O THR b 102 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU b 101 " --> pdb=" O THR b 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'e' and resid 84 through 90 removed outlier: 3.738A pdb=" N THR z 28 " --> pdb=" O ASP z 42 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP z 42 " --> pdb=" O THR z 28 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN z 30 " --> pdb=" O LEU z 40 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU z 40 " --> pdb=" O GLN z 30 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL z 32 " --> pdb=" O ALA z 38 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA z 38 " --> pdb=" O VAL z 32 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'z' and resid 79 through 83 current: chain 's' and resid 92 through 97 removed outlier: 6.729A pdb=" N LEU s 23 " --> pdb=" O LEU s 93 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR s 95 " --> pdb=" O ARG s 21 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG s 21 " --> pdb=" O THR s 95 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL s 97 " --> pdb=" O LYS s 19 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LYS s 19 " --> pdb=" O VAL s 97 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN s 33 " --> pdb=" O GLU s 47 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLU s 47 " --> pdb=" O GLN s 33 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL s 44 " --> pdb=" O ILE s 86 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE s 86 " --> pdb=" O VAL s 44 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN s 46 " --> pdb=" O LEU s 84 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU y 22 " --> pdb=" O LYS y 70 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE y 72 " --> pdb=" O SER y 20 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER y 20 " --> pdb=" O ILE y 72 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR y 28 " --> pdb=" O ALA y 49 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA y 49 " --> pdb=" O THR y 28 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG y 30 " --> pdb=" O VAL y 47 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL y 47 " --> pdb=" O ARG y 30 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN y 43 " --> pdb=" O VAL y 34 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL y 42 " --> pdb=" O VAL y 64 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP y 60 " --> pdb=" O ASP y 46 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE y 48 " --> pdb=" O HIS y 58 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS y 58 " --> pdb=" O ILE y 48 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR y 50 " --> pdb=" O VAL y 56 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL y 56 " --> pdb=" O THR y 50 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLN y 61 " --> pdb=" O ALA x 73 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA x 73 " --> pdb=" O GLN y 61 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER x 70 " --> pdb=" O ASN x 18 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE x 28 " --> pdb=" O ASP x 42 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP x 42 " --> pdb=" O ILE x 28 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG x 30 " --> pdb=" O LEU x 40 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU x 40 " --> pdb=" O ARG x 30 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR x 32 " --> pdb=" O VAL x 38 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL x 38 " --> pdb=" O TYR x 32 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS x 55 " --> pdb=" O GLU x 45 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'x' and resid 55 through 56 removed outlier: 3.758A pdb=" N HIS x 55 " --> pdb=" O GLU x 45 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU u 31 " --> pdb=" O ILE u 37 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE u 37 " --> pdb=" O LEU u 31 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS u 42 " --> pdb=" O GLU u 56 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU u 56 " --> pdb=" O LYS u 42 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL u 44 " --> pdb=" O ILE u 54 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE u 54 " --> pdb=" O VAL u 44 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE u 46 " --> pdb=" O VAL u 52 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL u 52 " --> pdb=" O PHE u 46 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL u 53 " --> pdb=" O LEU u 81 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU u 81 " --> pdb=" O VAL u 53 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP u 55 " --> pdb=" O LYS u 79 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS u 79 " --> pdb=" O ASP u 55 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA u 57 " --> pdb=" O LEU u 77 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS w 30 " --> pdb=" O LEU w 79 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE w 81 " --> pdb=" O GLY w 28 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY w 28 " --> pdb=" O ILE w 81 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU w 37 " --> pdb=" O GLU w 58 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU w 58 " --> pdb=" O GLU w 37 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG w 39 " --> pdb=" O ALA w 56 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA w 56 " --> pdb=" O ARG w 39 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN w 52 " --> pdb=" O VAL w 43 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN w 52 " --> pdb=" O PHE w 72 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE w 72 " --> pdb=" O GLN w 52 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN w 54 " --> pdb=" O GLU w 70 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU w 70 " --> pdb=" O ASN w 54 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU w 70 " --> pdb=" O LYS e 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS e 106 " --> pdb=" O GLU w 70 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER e 47 " --> pdb=" O ILE e 102 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL e 104 " --> pdb=" O ILE e 45 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE e 45 " --> pdb=" O VAL e 104 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG e 57 " --> pdb=" O ASN e 71 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASN e 71 " --> pdb=" O ARG e 57 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS e 59 " --> pdb=" O LEU e 69 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU e 69 " --> pdb=" O LYS e 59 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'm' and resid 79 through 83 removed outlier: 6.812A pdb=" N ALA m 38 " --> pdb=" O VAL m 32 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL m 32 " --> pdb=" O ALA m 38 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU m 40 " --> pdb=" O GLN m 30 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN m 30 " --> pdb=" O LEU m 40 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP m 42 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR m 28 " --> pdb=" O ASP m 42 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL g 84 " --> pdb=" O LYS g 79 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS g 79 " --> pdb=" O VAL g 84 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN g 86 " --> pdb=" O THR g 77 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR g 77 " --> pdb=" O ASN g 86 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLU g 88 " --> pdb=" O LEU g 75 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU g 75 " --> pdb=" O GLU g 88 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE g 90 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS g 73 " --> pdb=" O PHE g 90 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER g 92 " --> pdb=" O ASN g 71 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL g 68 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL g 72 " --> pdb=" O ILE g 55 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE g 55 " --> pdb=" O VAL g 72 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU g 74 " --> pdb=" O LYS g 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS g 53 " --> pdb=" O GLU g 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL g 44 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL g 103 " --> pdb=" O SER g 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS g 106 " --> pdb=" O GLU h 70 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU h 70 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU h 70 " --> pdb=" O ASN h 54 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN h 54 " --> pdb=" O GLU h 70 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE h 72 " --> pdb=" O GLN h 52 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN h 52 " --> pdb=" O PHE h 72 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN h 52 " --> pdb=" O VAL h 43 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA h 56 " --> pdb=" O ARG h 39 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG h 39 " --> pdb=" O ALA h 56 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU h 58 " --> pdb=" O GLU h 37 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU h 37 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY h 28 " --> pdb=" O ILE h 81 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE h 81 " --> pdb=" O GLY h 28 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS h 30 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA i 57 " --> pdb=" O LEU i 77 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS i 79 " --> pdb=" O ASP i 55 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP i 55 " --> pdb=" O LYS i 79 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU i 81 " --> pdb=" O VAL i 53 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL i 53 " --> pdb=" O LEU i 81 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL i 52 " --> pdb=" O PHE i 46 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE i 46 " --> pdb=" O VAL i 52 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE i 54 " --> pdb=" O VAL i 44 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL i 44 " --> pdb=" O ILE i 54 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU i 56 " --> pdb=" O LYS i 42 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS i 42 " --> pdb=" O GLU i 56 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS j 55 " --> pdb=" O GLU j 45 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'm' and resid 79 through 83 removed outlier: 6.728A pdb=" N LEU k 23 " --> pdb=" O LEU k 93 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR k 95 " --> pdb=" O ARG k 21 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG k 21 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL k 97 " --> pdb=" O LYS k 19 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LYS k 19 " --> pdb=" O VAL k 97 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN k 33 " --> pdb=" O GLU k 47 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU k 47 " --> pdb=" O GLN k 33 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL k 44 " --> pdb=" O ILE k 86 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE k 86 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN k 46 " --> pdb=" O LEU k 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS k 48 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG k 80 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE l 71 " --> pdb=" O GLU l 22 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS l 32 " --> pdb=" O ASP l 46 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP l 46 " --> pdb=" O LYS l 32 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL l 34 " --> pdb=" O LEU l 44 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU l 44 " --> pdb=" O VAL l 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP l 60 " --> pdb=" O ASP l 46 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE l 48 " --> pdb=" O HIS l 58 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N HIS l 58 " --> pdb=" O ILE l 48 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR l 50 " --> pdb=" O VAL l 56 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL l 56 " --> pdb=" O THR l 50 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN l 61 " --> pdb=" O ALA j 73 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA j 73 " --> pdb=" O GLN l 61 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER j 70 " --> pdb=" O ASN j 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG j 23 " --> pdb=" O ILE j 19 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS j 24 " --> pdb=" O GLU j 45 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU j 45 " --> pdb=" O LYS j 24 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA j 26 " --> pdb=" O ALA j 43 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA j 43 " --> pdb=" O ALA j 26 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL j 39 " --> pdb=" O ARG j 30 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS j 55 " --> pdb=" O GLU j 45 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'r' and resid 21 through 24 removed outlier: 4.413A pdb=" N THR r 21 " --> pdb=" O SER r 16 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'p' and resid 13 through 15 Processing sheet with id=AF9, first strand: chain 'q' and resid 13 through 15 Processing sheet with id=AG1, first strand: chain 'o' and resid 13 through 15 3348 hydrogen bonds defined for protein. 9717 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 614 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 49.92 Time building geometry restraints manager: 17.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 12279 1.32 - 1.45: 23836 1.45 - 1.58: 43775 1.58 - 1.70: 1081 1.70 - 1.83: 395 Bond restraints: 81366 Sorted by residual: bond pdb=" C GLU d 163 " pdb=" O GLU d 163 " ideal model delta sigma weight residual 1.235 1.264 -0.029 4.70e-03 4.53e+04 3.87e+01 bond pdb=" O3' U L 12 " pdb=" P G L 13 " ideal model delta sigma weight residual 1.607 1.692 -0.085 1.50e-02 4.44e+03 3.20e+01 bond pdb=" CA ILE Z 73 " pdb=" CB ILE Z 73 " ideal model delta sigma weight residual 1.539 1.511 0.028 5.40e-03 3.43e+04 2.77e+01 bond pdb=" O3' G L1120 " pdb=" P U L1121 " ideal model delta sigma weight residual 1.607 1.541 0.066 1.50e-02 4.44e+03 1.92e+01 bond pdb=" O3' G E 81 " pdb=" P A E 82 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.50e-02 4.44e+03 1.67e+01 ... (remaining 81361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 109995 2.81 - 5.63: 2425 5.63 - 8.44: 230 8.44 - 11.26: 49 11.26 - 14.07: 5 Bond angle restraints: 112704 Sorted by residual: angle pdb=" C MET b 43 " pdb=" N PRO b 44 " pdb=" CA PRO b 44 " ideal model delta sigma weight residual 119.28 128.69 -9.41 1.10e+00 8.26e-01 7.32e+01 angle pdb=" C THR b 4 " pdb=" N PRO b 5 " pdb=" CA PRO b 5 " ideal model delta sigma weight residual 118.85 127.46 -8.61 1.09e+00 8.42e-01 6.24e+01 angle pdb=" C PHE d 98 " pdb=" N ILE d 99 " pdb=" CA ILE d 99 " ideal model delta sigma weight residual 120.24 124.67 -4.43 6.30e-01 2.52e+00 4.94e+01 angle pdb=" N SER v 681 " pdb=" CA SER v 681 " pdb=" C SER v 681 " ideal model delta sigma weight residual 113.16 105.07 8.09 1.24e+00 6.50e-01 4.25e+01 angle pdb=" C ALA b 11 " pdb=" N PRO b 12 " pdb=" CA PRO b 12 " ideal model delta sigma weight residual 119.84 127.97 -8.13 1.25e+00 6.40e-01 4.23e+01 ... (remaining 112699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 48108 35.95 - 71.91: 1767 71.91 - 107.86: 197 107.86 - 143.81: 30 143.81 - 179.77: 17 Dihedral angle restraints: 50119 sinusoidal: 23827 harmonic: 26292 Sorted by residual: dihedral pdb=" O4' U B 2 " pdb=" C1' U B 2 " pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sinusoidal sigma weight residual 200.00 41.86 158.14 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' C D 79 " pdb=" C1' C D 79 " pdb=" N1 C D 79 " pdb=" C2 C D 79 " ideal model delta sinusoidal sigma weight residual 200.00 50.05 149.95 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" O4' C D 164 " pdb=" C1' C D 164 " pdb=" N1 C D 164 " pdb=" C2 C D 164 " ideal model delta sinusoidal sigma weight residual 232.00 52.23 179.77 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 50116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.024: 13431 1.024 - 2.048: 0 2.048 - 3.072: 0 3.072 - 4.096: 0 4.096 - 5.120: 2 Chirality restraints: 13433 Sorted by residual: chirality pdb=" C2 IHP A3000 " pdb=" C1 IHP A3000 " pdb=" C3 IHP A3000 " pdb=" O12 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.52 2.60 -5.12 2.00e-01 2.50e+01 6.55e+02 chirality pdb=" C3 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C4 IHP A3000 " pdb=" O13 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.34 2.76 -5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" C3' G L 120 " pdb=" C4' G L 120 " pdb=" O3' G L 120 " pdb=" C2' G L 120 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 13430 not shown) Planarity restraints: 12405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 262 " -0.096 5.00e-02 4.00e+02 1.47e-01 3.48e+01 pdb=" N PRO A 263 " 0.255 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP P 159 " -0.084 5.00e-02 4.00e+02 1.29e-01 2.67e+01 pdb=" N PRO P 160 " 0.223 5.00e-02 4.00e+02 pdb=" CA PRO P 160 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO P 160 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR g 42 " -0.084 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO g 43 " 0.223 5.00e-02 4.00e+02 pdb=" CA PRO g 43 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO g 43 " -0.069 5.00e-02 4.00e+02 ... (remaining 12402 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 308 2.44 - 3.05: 46036 3.05 - 3.67: 124954 3.67 - 4.28: 180287 4.28 - 4.90: 282535 Nonbonded interactions: 634120 Sorted by model distance: nonbonded pdb=" O2' U B -11 " pdb=" O5' G B -10 " model vdw 1.820 3.040 nonbonded pdb=" O TRP A 402 " pdb=" O TYR A 403 " model vdw 1.829 3.040 nonbonded pdb=" O2' C D 83 " pdb=" O5' A D 84 " model vdw 1.853 3.040 nonbonded pdb=" O2' U L1154 " pdb=" C5' C L1155 " model vdw 1.903 3.440 nonbonded pdb=" OP1 G E 78 " pdb="MG MG E 200 " model vdw 1.907 2.170 ... (remaining 634115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'h' selection = chain 'w' } ncs_group { reference = (chain 'i' and (resid 10 through 31 or (resid 32 through 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 37 or (resid 38 and (na \ me N or name CA or name C or name O or name CB )) or resid 39 through 53 or (res \ id 54 through 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 through 92)) selection = chain 'u' } ncs_group { reference = chain 'j' selection = chain 'x' } ncs_group { reference = (chain 'k' and resid 3 through 102) selection = chain 's' } ncs_group { reference = (chain 'l' and (resid 5 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 36 or (resid 37 and (nam \ e N or name CA or name C or name O or name CB )) or resid 38 through 85)) selection = chain 'y' } ncs_group { reference = (chain 'm' and resid 1 through 108) selection = chain 'z' } ncs_group { reference = (chain 'o' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 or resid \ 65 through 139)) selection = (chain 'p' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 or resid \ 65 through 139)) selection = (chain 'q' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 or (resid \ 76 and (name N or name CA or name C or name O or name CB )) or resid 77 through \ 139)) selection = (chain 'r' and (resid 1 through 52 or resid 57 through 61 or resid 65 through 13 \ 9)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.310 Check model and map are aligned: 0.450 Set scattering table: 0.560 Process input model: 181.540 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.500 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: 0.030 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 194.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 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 : 0.008 0.096 81366 Z= 0.499 Angle : 1.017 14.070 112704 Z= 0.603 Chirality : 0.087 5.120 13433 Planarity : 0.007 0.147 12405 Dihedral : 17.309 179.768 32929 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.05 % Favored : 94.18 % Rotamer: Outliers : 2.51 % Allowed : 5.03 % Favored : 92.46 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.07), residues: 8731 helix: -2.75 (0.06), residues: 3919 sheet: -0.62 (0.15), residues: 1043 loop : -2.03 (0.09), residues: 3769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP d 205 HIS 0.022 0.003 HIS O 306 PHE 0.054 0.003 PHE d 172 TYR 0.047 0.003 TYR d 105 ARG 0.022 0.001 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1657 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1465 time to evaluate : 6.029 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 168 LEU cc_start: 0.8981 (tp) cc_final: 0.8780 (tt) REVERT: A 403 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.6418 (t80) REVERT: A 578 MET cc_start: 0.7888 (mtt) cc_final: 0.7652 (mtm) REVERT: A 625 LEU cc_start: 0.9008 (tp) cc_final: 0.8699 (tt) REVERT: A 797 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8120 (mm) REVERT: A 1116 TYR cc_start: 0.8433 (t80) cc_final: 0.8154 (t80) REVERT: A 1259 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7515 (pt) REVERT: A 1379 MET cc_start: 0.8321 (mmm) cc_final: 0.8105 (tpp) REVERT: A 1851 PHE cc_start: 0.4134 (m-80) cc_final: 0.3880 (m-80) REVERT: A 2055 MET cc_start: 0.4242 (mtt) cc_final: 0.3564 (ptt) REVERT: C 74 VAL cc_start: 0.8253 (t) cc_final: 0.7998 (t) REVERT: C 90 LEU cc_start: 0.8634 (tp) cc_final: 0.8394 (mp) REVERT: C 187 ARG cc_start: 0.8393 (mmt90) cc_final: 0.7642 (mmt-90) REVERT: C 933 TRP cc_start: 0.7928 (m-10) cc_final: 0.7572 (m-10) REVERT: O 437 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6897 (mm-30) REVERT: P 234 MET cc_start: 0.0844 (mtp) cc_final: 0.0491 (mtt) REVERT: Q 108 MET cc_start: 0.8994 (mmm) cc_final: 0.8628 (mmm) REVERT: R 80 MET cc_start: 0.7809 (mtp) cc_final: 0.7300 (ttp) REVERT: S 169 PHE cc_start: 0.5865 (t80) cc_final: 0.5556 (t80) REVERT: T 53 MET cc_start: 0.7914 (mmm) cc_final: 0.7529 (mmp) REVERT: T 114 THR cc_start: 0.7884 (p) cc_final: 0.7679 (p) REVERT: Z 345 ILE cc_start: 0.8721 (tt) cc_final: 0.8261 (mm) REVERT: c 151 MET cc_start: 0.7342 (ttm) cc_final: 0.6968 (ttm) REVERT: d 132 VAL cc_start: 0.8733 (t) cc_final: 0.8315 (m) REVERT: I 197 ASN cc_start: 0.7232 (p0) cc_final: 0.6801 (p0) REVERT: H 84 ASN cc_start: 0.7249 (m-40) cc_final: 0.7036 (m-40) REVERT: v 392 TYR cc_start: 0.2684 (m-10) cc_final: 0.1948 (t80) REVERT: m 109 ASP cc_start: 0.1879 (m-30) cc_final: 0.1462 (t0) REVERT: j 46 ILE cc_start: 0.7298 (mm) cc_final: 0.6967 (tp) REVERT: i 46 PHE cc_start: 0.1062 (p90) cc_final: 0.0612 (p90) REVERT: y 35 GLU cc_start: 0.5892 (mm-30) cc_final: 0.5621 (tm-30) outliers start: 192 outliers final: 61 residues processed: 1619 average time/residue: 0.7683 time to fit residues: 2109.9258 Evaluate side-chains 736 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 671 time to evaluate : 6.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1574 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 437 GLU Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 506 THR Chi-restraints excluded: chain c residue 517 VAL Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 258 THR Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain v residue 529 HIS Chi-restraints excluded: chain v residue 576 THR Chi-restraints excluded: chain v residue 719 THR Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 76 THR Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 85 THR Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 100 THR Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain j residue 18 ASN Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain j residue 64 ARG Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain k residue 43 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 64 VAL Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 63 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 787 optimal weight: 8.9990 chunk 707 optimal weight: 1.9990 chunk 392 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 477 optimal weight: 2.9990 chunk 377 optimal weight: 0.9980 chunk 731 optimal weight: 8.9990 chunk 282 optimal weight: 0.6980 chunk 444 optimal weight: 0.9980 chunk 544 optimal weight: 50.0000 chunk 847 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 233 HIS A 253 GLN A 405 ASN A 541 ASN A 596 ASN A 658 ASN A 662 GLN A 685 HIS A 760 ASN A 784 GLN A 848 ASN ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A1034 ASN A1099 ASN A1140 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1254 ASN A1281 ASN A1368 GLN ** A1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN A1496 GLN A1532 HIS A1652 HIS A1730 ASN A1809 ASN A1863 HIS A2068 ASN C 82 ASN C 103 HIS C 167 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN C 294 ASN C 310 ASN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 683 ASN C 726 ASN C 733 ASN C 929 GLN C 934 HIS J 19 HIS O 99 ASN O 113 ASN ** O 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 306 HIS ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 ASN P 107 ASN P 161 ASN Q 69 ASN Q 106 ASN Q 141 ASN ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 254 GLN R 44 ASN R 147 ASN R 189 GLN S 34 HIS S 171 HIS S 173 HIS T 56 HIS T 57 HIS T 110 GLN T 112 ASN T 128 GLN ** T 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 147 HIS ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 69 ASN Z 105 GLN ** Z 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 223 HIS ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 354 HIS Z 368 ASN Z 441 ASN c 163 GLN d 123 ASN d 147 ASN d 196 HIS d 316 ASN I 185 ASN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 HIS ** v 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 596 GLN v 620 GLN v 643 HIS ** v 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 21 ASN m 35 GLN m 37 ASN m 78 ASN ** m 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 18 ASN j 20 ASN j 54 ASN h 50 ASN g 35 ASN g 50 ASN e 86 ASN l 12 ASN ** l 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 15 ASN i 23 GLN ** i 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 50 ASN x 20 ASN z 21 ASN ** z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 81366 Z= 0.218 Angle : 0.719 14.237 112704 Z= 0.372 Chirality : 0.044 0.546 13433 Planarity : 0.005 0.083 12405 Dihedral : 18.973 178.336 17938 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 2.65 % Allowed : 11.74 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.08), residues: 8731 helix: -0.50 (0.07), residues: 4072 sheet: -0.43 (0.15), residues: 1127 loop : -1.68 (0.10), residues: 3532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 212 HIS 0.009 0.001 HIS H 95 PHE 0.029 0.002 PHE Z 396 TYR 0.027 0.002 TYR d 105 ARG 0.011 0.001 ARG c 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 818 time to evaluate : 6.199 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping revert: symmetry clash Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 763 MET cc_start: 0.6719 (tpp) cc_final: 0.6388 (tpp) REVERT: A 1412 LEU cc_start: 0.6967 (pp) cc_final: 0.6502 (tp) REVERT: A 1851 PHE cc_start: 0.4425 (m-80) cc_final: 0.4181 (m-80) REVERT: A 1965 PHE cc_start: 0.2474 (OUTLIER) cc_final: 0.2172 (t80) REVERT: C 652 MET cc_start: 0.8043 (mmm) cc_final: 0.7501 (mmm) REVERT: C 719 MET cc_start: 0.7738 (tpp) cc_final: 0.7492 (tpp) REVERT: O 253 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8267 (mmm) REVERT: O 334 TRP cc_start: 0.8025 (m100) cc_final: 0.7794 (m100) REVERT: Q 108 MET cc_start: 0.8911 (mmm) cc_final: 0.8649 (mmm) REVERT: R 199 MET cc_start: 0.8062 (mmp) cc_final: 0.7770 (mmm) REVERT: T 1 MET cc_start: 0.4362 (OUTLIER) cc_final: 0.4017 (mmp) REVERT: T 46 ASN cc_start: 0.7463 (m-40) cc_final: 0.6242 (m-40) REVERT: T 47 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7813 (mm-30) REVERT: Z 124 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7145 (tt) REVERT: c 163 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: c 176 LEU cc_start: 0.8670 (mt) cc_final: 0.8219 (tt) REVERT: c 223 PRO cc_start: 0.8008 (Cg_exo) cc_final: 0.7668 (Cg_endo) REVERT: I 156 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5738 (m-30) REVERT: I 197 ASN cc_start: 0.7440 (p0) cc_final: 0.7044 (p0) REVERT: v 392 TYR cc_start: 0.2355 (m-10) cc_final: 0.2035 (t80) REVERT: v 456 LEU cc_start: 0.7860 (pp) cc_final: 0.7471 (mm) REVERT: v 602 MET cc_start: 0.6102 (mpp) cc_final: 0.5874 (mpp) REVERT: m 10 LEU cc_start: 0.6992 (mt) cc_final: 0.6286 (tt) REVERT: m 109 ASP cc_start: 0.2559 (m-30) cc_final: 0.2058 (t0) REVERT: j 46 ILE cc_start: 0.7384 (mm) cc_final: 0.6967 (tp) REVERT: g 35 ASN cc_start: 0.3209 (OUTLIER) cc_final: 0.2975 (t0) REVERT: g 76 TRP cc_start: 0.3864 (p90) cc_final: 0.3639 (p90) REVERT: e 35 ASN cc_start: 0.6146 (t0) cc_final: 0.5884 (t0) REVERT: e 90 PHE cc_start: 0.3981 (m-80) cc_final: 0.3235 (t80) REVERT: s 26 ASP cc_start: 0.4888 (p0) cc_final: 0.4569 (t70) REVERT: y 30 ARG cc_start: 0.4194 (ptt180) cc_final: 0.2849 (mtm180) outliers start: 201 outliers final: 114 residues processed: 968 average time/residue: 0.7036 time to fit residues: 1211.2982 Evaluate side-chains 727 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 606 time to evaluate : 6.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1281 ASN Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1399 MET Chi-restraints excluded: chain A residue 1418 THR Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1812 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain A residue 2040 TRP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain O residue 253 MET Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 197 ILE Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 125 ILE Chi-restraints excluded: chain Q residue 211 ASP Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 171 HIS Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 289 VAL Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 517 VAL Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 280 LEU Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain v residue 445 SER Chi-restraints excluded: chain v residue 509 GLU Chi-restraints excluded: chain v residue 520 ILE Chi-restraints excluded: chain v residue 525 TYR Chi-restraints excluded: chain v residue 576 THR Chi-restraints excluded: chain v residue 711 MET Chi-restraints excluded: chain v residue 719 THR Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 76 THR Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 85 THR Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 100 THR Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain j residue 18 ASN Chi-restraints excluded: chain h residue 80 TYR Chi-restraints excluded: chain g residue 35 ASN Chi-restraints excluded: chain g residue 50 ASN Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain e residue 92 SER Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain y residue 63 PHE Chi-restraints excluded: chain y residue 73 VAL Chi-restraints excluded: chain z residue 28 THR Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 101 THR Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 470 optimal weight: 0.9980 chunk 262 optimal weight: 9.9990 chunk 705 optimal weight: 4.9990 chunk 576 optimal weight: 20.0000 chunk 233 optimal weight: 0.9980 chunk 848 optimal weight: 6.9990 chunk 916 optimal weight: 5.9990 chunk 755 optimal weight: 30.0000 chunk 841 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 680 optimal weight: 30.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS A 675 HIS A 839 HIS A 848 ASN ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1281 ASN A1369 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN A1667 GLN A1707 HIS A2018 ASN C 108 GLN C 180 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN C 309 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 GLN C 721 GLN C 929 GLN O 194 HIS ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN P 161 ASN ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 ASN ** T 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 HIS ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 116 ASN ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 79 HIS ** d 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN v 397 ASN v 403 GLN ** v 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 634 HIS m 21 ASN ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN ** m 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 35 ASN s 46 ASN ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 GLN ** l 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 15 ASN ** i 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 85 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 81366 Z= 0.320 Angle : 0.712 14.244 112704 Z= 0.367 Chirality : 0.045 0.310 13433 Planarity : 0.005 0.057 12405 Dihedral : 18.570 179.158 17899 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.10 % Favored : 94.73 % Rotamer: Outliers : 3.57 % Allowed : 12.94 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.09), residues: 8731 helix: 0.53 (0.08), residues: 4061 sheet: -0.45 (0.15), residues: 1099 loop : -1.57 (0.10), residues: 3571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP v 624 HIS 0.028 0.002 HIS S 171 PHE 0.031 0.002 PHE A1844 TYR 0.029 0.002 TYR C 387 ARG 0.031 0.001 ARG c 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 646 time to evaluate : 6.108 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping revert: symmetry clash Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 636 HIS cc_start: 0.8612 (m-70) cc_final: 0.8396 (m-70) REVERT: A 1262 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7873 (ttm) REVERT: A 1748 ILE cc_start: 0.8183 (pt) cc_final: 0.7780 (tp) REVERT: A 1851 PHE cc_start: 0.4612 (m-80) cc_final: 0.4193 (m-80) REVERT: C 78 MET cc_start: 0.8076 (tpt) cc_final: 0.7801 (mmm) REVERT: C 189 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8197 (pp) REVERT: C 652 MET cc_start: 0.8523 (mmm) cc_final: 0.7952 (mmm) REVERT: O 111 ILE cc_start: 0.8792 (tp) cc_final: 0.8510 (tt) REVERT: O 227 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8431 (t) REVERT: Q 108 MET cc_start: 0.8979 (mmm) cc_final: 0.8726 (mmm) REVERT: R 33 TRP cc_start: 0.7435 (t-100) cc_final: 0.7143 (t-100) REVERT: R 199 MET cc_start: 0.8220 (mmp) cc_final: 0.7960 (mmm) REVERT: R 242 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7768 (tp) REVERT: T 1 MET cc_start: 0.4130 (OUTLIER) cc_final: 0.3770 (mmp) REVERT: T 46 ASN cc_start: 0.7381 (m-40) cc_final: 0.6529 (m-40) REVERT: T 50 TRP cc_start: 0.7440 (m-10) cc_final: 0.7173 (m-10) REVERT: T 114 THR cc_start: 0.8023 (p) cc_final: 0.7791 (t) REVERT: Z 124 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7234 (tt) REVERT: Z 195 GLU cc_start: 0.7269 (pp20) cc_final: 0.6896 (pp20) REVERT: c 91 MET cc_start: 0.7135 (mmt) cc_final: 0.6226 (mtt) REVERT: c 163 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6970 (mm-40) REVERT: d 58 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8959 (mp) REVERT: d 198 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6621 (mp10) REVERT: I 197 ASN cc_start: 0.7602 (p0) cc_final: 0.7202 (p0) REVERT: n 227 ASP cc_start: 0.6445 (p0) cc_final: 0.6065 (p0) REVERT: H 82 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6055 (pp) REVERT: v 392 TYR cc_start: 0.2024 (m-10) cc_final: 0.1815 (t80) REVERT: v 711 MET cc_start: 0.4380 (OUTLIER) cc_final: 0.4114 (mmm) REVERT: j 46 ILE cc_start: 0.7524 (mm) cc_final: 0.7047 (tp) REVERT: g 11 HIS cc_start: 0.3856 (p-80) cc_final: 0.2450 (t70) REVERT: e 35 ASN cc_start: 0.6514 (t0) cc_final: 0.6272 (t0) REVERT: s 26 ASP cc_start: 0.5332 (p0) cc_final: 0.4583 (t0) REVERT: l 84 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6807 (m-10) REVERT: y 30 ARG cc_start: 0.4572 (ptt180) cc_final: 0.3199 (mtm180) REVERT: z 62 MET cc_start: 0.1371 (ttm) cc_final: 0.1170 (ttm) REVERT: r 126 LEU cc_start: 0.0658 (mm) cc_final: -0.0276 (pp) outliers start: 260 outliers final: 145 residues processed: 861 average time/residue: 0.6781 time to fit residues: 1044.9927 Evaluate side-chains 702 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 545 time to evaluate : 6.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain A residue 2040 TRP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain O residue 227 VAL Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 404 CYS Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 125 ILE Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 306 THR Chi-restraints excluded: chain R residue 34 TYR Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 16 GLU Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 193 SER Chi-restraints excluded: chain Z residue 198 PHE Chi-restraints excluded: chain Z residue 289 VAL Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 65 PHE Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 517 VAL Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 65 MET Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain d residue 198 GLN Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 428 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain v residue 440 VAL Chi-restraints excluded: chain v residue 525 TYR Chi-restraints excluded: chain v residue 576 THR Chi-restraints excluded: chain v residue 711 MET Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 76 THR Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 100 THR Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 104 SER Chi-restraints excluded: chain k residue 109 LEU Chi-restraints excluded: chain e residue 92 SER Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 84 PHE Chi-restraints excluded: chain i residue 22 GLN Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain y residue 73 VAL Chi-restraints excluded: chain z residue 28 THR Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 27 LEU Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 102 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 838 optimal weight: 6.9990 chunk 638 optimal weight: 9.9990 chunk 440 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 405 optimal weight: 7.9990 chunk 569 optimal weight: 10.0000 chunk 851 optimal weight: 10.0000 chunk 901 optimal weight: 20.0000 chunk 445 optimal weight: 3.9990 chunk 807 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 257 ASN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN A 864 GLN A1156 HIS A1197 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1540 ASN A1990 ASN C 167 ASN C 180 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 HIS ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 ASN ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 HIS T 143 HIS ** T 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 170 HIS ** Z 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN ** c 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN d 316 ASN ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN ** v 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN ** m 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 8 HIS ** l 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 47 ASN w 50 ASN y 58 HIS y 61 GLN ** z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 94 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 81366 Z= 0.337 Angle : 0.703 10.212 112704 Z= 0.365 Chirality : 0.045 0.281 13433 Planarity : 0.005 0.063 12405 Dihedral : 18.418 179.286 17893 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.11 % Favored : 94.72 % Rotamer: Outliers : 4.20 % Allowed : 14.01 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.09), residues: 8731 helix: 0.87 (0.08), residues: 4064 sheet: -0.57 (0.15), residues: 1049 loop : -1.49 (0.10), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP v 411 HIS 0.010 0.002 HIS S 171 PHE 0.030 0.002 PHE Z 396 TYR 0.024 0.002 TYR O 221 ARG 0.021 0.001 ARG e 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 612 time to evaluate : 6.142 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping revert: symmetry clash Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 165 LEU cc_start: 0.8369 (tp) cc_final: 0.8162 (tp) REVERT: A 238 ARG cc_start: 0.4467 (mmm160) cc_final: 0.4209 (mmm160) REVERT: A 271 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7876 (pm20) REVERT: A 615 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7483 (mm) REVERT: A 716 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7578 (ttt-90) REVERT: A 743 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8414 (mmmt) REVERT: A 757 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7039 (mm-30) REVERT: A 1213 MET cc_start: 0.7886 (tpp) cc_final: 0.6825 (tpp) REVERT: A 1275 MET cc_start: 0.7086 (mpp) cc_final: 0.6220 (mtm) REVERT: A 1299 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8190 (mtpt) REVERT: A 1748 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7775 (tp) REVERT: A 1851 PHE cc_start: 0.4629 (m-80) cc_final: 0.4153 (m-80) REVERT: C 189 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8348 (pp) REVERT: C 652 MET cc_start: 0.8786 (mmm) cc_final: 0.8188 (mmm) REVERT: O 194 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.8174 (p90) REVERT: R 252 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.6758 (t70) REVERT: S 167 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8147 (mp10) REVERT: c 91 MET cc_start: 0.7444 (mmt) cc_final: 0.6455 (mtt) REVERT: c 176 LEU cc_start: 0.8686 (mt) cc_final: 0.8481 (tt) REVERT: I 197 ASN cc_start: 0.7650 (p0) cc_final: 0.7313 (p0) REVERT: n 227 ASP cc_start: 0.6607 (p0) cc_final: 0.6329 (p0) REVERT: H 82 LEU cc_start: 0.6719 (mt) cc_final: 0.6287 (pp) REVERT: j 46 ILE cc_start: 0.7662 (mm) cc_final: 0.7092 (tp) REVERT: g 11 HIS cc_start: 0.3731 (p-80) cc_final: 0.2430 (t70) REVERT: g 46 ILE cc_start: 0.6310 (mp) cc_final: 0.6076 (mt) REVERT: e 45 ILE cc_start: 0.0395 (mm) cc_final: 0.0153 (mm) REVERT: l 84 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6677 (m-10) REVERT: y 30 ARG cc_start: 0.4526 (ptt180) cc_final: 0.3338 (mtm180) REVERT: z 62 MET cc_start: 0.0850 (ttm) cc_final: 0.0258 (ttm) REVERT: r 126 LEU cc_start: 0.0610 (mm) cc_final: -0.0292 (pp) outliers start: 300 outliers final: 174 residues processed: 857 average time/residue: 0.7056 time to fit residues: 1082.0150 Evaluate side-chains 704 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 522 time to evaluate : 6.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1299 LYS Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1418 THR Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 194 HIS Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 275 THR Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 404 CYS Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 125 ILE Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain Q residue 282 LEU Chi-restraints excluded: chain Q residue 306 THR Chi-restraints excluded: chain R residue 34 TYR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 210 LYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 252 HIS Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 16 GLU Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 198 PHE Chi-restraints excluded: chain Z residue 289 VAL Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain d residue 316 ASN Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 292 HIS Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain v residue 432 ILE Chi-restraints excluded: chain v residue 445 SER Chi-restraints excluded: chain v residue 525 TYR Chi-restraints excluded: chain v residue 576 THR Chi-restraints excluded: chain v residue 679 LEU Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 100 THR Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain u residue 60 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 100 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain g residue 26 PHE Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 86 ILE Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 104 SER Chi-restraints excluded: chain e residue 90 PHE Chi-restraints excluded: chain e residue 92 SER Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 64 VAL Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 84 PHE Chi-restraints excluded: chain i residue 22 GLN Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 27 LEU Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 102 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 751 optimal weight: 20.0000 chunk 511 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 671 optimal weight: 20.0000 chunk 372 optimal weight: 0.7980 chunk 769 optimal weight: 10.0000 chunk 623 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 460 optimal weight: 6.9990 chunk 809 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 ASN ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 197 ASN ** c 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** v 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 71 GLN ** m 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 ASN ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 GLN w 24 ASN ** z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 81366 Z= 0.230 Angle : 0.635 16.112 112704 Z= 0.323 Chirality : 0.042 0.256 13433 Planarity : 0.004 0.099 12405 Dihedral : 18.281 179.468 17889 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.91 % Favored : 94.95 % Rotamer: Outliers : 3.35 % Allowed : 15.37 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.09), residues: 8731 helix: 1.26 (0.08), residues: 4074 sheet: -0.52 (0.15), residues: 1084 loop : -1.43 (0.10), residues: 3573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP v 411 HIS 0.009 0.001 HIS g 52 PHE 0.034 0.002 PHE A1965 TYR 0.020 0.002 TYR C 387 ARG 0.012 0.001 ARG Z 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 606 time to evaluate : 6.146 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 172 ILE cc_start: 0.9117 (mt) cc_final: 0.8899 (mm) REVERT: A 176 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8932 (mp) REVERT: A 271 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7886 (pm20) REVERT: A 622 MET cc_start: 0.8524 (tpp) cc_final: 0.8149 (tpp) REVERT: A 1213 MET cc_start: 0.7649 (tpp) cc_final: 0.6780 (tpp) REVERT: A 1275 MET cc_start: 0.6739 (mpp) cc_final: 0.6067 (mtm) REVERT: A 1748 ILE cc_start: 0.8206 (pt) cc_final: 0.7799 (tp) REVERT: A 1851 PHE cc_start: 0.3862 (m-80) cc_final: 0.3475 (m-80) REVERT: A 2024 MET cc_start: 0.4419 (mmm) cc_final: 0.4151 (mpp) REVERT: C 78 MET cc_start: 0.7930 (tpp) cc_final: 0.7572 (mmm) REVERT: C 156 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: C 189 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8280 (pp) REVERT: C 276 ASP cc_start: 0.5914 (t0) cc_final: 0.5605 (t0) REVERT: C 652 MET cc_start: 0.8714 (mmm) cc_final: 0.8049 (mmm) REVERT: C 842 MET cc_start: 0.6974 (tpt) cc_final: 0.6693 (tpp) REVERT: C 927 MET cc_start: 0.7356 (tpp) cc_final: 0.7050 (tpt) REVERT: O 227 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8328 (t) REVERT: O 334 TRP cc_start: 0.8185 (m100) cc_final: 0.7928 (m100) REVERT: P 202 MET cc_start: 0.6444 (mpp) cc_final: 0.6167 (ptp) REVERT: Q 238 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6174 (pp) REVERT: Q 248 CYS cc_start: 0.5801 (OUTLIER) cc_final: 0.5028 (p) REVERT: R 199 MET cc_start: 0.7947 (mmm) cc_final: 0.7628 (mmm) REVERT: R 252 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6664 (t70) REVERT: S 167 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8152 (mt0) REVERT: Z 34 MET cc_start: 0.2110 (mmp) cc_final: 0.1403 (mmp) REVERT: c 91 MET cc_start: 0.7253 (mmt) cc_final: 0.6339 (mtt) REVERT: I 197 ASN cc_start: 0.7565 (p0) cc_final: 0.7254 (p0) REVERT: n 227 ASP cc_start: 0.6590 (p0) cc_final: 0.6313 (p0) REVERT: H 82 LEU cc_start: 0.6661 (mt) cc_final: 0.6234 (pp) REVERT: v 386 GLU cc_start: 0.4460 (OUTLIER) cc_final: 0.3363 (mm-30) REVERT: j 46 ILE cc_start: 0.7731 (mm) cc_final: 0.7202 (tp) REVERT: g 11 HIS cc_start: 0.3485 (p-80) cc_final: 0.2301 (t70) REVERT: k 76 LYS cc_start: 0.5013 (pttp) cc_final: 0.4488 (ptmt) REVERT: l 84 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6814 (m-10) REVERT: y 30 ARG cc_start: 0.4600 (ptt180) cc_final: 0.3303 (mtm180) REVERT: z 62 MET cc_start: 0.0727 (ttm) cc_final: 0.0308 (ttm) REVERT: r 126 LEU cc_start: 0.0617 (mm) cc_final: -0.0280 (pp) outliers start: 245 outliers final: 160 residues processed: 813 average time/residue: 0.6849 time to fit residues: 1003.9199 Evaluate side-chains 712 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 543 time to evaluate : 6.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1548 GLN Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain O residue 227 VAL Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 262 LEU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 125 ILE Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 248 CYS Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 280 VAL Chi-restraints excluded: chain Q residue 282 LEU Chi-restraints excluded: chain Q residue 306 THR Chi-restraints excluded: chain R residue 34 TYR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 252 HIS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 171 HIS Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 114 THR Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 16 GLU Chi-restraints excluded: chain Z residue 158 CYS Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 198 PHE Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain d residue 316 ASN Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 258 THR Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 292 HIS Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain v residue 386 GLU Chi-restraints excluded: chain v residue 440 VAL Chi-restraints excluded: chain v residue 525 TYR Chi-restraints excluded: chain v residue 532 ILE Chi-restraints excluded: chain v residue 576 THR Chi-restraints excluded: chain v residue 676 ILE Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain g residue 26 PHE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 86 ILE Chi-restraints excluded: chain k residue 109 LEU Chi-restraints excluded: chain e residue 92 SER Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 84 PHE Chi-restraints excluded: chain i residue 22 GLN Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain z residue 28 THR Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 27 LEU Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 102 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 303 optimal weight: 8.9990 chunk 812 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 529 optimal weight: 0.9980 chunk 222 optimal weight: 0.8980 chunk 902 optimal weight: 20.0000 chunk 749 optimal weight: 40.0000 chunk 417 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 chunk 473 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1281 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 ASN P 161 ASN Q 141 ASN ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN ** c 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 316 ASN ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 654 ASN ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 21 ASN ** z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 81366 Z= 0.205 Angle : 0.614 12.142 112704 Z= 0.310 Chirality : 0.041 0.236 13433 Planarity : 0.004 0.060 12405 Dihedral : 18.171 178.895 17887 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.81 % Favored : 95.04 % Rotamer: Outliers : 3.28 % Allowed : 16.04 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.09), residues: 8731 helix: 1.49 (0.08), residues: 4077 sheet: -0.49 (0.15), residues: 1090 loop : -1.35 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 933 HIS 0.007 0.001 HIS n 292 PHE 0.033 0.002 PHE A1965 TYR 0.034 0.001 TYR d 267 ARG 0.008 0.000 ARG c 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 601 time to evaluate : 6.217 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 175 LEU cc_start: 0.9046 (tp) cc_final: 0.8657 (tt) REVERT: A 271 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7862 (pm20) REVERT: A 622 MET cc_start: 0.8513 (tpp) cc_final: 0.8044 (tpp) REVERT: A 716 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7292 (ttt-90) REVERT: A 811 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8492 (mt) REVERT: A 1213 MET cc_start: 0.7585 (tpp) cc_final: 0.6666 (tpp) REVERT: A 1350 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7997 (mt) REVERT: A 1851 PHE cc_start: 0.3939 (m-80) cc_final: 0.3510 (m-80) REVERT: A 1948 MET cc_start: 0.7360 (ptp) cc_final: 0.6883 (ptp) REVERT: A 2024 MET cc_start: 0.4861 (mmm) cc_final: 0.4615 (mpp) REVERT: A 2055 MET cc_start: 0.1498 (mmt) cc_final: 0.0781 (mmm) REVERT: C 156 ASP cc_start: 0.6910 (m-30) cc_final: 0.6576 (m-30) REVERT: C 186 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7512 (t0) REVERT: C 189 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8217 (pp) REVERT: C 200 CYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7609 (p) REVERT: C 276 ASP cc_start: 0.6073 (t0) cc_final: 0.5781 (t0) REVERT: C 391 MET cc_start: 0.8848 (ttm) cc_final: 0.8639 (ttt) REVERT: C 652 MET cc_start: 0.8752 (mmm) cc_final: 0.8070 (mmm) REVERT: C 927 MET cc_start: 0.7373 (tpp) cc_final: 0.6892 (tpt) REVERT: O 194 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.7879 (p90) REVERT: O 227 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8322 (t) REVERT: O 334 TRP cc_start: 0.8039 (m100) cc_final: 0.7813 (m100) REVERT: Q 238 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6155 (pp) REVERT: Q 248 CYS cc_start: 0.5566 (OUTLIER) cc_final: 0.4932 (p) REVERT: S 167 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8086 (mp10) REVERT: T 134 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6604 (tpt170) REVERT: Z 193 SER cc_start: 0.7673 (m) cc_final: 0.7159 (p) REVERT: Z 345 ILE cc_start: 0.8494 (tp) cc_final: 0.8243 (tp) REVERT: c 91 MET cc_start: 0.7033 (mmt) cc_final: 0.6181 (mtt) REVERT: I 197 ASN cc_start: 0.7551 (p0) cc_final: 0.7261 (p0) REVERT: n 227 ASP cc_start: 0.6606 (p0) cc_final: 0.6111 (p0) REVERT: H 82 LEU cc_start: 0.6420 (mt) cc_final: 0.6052 (pp) REVERT: v 386 GLU cc_start: 0.4219 (OUTLIER) cc_final: 0.3112 (mm-30) REVERT: m 1 MET cc_start: 0.4243 (tmm) cc_final: 0.3859 (tmm) REVERT: j 46 ILE cc_start: 0.7770 (mm) cc_final: 0.7272 (tp) REVERT: g 11 HIS cc_start: 0.3497 (p-80) cc_final: 0.2336 (t70) REVERT: k 76 LYS cc_start: 0.5069 (pttp) cc_final: 0.4779 (ptmt) REVERT: l 21 LEU cc_start: 0.7165 (pp) cc_final: 0.6854 (pp) REVERT: l 84 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6711 (m-10) REVERT: y 30 ARG cc_start: 0.4691 (ptt180) cc_final: 0.3545 (mtm180) REVERT: z 62 MET cc_start: 0.0722 (ttm) cc_final: 0.0460 (ttm) outliers start: 241 outliers final: 162 residues processed: 808 average time/residue: 0.6707 time to fit residues: 980.4403 Evaluate side-chains 719 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 544 time to evaluate : 6.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1548 GLN Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1812 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain O residue 194 HIS Chi-restraints excluded: chain O residue 227 VAL Chi-restraints excluded: chain O residue 262 LEU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 161 ASN Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 125 ILE Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 248 CYS Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 280 VAL Chi-restraints excluded: chain Q residue 282 LEU Chi-restraints excluded: chain Q residue 306 THR Chi-restraints excluded: chain R residue 34 TYR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 210 LYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 114 THR Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 16 GLU Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 158 CYS Chi-restraints excluded: chain Z residue 198 PHE Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 121 LEU Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 258 THR Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 292 HIS Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain v residue 386 GLU Chi-restraints excluded: chain v residue 440 VAL Chi-restraints excluded: chain v residue 525 TYR Chi-restraints excluded: chain v residue 532 ILE Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain g residue 26 PHE Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain e residue 92 SER Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 84 PHE Chi-restraints excluded: chain i residue 22 GLN Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain z residue 28 THR Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 102 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 870 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 514 optimal weight: 7.9990 chunk 659 optimal weight: 7.9990 chunk 510 optimal weight: 5.9990 chunk 759 optimal weight: 0.0040 chunk 504 optimal weight: 0.6980 chunk 899 optimal weight: 7.9990 chunk 562 optimal weight: 8.9990 chunk 548 optimal weight: 50.0000 chunk 415 optimal weight: 9.9990 overall best weight: 3.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 839 HIS A 948 HIS A 952 ASN A1005 GLN A1281 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 ASN Q 243 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 166 HIS ** T 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN ** v 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 81366 Z= 0.267 Angle : 0.648 15.699 112704 Z= 0.328 Chirality : 0.042 0.233 13433 Planarity : 0.004 0.061 12405 Dihedral : 18.153 179.583 17886 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.37 % Favored : 94.48 % Rotamer: Outliers : 3.32 % Allowed : 16.38 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.09), residues: 8731 helix: 1.51 (0.08), residues: 4073 sheet: -0.50 (0.15), residues: 1073 loop : -1.38 (0.10), residues: 3585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP C 933 HIS 0.008 0.001 HIS S 166 PHE 0.029 0.002 PHE C 212 TYR 0.032 0.002 TYR v 574 ARG 0.007 0.001 ARG x 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 565 time to evaluate : 6.141 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 208 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping revert: symmetry clash Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 175 LEU cc_start: 0.9115 (tp) cc_final: 0.8726 (tt) REVERT: A 271 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7876 (pm20) REVERT: A 622 MET cc_start: 0.8616 (tpp) cc_final: 0.8258 (tpp) REVERT: A 625 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8241 (tt) REVERT: A 716 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7468 (ttt-90) REVERT: A 811 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8649 (mt) REVERT: A 862 GLU cc_start: 0.8007 (tp30) cc_final: 0.7716 (tp30) REVERT: A 1187 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7646 (mm) REVERT: A 1350 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8079 (mt) REVERT: A 1851 PHE cc_start: 0.3934 (m-80) cc_final: 0.3485 (m-80) REVERT: A 2055 MET cc_start: 0.1071 (mmt) cc_final: 0.0340 (mmm) REVERT: C 156 ASP cc_start: 0.7024 (m-30) cc_final: 0.6711 (m-30) REVERT: C 186 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7559 (t0) REVERT: C 189 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8285 (pp) REVERT: C 200 CYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7773 (p) REVERT: C 276 ASP cc_start: 0.5774 (t0) cc_final: 0.5427 (t0) REVERT: C 391 MET cc_start: 0.8970 (ttm) cc_final: 0.8449 (ttm) REVERT: C 834 MET cc_start: 0.7069 (mmm) cc_final: 0.6515 (tpp) REVERT: C 927 MET cc_start: 0.7600 (tpp) cc_final: 0.7105 (tpt) REVERT: O 194 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8074 (p90) REVERT: O 227 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8307 (t) REVERT: O 334 TRP cc_start: 0.8113 (m100) cc_final: 0.7907 (m100) REVERT: P 84 ASN cc_start: 0.8630 (m-40) cc_final: 0.8272 (m-40) REVERT: Q 238 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6234 (pp) REVERT: R 199 MET cc_start: 0.7718 (mmm) cc_final: 0.7282 (mmm) REVERT: R 252 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6712 (t70) REVERT: S 167 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8194 (mt0) REVERT: T 134 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6594 (tpt170) REVERT: Z 193 SER cc_start: 0.7571 (m) cc_final: 0.7296 (t) REVERT: Z 345 ILE cc_start: 0.8522 (tp) cc_final: 0.8277 (tp) REVERT: c 91 MET cc_start: 0.7029 (mmt) cc_final: 0.6223 (mtt) REVERT: I 197 ASN cc_start: 0.7671 (p0) cc_final: 0.7388 (p0) REVERT: n 227 ASP cc_start: 0.6658 (p0) cc_final: 0.6177 (p0) REVERT: H 82 LEU cc_start: 0.6411 (mt) cc_final: 0.6043 (pp) REVERT: v 386 GLU cc_start: 0.4259 (OUTLIER) cc_final: 0.3226 (mm-30) REVERT: m 1 MET cc_start: 0.4879 (tmm) cc_final: 0.4398 (tmm) REVERT: j 46 ILE cc_start: 0.7873 (mm) cc_final: 0.7385 (tp) REVERT: g 11 HIS cc_start: 0.3512 (p-80) cc_final: 0.2434 (t70) REVERT: g 46 ILE cc_start: 0.6297 (mp) cc_final: 0.6039 (mt) REVERT: l 21 LEU cc_start: 0.7191 (pp) cc_final: 0.6927 (pp) REVERT: l 79 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6663 (ptmm) REVERT: l 84 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6746 (m-10) REVERT: y 30 ARG cc_start: 0.4586 (ptt180) cc_final: 0.3536 (mtm180) REVERT: y 40 MET cc_start: 0.2921 (mmm) cc_final: 0.2200 (mmt) outliers start: 243 outliers final: 175 residues processed: 769 average time/residue: 0.6852 time to fit residues: 952.4379 Evaluate side-chains 731 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 540 time to evaluate : 6.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1548 GLN Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2005 PHE Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 818 TYR Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 194 HIS Chi-restraints excluded: chain O residue 227 VAL Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 262 LEU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 404 CYS Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 125 ILE Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 280 VAL Chi-restraints excluded: chain Q residue 282 LEU Chi-restraints excluded: chain Q residue 306 THR Chi-restraints excluded: chain R residue 34 TYR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 210 LYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 HIS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 114 THR Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 16 GLU Chi-restraints excluded: chain Z residue 73 ILE Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 158 CYS Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 198 PHE Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 208 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 258 THR Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 292 HIS Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain v residue 386 GLU Chi-restraints excluded: chain v residue 440 VAL Chi-restraints excluded: chain v residue 525 TYR Chi-restraints excluded: chain v residue 532 ILE Chi-restraints excluded: chain v residue 676 ILE Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 86 ILE Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain e residue 92 SER Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain s residue 6 VAL Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 84 PHE Chi-restraints excluded: chain i residue 22 GLN Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 27 LEU Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 102 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 556 optimal weight: 40.0000 chunk 359 optimal weight: 10.0000 chunk 537 optimal weight: 20.0000 chunk 270 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 571 optimal weight: 6.9990 chunk 612 optimal weight: 30.0000 chunk 444 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 706 optimal weight: 0.9980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 HIS A 952 ASN A1281 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 GLN ** C 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 194 HIS O 223 HIS ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 HIS T 112 ASN T 116 ASN ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN ** v 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 81366 Z= 0.289 Angle : 0.663 15.638 112704 Z= 0.336 Chirality : 0.043 0.294 13433 Planarity : 0.004 0.058 12405 Dihedral : 18.178 179.343 17886 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.38 % Favored : 94.47 % Rotamer: Outliers : 3.37 % Allowed : 16.89 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.09), residues: 8731 helix: 1.48 (0.08), residues: 4077 sheet: -0.54 (0.16), residues: 1039 loop : -1.37 (0.10), residues: 3615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP A1995 HIS 0.009 0.001 HIS Q 185 PHE 0.030 0.002 PHE A 423 TYR 0.028 0.002 TYR d 267 ARG 0.011 0.001 ARG c 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 575 time to evaluate : 6.126 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 55 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 175 LEU cc_start: 0.9134 (tp) cc_final: 0.8689 (tt) REVERT: A 271 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7932 (pm20) REVERT: A 284 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7660 (mmt90) REVERT: A 622 MET cc_start: 0.8618 (tpp) cc_final: 0.8270 (tpp) REVERT: A 716 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7548 (ttt-90) REVERT: A 763 MET cc_start: 0.7077 (tpt) cc_final: 0.6148 (tpp) REVERT: A 811 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8703 (mt) REVERT: A 862 GLU cc_start: 0.8065 (tp30) cc_final: 0.7769 (tp30) REVERT: A 1187 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7595 (mm) REVERT: A 1213 MET cc_start: 0.7588 (tpp) cc_final: 0.6901 (ttt) REVERT: A 1350 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8156 (mt) REVERT: A 1673 LEU cc_start: 0.6771 (tt) cc_final: 0.6532 (tt) REVERT: A 1823 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8752 (mp) REVERT: A 1851 PHE cc_start: 0.3756 (m-80) cc_final: 0.3367 (m-80) REVERT: A 2055 MET cc_start: 0.1110 (mmt) cc_final: 0.0631 (mmm) REVERT: C 156 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6720 (m-30) REVERT: C 186 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7670 (t0) REVERT: C 189 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8284 (pp) REVERT: C 200 CYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7864 (p) REVERT: C 263 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6710 (mtt) REVERT: C 276 ASP cc_start: 0.6146 (t0) cc_final: 0.5857 (t0) REVERT: C 391 MET cc_start: 0.9036 (ttm) cc_final: 0.8376 (ttm) REVERT: C 652 MET cc_start: 0.8968 (mmm) cc_final: 0.8751 (mmm) REVERT: C 834 MET cc_start: 0.7285 (mmm) cc_final: 0.6787 (tpp) REVERT: C 927 MET cc_start: 0.7606 (tpp) cc_final: 0.7047 (tpt) REVERT: O 194 HIS cc_start: 0.9041 (OUTLIER) cc_final: 0.8498 (p-80) REVERT: P 84 ASN cc_start: 0.8776 (m-40) cc_final: 0.8494 (m-40) REVERT: Q 5 ILE cc_start: 0.7649 (pt) cc_final: 0.7393 (mp) REVERT: Q 238 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5859 (pp) REVERT: Q 248 CYS cc_start: 0.5870 (OUTLIER) cc_final: 0.5623 (p) REVERT: R 199 MET cc_start: 0.7723 (mmm) cc_final: 0.7334 (mmm) REVERT: R 252 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6782 (t70) REVERT: S 167 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8114 (mt0) REVERT: T 134 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6650 (tpt170) REVERT: Z 345 ILE cc_start: 0.8588 (tp) cc_final: 0.8379 (tp) REVERT: Z 350 MET cc_start: 0.8643 (mmp) cc_final: 0.8414 (mmp) REVERT: c 91 MET cc_start: 0.7045 (mmt) cc_final: 0.6246 (mtt) REVERT: c 176 LEU cc_start: 0.8389 (mt) cc_final: 0.8186 (tt) REVERT: I 197 ASN cc_start: 0.7719 (p0) cc_final: 0.7390 (p0) REVERT: n 227 ASP cc_start: 0.6959 (p0) cc_final: 0.6556 (p0) REVERT: n 296 ILE cc_start: -0.1347 (mm) cc_final: -0.1654 (mm) REVERT: H 82 LEU cc_start: 0.6532 (mt) cc_final: 0.6253 (pp) REVERT: v 386 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.3250 (mm-30) REVERT: v 411 TRP cc_start: 0.6665 (OUTLIER) cc_final: 0.6323 (t-100) REVERT: v 602 MET cc_start: 0.5833 (mpp) cc_final: 0.5539 (mpp) REVERT: m 1 MET cc_start: 0.4508 (tmm) cc_final: 0.4228 (tmm) REVERT: m 16 THR cc_start: 0.5108 (t) cc_final: 0.4886 (t) REVERT: j 46 ILE cc_start: 0.8014 (mm) cc_final: 0.7557 (tp) REVERT: g 11 HIS cc_start: 0.3863 (p-80) cc_final: 0.2546 (t70) REVERT: g 46 ILE cc_start: 0.6702 (mp) cc_final: 0.6440 (mt) REVERT: k 76 LYS cc_start: 0.4391 (pttp) cc_final: 0.4133 (ptmt) REVERT: l 21 LEU cc_start: 0.7251 (pp) cc_final: 0.7015 (pp) REVERT: l 84 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6336 (m-10) REVERT: y 30 ARG cc_start: 0.4617 (ptt180) cc_final: 0.3195 (mtm180) REVERT: y 38 ASP cc_start: 0.6544 (p0) cc_final: 0.6189 (p0) REVERT: y 40 MET cc_start: 0.2905 (mmm) cc_final: 0.1288 (mmt) REVERT: r 126 LEU cc_start: 0.1204 (mm) cc_final: 0.0249 (pp) outliers start: 246 outliers final: 181 residues processed: 780 average time/residue: 0.6884 time to fit residues: 973.1116 Evaluate side-chains 745 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 546 time to evaluate : 6.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1548 GLN Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1823 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1956 ILE Chi-restraints excluded: chain A residue 2005 PHE Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 818 TYR Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 194 HIS Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 262 LEU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 404 CYS Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 125 ILE Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 248 CYS Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 280 VAL Chi-restraints excluded: chain Q residue 282 LEU Chi-restraints excluded: chain Q residue 306 THR Chi-restraints excluded: chain R residue 34 TYR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 210 LYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 HIS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 114 THR Chi-restraints excluded: chain T residue 116 ASN Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 16 GLU Chi-restraints excluded: chain Z residue 73 ILE Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 158 CYS Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 198 PHE Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 506 THR Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 245 LYS Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 292 HIS Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain v residue 386 GLU Chi-restraints excluded: chain v residue 411 TRP Chi-restraints excluded: chain v residue 440 VAL Chi-restraints excluded: chain v residue 445 SER Chi-restraints excluded: chain v residue 525 TYR Chi-restraints excluded: chain v residue 532 ILE Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 86 ILE Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain e residue 92 SER Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain s residue 6 VAL Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 84 PHE Chi-restraints excluded: chain i residue 22 GLN Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain y residue 56 VAL Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain q residue 55 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 102 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 818 optimal weight: 20.0000 chunk 861 optimal weight: 10.0000 chunk 786 optimal weight: 20.0000 chunk 837 optimal weight: 10.0000 chunk 504 optimal weight: 1.9990 chunk 365 optimal weight: 6.9990 chunk 658 optimal weight: 20.0000 chunk 257 optimal weight: 3.9990 chunk 757 optimal weight: 50.0000 chunk 792 optimal weight: 0.7980 chunk 835 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A1281 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1600 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 ASN Q 199 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 ASN ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 205 HIS ** n 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 81366 Z= 0.326 Angle : 0.699 19.752 112704 Z= 0.354 Chirality : 0.044 0.255 13433 Planarity : 0.004 0.059 12405 Dihedral : 18.237 178.778 17882 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.93 % Favored : 93.92 % Rotamer: Outliers : 3.20 % Allowed : 17.46 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.09), residues: 8731 helix: 1.34 (0.08), residues: 4091 sheet: -0.62 (0.16), residues: 1017 loop : -1.46 (0.10), residues: 3623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 933 HIS 0.042 0.002 HIS O 194 PHE 0.033 0.002 PHE c 65 TYR 0.027 0.002 TYR O 196 ARG 0.011 0.001 ARG O 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 556 time to evaluate : 6.286 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping revert: symmetry clash Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 175 LEU cc_start: 0.9160 (tp) cc_final: 0.8741 (tt) REVERT: A 271 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7950 (pm20) REVERT: A 284 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7566 (mmt90) REVERT: A 622 MET cc_start: 0.8662 (tpp) cc_final: 0.8368 (tpp) REVERT: A 625 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8358 (tt) REVERT: A 1187 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7736 (mm) REVERT: A 1851 PHE cc_start: 0.3570 (m-80) cc_final: 0.3209 (m-80) REVERT: A 2024 MET cc_start: 0.4900 (mmm) cc_final: 0.4692 (mpp) REVERT: A 2055 MET cc_start: 0.0956 (mmt) cc_final: 0.0489 (mmm) REVERT: C 186 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7699 (t0) REVERT: C 189 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8320 (pp) REVERT: C 200 CYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7904 (p) REVERT: C 276 ASP cc_start: 0.6282 (t0) cc_final: 0.5986 (t0) REVERT: C 391 MET cc_start: 0.8973 (ttm) cc_final: 0.8306 (ttm) REVERT: C 834 MET cc_start: 0.7428 (mmm) cc_final: 0.7067 (tpp) REVERT: C 886 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8340 (p) REVERT: C 927 MET cc_start: 0.7671 (tpp) cc_final: 0.7149 (tpt) REVERT: C 968 MET cc_start: 0.8650 (mmm) cc_final: 0.8414 (mmm) REVERT: O 334 TRP cc_start: 0.8191 (m100) cc_final: 0.7952 (m100) REVERT: P 84 ASN cc_start: 0.8822 (m-40) cc_final: 0.8537 (m-40) REVERT: Q 238 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.5877 (pp) REVERT: Q 248 CYS cc_start: 0.5906 (OUTLIER) cc_final: 0.5669 (p) REVERT: R 199 MET cc_start: 0.7699 (mmm) cc_final: 0.7308 (mmm) REVERT: R 252 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6763 (t70) REVERT: S 167 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7947 (mt0) REVERT: T 134 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6637 (tpt170) REVERT: Z 73 ILE cc_start: 0.2559 (OUTLIER) cc_final: 0.2287 (mt) REVERT: Z 345 ILE cc_start: 0.8632 (tp) cc_final: 0.8417 (tp) REVERT: Z 350 MET cc_start: 0.8687 (mmp) cc_final: 0.8482 (mmp) REVERT: c 91 MET cc_start: 0.6963 (mmt) cc_final: 0.6194 (mtt) REVERT: I 197 ASN cc_start: 0.7733 (p0) cc_final: 0.7343 (p0) REVERT: n 227 ASP cc_start: 0.7018 (p0) cc_final: 0.6618 (p0) REVERT: n 296 ILE cc_start: -0.1445 (mm) cc_final: -0.1718 (mm) REVERT: H 82 LEU cc_start: 0.6519 (mt) cc_final: 0.6239 (pp) REVERT: v 386 GLU cc_start: 0.4489 (OUTLIER) cc_final: 0.3225 (mm-30) REVERT: v 411 TRP cc_start: 0.6648 (OUTLIER) cc_final: 0.6238 (t-100) REVERT: v 730 GLN cc_start: 0.4402 (mm-40) cc_final: 0.4137 (mt0) REVERT: m 1 MET cc_start: 0.4386 (tmm) cc_final: 0.4078 (tmm) REVERT: m 16 THR cc_start: 0.5439 (t) cc_final: 0.5201 (t) REVERT: j 46 ILE cc_start: 0.8060 (mm) cc_final: 0.7613 (tp) REVERT: g 11 HIS cc_start: 0.3321 (p-80) cc_final: 0.2585 (t70) REVERT: l 21 LEU cc_start: 0.7451 (pp) cc_final: 0.7230 (pp) REVERT: l 84 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6369 (m-10) REVERT: y 30 ARG cc_start: 0.4683 (ptt180) cc_final: 0.3246 (mtm180) REVERT: y 38 ASP cc_start: 0.6894 (p0) cc_final: 0.6545 (p0) REVERT: y 40 MET cc_start: 0.2734 (mmm) cc_final: 0.1207 (mmt) REVERT: z 1 MET cc_start: 0.5437 (tpt) cc_final: 0.5096 (tpt) REVERT: r 126 LEU cc_start: 0.1333 (mm) cc_final: 0.0271 (pp) outliers start: 234 outliers final: 190 residues processed: 759 average time/residue: 0.6871 time to fit residues: 946.3414 Evaluate side-chains 745 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 541 time to evaluate : 6.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1548 GLN Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1956 ILE Chi-restraints excluded: chain A residue 2005 PHE Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 818 TYR Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 194 HIS Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 262 LEU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 404 CYS Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 125 ILE Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 248 CYS Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 280 VAL Chi-restraints excluded: chain Q residue 282 LEU Chi-restraints excluded: chain Q residue 306 THR Chi-restraints excluded: chain R residue 34 TYR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 210 LYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 HIS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 114 THR Chi-restraints excluded: chain T residue 116 ASN Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 16 GLU Chi-restraints excluded: chain Z residue 73 ILE Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 158 CYS Chi-restraints excluded: chain Z residue 198 PHE Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 506 THR Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 245 LYS Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 292 HIS Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain v residue 386 GLU Chi-restraints excluded: chain v residue 411 TRP Chi-restraints excluded: chain v residue 440 VAL Chi-restraints excluded: chain v residue 445 SER Chi-restraints excluded: chain v residue 525 TYR Chi-restraints excluded: chain v residue 532 ILE Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 86 ILE Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 104 SER Chi-restraints excluded: chain e residue 92 SER Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain s residue 6 VAL Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 84 PHE Chi-restraints excluded: chain i residue 22 GLN Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain x residue 34 ILE Chi-restraints excluded: chain y residue 56 VAL Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 550 optimal weight: 50.0000 chunk 886 optimal weight: 0.6980 chunk 540 optimal weight: 30.0000 chunk 420 optimal weight: 9.9990 chunk 616 optimal weight: 20.0000 chunk 929 optimal weight: 7.9990 chunk 855 optimal weight: 7.9990 chunk 740 optimal weight: 50.0000 chunk 76 optimal weight: 3.9990 chunk 571 optimal weight: 4.9990 chunk 453 optimal weight: 0.0070 overall best weight: 3.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 ASN ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1655 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 194 HIS ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 ASN ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN ** n 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 529 HIS v 654 ASN ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 81366 Z= 0.285 Angle : 0.674 15.618 112704 Z= 0.341 Chirality : 0.043 0.259 13433 Planarity : 0.004 0.127 12405 Dihedral : 18.212 178.535 17881 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 2.91 % Allowed : 17.94 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.09), residues: 8731 helix: 1.43 (0.08), residues: 4084 sheet: -0.72 (0.16), residues: 1012 loop : -1.43 (0.10), residues: 3635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP C 933 HIS 0.015 0.001 HIS O 194 PHE 0.035 0.002 PHE A 423 TYR 0.026 0.002 TYR d 267 ARG 0.014 0.001 ARG v 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17462 Ramachandran restraints generated. 8731 Oldfield, 0 Emsley, 8731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 557 time to evaluate : 6.208 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 Corrupt residue: chain: c residue: PRO 504 >>> skipping Corrupt residue: chain: c residue: PRO 505 >>> skipping Corrupt residue: chain: c residue: PRO 532 >>> skipping Corrupt residue: chain: c residue: PRO 550 >>> skipping Corrupt residue: chain: n residue: PRO 159 >>> skipping Corrupt residue: chain: n residue: PRO 162 >>> skipping Corrupt residue: chain: n residue: PRO 257 >>> skipping Corrupt residue: chain: n residue: PRO 260 >>> skipping Corrupt residue: chain: n residue: PRO 327 >>> skipping Corrupt residue: chain: n residue: PRO 340 >>> skipping Corrupt residue: chain: n residue: PRO 373 >>> skipping Corrupt residue: chain: n residue: PRO 424 >>> skipping Corrupt residue: chain: n residue: PRO 428 >>> skipping Corrupt residue: chain: n residue: PRO 436 >>> skipping Corrupt residue: chain: t residue: PRO 13 >>> skipping Corrupt residue: chain: t residue: PRO 77 >>> skipping Corrupt residue: chain: t residue: PRO 96 >>> skipping Corrupt residue: chain: t residue: PRO 105 >>> skipping Corrupt residue: chain: t residue: PRO 133 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: r residue: PRO 17 >>> skipping Corrupt residue: chain: r residue: PRO 44 >>> skipping Corrupt residue: chain: p residue: PRO 17 >>> skipping Corrupt residue: chain: p residue: PRO 44 >>> skipping Corrupt residue: chain: q residue: PRO 17 >>> skipping Corrupt residue: chain: q residue: PRO 44 >>> skipping Corrupt residue: chain: o residue: PRO 17 >>> skipping Corrupt residue: chain: o residue: PRO 44 >>> skipping REVERT: A 175 LEU cc_start: 0.9099 (tp) cc_final: 0.8711 (tt) REVERT: A 271 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7954 (pm20) REVERT: A 284 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7458 (mmt90) REVERT: A 622 MET cc_start: 0.8603 (tpp) cc_final: 0.8251 (tpp) REVERT: A 625 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 811 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8673 (mt) REVERT: A 862 GLU cc_start: 0.8246 (tp30) cc_final: 0.7393 (tp30) REVERT: A 1187 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7720 (mm) REVERT: A 1350 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 1703 MET cc_start: 0.7875 (mmm) cc_final: 0.6707 (ttt) REVERT: A 1823 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8607 (mp) REVERT: A 1851 PHE cc_start: 0.3504 (m-80) cc_final: 0.3126 (m-80) REVERT: A 1995 TRP cc_start: 0.5287 (m-90) cc_final: 0.4883 (m-90) REVERT: A 2055 MET cc_start: 0.0619 (mmt) cc_final: 0.0179 (mmm) REVERT: C 186 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7667 (t0) REVERT: C 189 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8254 (pp) REVERT: C 200 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7913 (p) REVERT: C 276 ASP cc_start: 0.6343 (t0) cc_final: 0.6041 (t0) REVERT: C 391 MET cc_start: 0.8946 (ttm) cc_final: 0.8482 (ttm) REVERT: C 719 MET cc_start: 0.7900 (tpp) cc_final: 0.7287 (tpp) REVERT: C 741 MET cc_start: 0.6564 (mmm) cc_final: 0.6324 (mmm) REVERT: C 834 MET cc_start: 0.7352 (mmm) cc_final: 0.6968 (tpp) REVERT: C 927 MET cc_start: 0.7560 (tpp) cc_final: 0.7174 (tpt) REVERT: C 968 MET cc_start: 0.8631 (mmm) cc_final: 0.8416 (mmm) REVERT: O 334 TRP cc_start: 0.8124 (m100) cc_final: 0.7901 (m100) REVERT: Q 238 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.5848 (pp) REVERT: R 199 MET cc_start: 0.7691 (mmm) cc_final: 0.7324 (mmm) REVERT: R 217 GLU cc_start: 0.6784 (mp0) cc_final: 0.6464 (mm-30) REVERT: R 252 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.6681 (t70) REVERT: T 134 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6602 (tpt170) REVERT: Z 73 ILE cc_start: 0.2811 (OUTLIER) cc_final: 0.2517 (mt) REVERT: Z 193 SER cc_start: 0.7663 (m) cc_final: 0.7459 (t) REVERT: Z 345 ILE cc_start: 0.8637 (tp) cc_final: 0.8391 (tp) REVERT: c 91 MET cc_start: 0.7068 (mmt) cc_final: 0.6290 (mtt) REVERT: I 197 ASN cc_start: 0.7723 (p0) cc_final: 0.7316 (p0) REVERT: n 227 ASP cc_start: 0.7011 (p0) cc_final: 0.6630 (p0) REVERT: H 82 LEU cc_start: 0.6453 (mt) cc_final: 0.6208 (pp) REVERT: v 386 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.3199 (mm-30) REVERT: v 411 TRP cc_start: 0.6576 (OUTLIER) cc_final: 0.6230 (t-100) REVERT: v 730 GLN cc_start: 0.4456 (mm-40) cc_final: 0.4192 (mt0) REVERT: m 16 THR cc_start: 0.5591 (t) cc_final: 0.5353 (t) REVERT: j 46 ILE cc_start: 0.8047 (mm) cc_final: 0.7618 (tp) REVERT: g 11 HIS cc_start: 0.3361 (p-80) cc_final: 0.2646 (t70) REVERT: l 21 LEU cc_start: 0.7423 (pp) cc_final: 0.7198 (pp) REVERT: l 84 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6558 (m-10) REVERT: w 54 ASN cc_start: 0.5073 (m-40) cc_final: 0.4531 (p0) REVERT: y 22 GLU cc_start: 0.1058 (mp0) cc_final: 0.0853 (mp0) REVERT: y 30 ARG cc_start: 0.4560 (ptt180) cc_final: 0.3139 (mtm180) REVERT: y 38 ASP cc_start: 0.6722 (p0) cc_final: 0.6353 (p0) REVERT: y 40 MET cc_start: 0.2625 (mmm) cc_final: 0.1095 (mmt) REVERT: z 1 MET cc_start: 0.5671 (tpt) cc_final: 0.5418 (tpt) REVERT: r 126 LEU cc_start: 0.1529 (mm) cc_final: 0.0399 (pp) outliers start: 215 outliers final: 182 residues processed: 742 average time/residue: 0.6747 time to fit residues: 908.8748 Evaluate side-chains 733 residues out of total 8149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 536 time to evaluate : 6.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1548 GLN Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1823 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1956 ILE Chi-restraints excluded: chain A residue 2005 PHE Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 818 TYR Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain O residue 182 VAL Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 262 LEU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 404 CYS Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 161 ASN Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 280 VAL Chi-restraints excluded: chain Q residue 282 LEU Chi-restraints excluded: chain Q residue 306 THR Chi-restraints excluded: chain R residue 34 TYR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 210 LYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 HIS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 116 ASN Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain Z residue 16 GLU Chi-restraints excluded: chain Z residue 73 ILE Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 158 CYS Chi-restraints excluded: chain Z residue 198 PHE Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain c residue 504 PRO Chi-restraints excluded: chain c residue 505 PRO Chi-restraints excluded: chain c residue 506 THR Chi-restraints excluded: chain c residue 532 PRO Chi-restraints excluded: chain c residue 550 PRO Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 201 THR Chi-restraints excluded: chain d residue 245 LYS Chi-restraints excluded: chain d residue 284 LEU Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 159 PRO Chi-restraints excluded: chain n residue 162 PRO Chi-restraints excluded: chain n residue 257 PRO Chi-restraints excluded: chain n residue 260 PRO Chi-restraints excluded: chain n residue 292 HIS Chi-restraints excluded: chain n residue 327 PRO Chi-restraints excluded: chain n residue 340 PRO Chi-restraints excluded: chain n residue 373 PRO Chi-restraints excluded: chain n residue 424 PRO Chi-restraints excluded: chain n residue 436 PRO Chi-restraints excluded: chain n residue 443 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain v residue 386 GLU Chi-restraints excluded: chain v residue 411 TRP Chi-restraints excluded: chain v residue 440 VAL Chi-restraints excluded: chain v residue 445 SER Chi-restraints excluded: chain v residue 525 TYR Chi-restraints excluded: chain v residue 532 ILE Chi-restraints excluded: chain v residue 676 ILE Chi-restraints excluded: chain t residue 13 PRO Chi-restraints excluded: chain t residue 77 PRO Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain t residue 96 PRO Chi-restraints excluded: chain t residue 105 PRO Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain t residue 111 VAL Chi-restraints excluded: chain t residue 133 PRO Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 81 SER Chi-restraints excluded: chain m residue 95 ILE Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 86 ILE Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 104 SER Chi-restraints excluded: chain e residue 92 SER Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain s residue 6 VAL Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain l residue 64 VAL Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 84 PHE Chi-restraints excluded: chain i residue 22 GLN Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain x residue 34 ILE Chi-restraints excluded: chain y residue 56 VAL Chi-restraints excluded: chain z residue 60 ILE Chi-restraints excluded: chain r residue 17 PRO Chi-restraints excluded: chain r residue 44 PRO Chi-restraints excluded: chain p residue 17 PRO Chi-restraints excluded: chain p residue 44 PRO Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 17 PRO Chi-restraints excluded: chain q residue 26 SER Chi-restraints excluded: chain q residue 44 PRO Chi-restraints excluded: chain o residue 17 PRO Chi-restraints excluded: chain o residue 44 PRO Chi-restraints excluded: chain o residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 933 random chunks: chunk 587 optimal weight: 10.0000 chunk 788 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 chunk 682 optimal weight: 40.0000 chunk 109 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 741 optimal weight: 50.0000 chunk 310 optimal weight: 2.9990 chunk 761 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 559 GLN ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN P 161 ASN Q 236 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 ASN ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.127491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.100432 restraints weight = 304911.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.097868 restraints weight = 215329.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.098556 restraints weight = 165935.392| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 81366 Z= 0.212 Angle : 0.645 14.648 112704 Z= 0.325 Chirality : 0.042 0.277 13433 Planarity : 0.004 0.057 12405 Dihedral : 18.142 178.681 17881 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 2.61 % Allowed : 18.44 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.09), residues: 8731 helix: 1.56 (0.08), residues: 4087 sheet: -0.61 (0.16), residues: 1010 loop : -1.38 (0.10), residues: 3634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP C 933 HIS 0.020 0.001 HIS A1888 PHE 0.026 0.002 PHE A1965 TYR 0.025 0.001 TYR d 267 ARG 0.008 0.000 ARG c 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17787.82 seconds wall clock time: 310 minutes 4.95 seconds (18604.95 seconds total)