Starting phenix.real_space_refine on Tue Apr 16 12:43:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd1_16566/04_2024/8cd1_16566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd1_16566/04_2024/8cd1_16566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd1_16566/04_2024/8cd1_16566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd1_16566/04_2024/8cd1_16566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd1_16566/04_2024/8cd1_16566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cd1_16566/04_2024/8cd1_16566.pdb" } resolution = 3.0 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= -0.008 sd= 0.894 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: 6 Type Number sf(0) Gaussians P 4603 5.49 5 Mg 171 5.21 5 S 144 5.16 5 C 72728 2.51 5 N 26945 2.21 5 O 40198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 92": "NH1" <-> "NH2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 144789 Number of models: 1 Model: "" Number of chains: 59 Chain: "2" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 423 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "4" Number of atoms: 376 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Conformer: "B" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} bond proxies already assigned to first conformer: 356 Chain: "5" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "6" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 303 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 61859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2883, 61859 Classifications: {'RNA': 2883} Modifications used: {'5*END': 1, 'rna2p_pur': 275, 'rna2p_pyr': 166, 'rna3p_pur': 1378, 'rna3p_pyr': 1064} Link IDs: {'rna2p': 441, 'rna3p': 2441} Chain breaks: 2 Chain: "B" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2555 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 51, 'rna3p_pyr': 51} Link IDs: {'rna2p': 17, 'rna3p': 102} Chain: "C" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2048 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 255} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1549 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 200} 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: "Dt" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain: "E" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1509 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1288 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "G" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1294 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 163} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 577 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "J" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1055 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 137} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Le" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 531 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "M" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1069 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "P" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "T" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 701 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "U" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "V" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1396 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 180} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'TRANS': 75} Chain: "X" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 473 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 58} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "a" Number of atoms: 32744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1526, 32744 Classifications: {'RNA': 1526} Modifications used: {'5*END': 1, 'rna2p_pur': 125, 'rna2p_pyr': 83, 'rna3p_pur': 747, 'rna3p_pyr': 571} Link IDs: {'rna2p': 208, 'rna3p': 1317} Chain: "b" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1821 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1627 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 198} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1603 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "e" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1145 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 853 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1190 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 148} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "h" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 982 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "i" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 765 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "k" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 838 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 107} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "m" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "n" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 777 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "o" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 686 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "p" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "q" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "r" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 566 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "s" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 635 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "t" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 654 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "u" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 519 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "v" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2262 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 258} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Unusual residues: {' MG': 150} Classifications: {'undetermined': 150} Link IDs: {None: 149} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' MG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG 4 41 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG 4 41 " occ=0.50 Time building chain proxies: 49.93, per 1000 atoms: 0.34 Number of scatterers: 144789 At special positions: 0 Unit cell: (247.796, 278.637, 257.367, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 4603 15.00 Mg 171 11.99 O 40198 8.00 N 26945 7.00 C 72728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS d 9 " - pdb=" SG CYS d 32 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.76 Conformation dependent library (CDL) restraints added in 5.9 seconds 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10804 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 73 sheets defined 34.6% alpha, 16.1% beta 1359 base pairs and 2200 stacking pairs defined. Time for finding SS restraints: 48.11 Creating SS restraints... Processing helix chain '2' and resid 9 through 17 removed outlier: 3.684A pdb=" N ARG 2 16 " --> pdb=" O ALA 2 12 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 2 17 " --> pdb=" O ARG 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 20 No H-bonds generated for 'chain '2' and resid 18 through 20' Processing helix chain '4' and resid 9 through 17 Processing helix chain '4' and resid 17 through 24 removed outlier: 4.173A pdb=" N THR 4 24 " --> pdb=" O ALA 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 38 Processing helix chain '5' and resid 7 through 14 Processing helix chain '5' and resid 36 through 42 Processing helix chain '5' and resid 50 through 61 removed outlier: 4.573A pdb=" N ALA 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG 5 56 " --> pdb=" O SER 5 52 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 34 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.239A pdb=" N SER C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 removed outlier: 4.117A pdb=" N THR C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 213' Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.599A pdb=" N VAL D 61 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 97 through 101 removed outlier: 4.290A pdb=" N LEU D 100 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 96 through 114 removed outlier: 3.599A pdb=" N ALA E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.966A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.564A pdb=" N LEU E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 199 removed outlier: 3.713A pdb=" N LYS E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS E 194 " --> pdb=" O SER E 190 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 Processing helix chain 'F' and resid 11 through 20 removed outlier: 3.628A pdb=" N LYS F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 removed outlier: 3.772A pdb=" N GLU F 27 " --> pdb=" O ASN F 24 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL F 28 " --> pdb=" O VAL F 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 28' Processing helix chain 'F' and resid 48 through 62 removed outlier: 4.137A pdb=" N ASN F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 100 removed outlier: 3.552A pdb=" N TYR F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 171 removed outlier: 3.574A pdb=" N GLY F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 7 Processing helix chain 'G' and resid 60 through 79 removed outlier: 3.758A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 43 through 50 removed outlier: 3.702A pdb=" N PHE H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 43 through 50' Processing helix chain 'H' and resid 50 through 73 removed outlier: 3.703A pdb=" N LYS H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU H 66 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLN H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 removed outlier: 3.899A pdb=" N VAL J 11 " --> pdb=" O PRO J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.991A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 69 removed outlier: 4.115A pdb=" N LYS J 68 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR J 69 " --> pdb=" O GLY J 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 65 through 69' Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.689A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 107 removed outlier: 3.827A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.534A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 removed outlier: 3.919A pdb=" N VAL K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER K 116 " --> pdb=" O MET K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.801A pdb=" N ARG L 41 " --> pdb=" O LEU L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 69 through 72 removed outlier: 3.534A pdb=" N MET L 72 " --> pdb=" O LEU L 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 69 through 72' Processing helix chain 'L' and resid 80 through 85 removed outlier: 4.024A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 98 removed outlier: 3.561A pdb=" N LEU L 95 " --> pdb=" O SER L 91 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'Le' and resid 55 through 64 Processing helix chain 'M' and resid 45 through 58 removed outlier: 3.862A pdb=" N VAL M 58 " --> pdb=" O LEU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 124 removed outlier: 3.593A pdb=" N LEU M 120 " --> pdb=" O GLU M 116 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.888A pdb=" N GLU N 30 " --> pdb=" O VAL N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 45 Processing helix chain 'N' and resid 47 through 55 removed outlier: 3.702A pdb=" N LEU N 51 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 68 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'O' and resid 3 through 23 removed outlier: 3.669A pdb=" N THR O 7 " --> pdb=" O VAL O 3 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA O 15 " --> pdb=" O ARG O 11 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 84 removed outlier: 3.866A pdb=" N ALA O 78 " --> pdb=" O GLY O 74 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU O 79 " --> pdb=" O GLN O 75 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 112 Processing helix chain 'P' and resid 5 through 14 removed outlier: 3.517A pdb=" N GLU P 10 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU P 12 " --> pdb=" O GLN P 8 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 103 removed outlier: 3.718A pdb=" N LEU P 101 " --> pdb=" O LEU P 98 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA P 103 " --> pdb=" O TYR P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 110 removed outlier: 3.666A pdb=" N ARG P 110 " --> pdb=" O LYS P 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 21 removed outlier: 3.893A pdb=" N ARG Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.587A pdb=" N SER Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 71 removed outlier: 4.466A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 removed outlier: 3.830A pdb=" N ALA Q 86 " --> pdb=" O GLY Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 101 removed outlier: 4.043A pdb=" N LEU Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.609A pdb=" N LYS Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.678A pdb=" N ALA S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.964A pdb=" N ASN S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 4.100A pdb=" N GLU S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 16 through 26 Processing helix chain 'T' and resid 38 through 50 removed outlier: 3.651A pdb=" N VAL T 46 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 25 removed outlier: 3.633A pdb=" N LEU V 22 " --> pdb=" O ALA V 18 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG V 23 " --> pdb=" O SER V 19 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG V 24 " --> pdb=" O ARG V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 56 removed outlier: 3.597A pdb=" N LEU V 53 " --> pdb=" O GLU V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 117 through 122 Processing helix chain 'V' and resid 173 through 178 Processing helix chain 'W' and resid 73 through 76 removed outlier: 4.229A pdb=" N GLY W 76 " --> pdb=" O GLY W 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 73 through 76' Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 63 through 74 removed outlier: 3.526A pdb=" N ARG X 74 " --> pdb=" O ASP X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 removed outlier: 3.544A pdb=" N GLU Y 7 " --> pdb=" O ASN Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 33 removed outlier: 4.073A pdb=" N LEU Y 18 " --> pdb=" O ASN Y 14 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY Y 19 " --> pdb=" O GLU Y 15 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU Y 20 " --> pdb=" O GLN Y 16 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ARG Y 22 " --> pdb=" O LEU Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 56 removed outlier: 4.010A pdb=" N SER Y 43 " --> pdb=" O SER Y 39 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG Y 47 " --> pdb=" O SER Y 43 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA Y 50 " --> pdb=" O LYS Y 46 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 27 removed outlier: 3.560A pdb=" N LYS Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 50 removed outlier: 3.873A pdb=" N ILE Z 47 " --> pdb=" O ASN Z 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.828A pdb=" N MET b 9 " --> pdb=" O ASN b 5 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.550A pdb=" N LYS b 29 " --> pdb=" O LYS b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 34 through 38 Processing helix chain 'b' and resid 45 through 62 removed outlier: 4.182A pdb=" N MET b 49 " --> pdb=" O LYS b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 83 Processing helix chain 'b' and resid 103 through 121 removed outlier: 3.518A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS b 112 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG b 113 " --> pdb=" O GLN b 109 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU b 114 " --> pdb=" O SER b 110 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU b 118 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR b 119 " --> pdb=" O ARG b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 148 removed outlier: 3.808A pdb=" N LEU b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP b 140 " --> pdb=" O MET b 136 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU b 142 " --> pdb=" O SER b 138 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS b 143 " --> pdb=" O ARG b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 180 removed outlier: 4.141A pdb=" N ILE b 173 " --> pdb=" O GLU b 169 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 237 removed outlier: 3.548A pdb=" N LEU b 214 " --> pdb=" O VAL b 210 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER b 216 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET b 217 " --> pdb=" O TYR b 213 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP b 233 " --> pdb=" O ALA b 229 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU b 234 " --> pdb=" O THR b 230 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL b 236 " --> pdb=" O ALA b 232 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 47 removed outlier: 3.524A pdb=" N ARG c 40 " --> pdb=" O ASP c 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU c 41 " --> pdb=" O LEU c 37 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 4.021A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 95 removed outlier: 3.744A pdb=" N LYS c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR c 92 " --> pdb=" O ARG c 88 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS c 93 " --> pdb=" O GLN c 89 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN c 94 " --> pdb=" O ASP c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 111 Processing helix chain 'c' and resid 112 through 126 Processing helix chain 'c' and resid 131 through 144 removed outlier: 4.230A pdb=" N ILE c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 3.711A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.883A pdb=" N TYR d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 82 Processing helix chain 'd' and resid 85 through 96 Processing helix chain 'd' and resid 97 through 106 Processing helix chain 'd' and resid 110 through 120 Processing helix chain 'd' and resid 152 through 161 removed outlier: 3.571A pdb=" N LEU d 159 " --> pdb=" O ILE d 155 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU d 161 " --> pdb=" O GLN d 157 " (cutoff:3.500A) Processing helix chain 'd' and resid 162 through 165 Processing helix chain 'd' and resid 196 through 204 removed outlier: 4.412A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR d 204 " --> pdb=" O ILE d 200 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 69 Processing helix chain 'e' and resid 110 through 119 removed outlier: 3.946A pdb=" N ALA e 114 " --> pdb=" O GLY e 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 146 removed outlier: 3.957A pdb=" N VAL e 138 " --> pdb=" O PRO e 134 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N TYR e 139 " --> pdb=" O VAL e 135 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA e 140 " --> pdb=" O ASN e 136 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 16 removed outlier: 4.673A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 33 removed outlier: 3.730A pdb=" N GLU f 23 " --> pdb=" O GLY f 19 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 80 removed outlier: 4.034A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 106 Processing helix chain 'g' and resid 21 through 31 removed outlier: 3.844A pdb=" N LYS g 25 " --> pdb=" O GLN g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.586A pdb=" N ARG g 41 " --> pdb=" O ALA g 37 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS g 49 " --> pdb=" O GLY g 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.634A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 94 through 110 removed outlier: 4.419A pdb=" N ALA g 98 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL g 105 " --> pdb=" O MET g 101 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 128 removed outlier: 3.781A pdb=" N ARG g 119 " --> pdb=" O SER g 115 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU g 120 " --> pdb=" O MET g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 Processing helix chain 'g' and resid 149 through 152 Processing helix chain 'h' and resid 5 through 20 removed outlier: 3.662A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.737A pdb=" N ALA h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 113 through 120 Processing helix chain 'i' and resid 35 through 39 Processing helix chain 'i' and resid 43 through 55 removed outlier: 3.522A pdb=" N ARG i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 91 Processing helix chain 'i' and resid 94 through 102 Processing helix chain 'j' and resid 14 through 31 removed outlier: 3.591A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN j 23 " --> pdb=" O ASP j 19 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU j 24 " --> pdb=" O GLN j 20 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 87 Processing helix chain 'j' and resid 87 through 92 removed outlier: 3.666A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 74 removed outlier: 3.726A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 75 through 78 Processing helix chain 'k' and resid 94 through 99 Processing helix chain 'k' and resid 100 through 104 Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'm' and resid 14 through 21 removed outlier: 4.000A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 38 Processing helix chain 'm' and resid 52 through 61 Processing helix chain 'm' and resid 65 through 82 removed outlier: 3.983A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.746A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 21 removed outlier: 3.624A pdb=" N LYS n 12 " --> pdb=" O ASN n 8 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR n 20 " --> pdb=" O THR n 16 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.549A pdb=" N ASN n 43 " --> pdb=" O GLU n 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA n 44 " --> pdb=" O GLU n 40 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA n 47 " --> pdb=" O ASN n 43 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 90 removed outlier: 3.623A pdb=" N GLU n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 15 Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.596A pdb=" N ALA o 30 " --> pdb=" O GLU o 26 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS o 44 " --> pdb=" O GLN o 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA o 45 " --> pdb=" O ASP o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.158A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.578A pdb=" N ARG o 84 " --> pdb=" O ALA o 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 62 Processing helix chain 'p' and resid 68 through 77 removed outlier: 3.925A pdb=" N GLN p 73 " --> pdb=" O GLU p 69 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 11 removed outlier: 3.530A pdb=" N LYS r 9 " --> pdb=" O PHE r 5 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE r 10 " --> pdb=" O ARG r 6 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS r 11 " --> pdb=" O ARG r 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 5 through 11' Processing helix chain 'r' and resid 13 through 15 No H-bonds generated for 'chain 'r' and resid 13 through 15' Processing helix chain 'r' and resid 25 through 30 Processing helix chain 'r' and resid 31 through 33 No H-bonds generated for 'chain 'r' and resid 31 through 33' Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.893A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 65 Processing helix chain 's' and resid 4 through 8 removed outlier: 3.581A pdb=" N GLY s 8 " --> pdb=" O LEU s 5 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 25 removed outlier: 3.591A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 removed outlier: 3.885A pdb=" N VAL s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 63 through 67 removed outlier: 4.167A pdb=" N VAL s 67 " --> pdb=" O GLU s 64 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 removed outlier: 3.564A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 41 removed outlier: 3.721A pdb=" N GLU t 15 " --> pdb=" O ALA t 11 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS t 16 " --> pdb=" O LYS t 12 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 't' and resid 44 through 53 Processing helix chain 't' and resid 54 through 64 removed outlier: 3.579A pdb=" N LYS t 64 " --> pdb=" O ARG t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 84 removed outlier: 3.635A pdb=" N HIS t 75 " --> pdb=" O LYS t 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS t 76 " --> pdb=" O ALA t 72 " (cutoff:3.500A) Processing helix chain 't' and resid 85 through 87 No H-bonds generated for 'chain 't' and resid 85 through 87' Processing helix chain 'u' and resid 11 through 27 removed outlier: 3.517A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) Processing helix chain 'u' and resid 29 through 34 removed outlier: 3.601A pdb=" N ARG u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 66 removed outlier: 3.535A pdb=" N VAL u 60 " --> pdb=" O HIS u 56 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU u 63 " --> pdb=" O LYS u 59 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN u 64 " --> pdb=" O VAL u 60 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG u 65 " --> pdb=" O GLN u 61 " (cutoff:3.500A) Processing helix chain 'v' and resid 12 through 30 Processing helix chain 'v' and resid 33 through 37 removed outlier: 3.659A pdb=" N PHE v 37 " --> pdb=" O ARG v 34 " (cutoff:3.500A) Processing helix chain 'v' and resid 125 through 131 Processing helix chain 'v' and resid 132 through 136 removed outlier: 3.639A pdb=" N ARG v 136 " --> pdb=" O TRP v 133 " (cutoff:3.500A) Processing helix chain 'v' and resid 158 through 163 Processing helix chain 'v' and resid 186 through 194 Processing helix chain 'v' and resid 211 through 222 Processing helix chain 'v' and resid 222 through 228 Processing helix chain 'v' and resid 243 through 254 Processing helix chain 'v' and resid 260 through 274 Processing sheet with id=AA1, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain '5' and resid 15 through 17 removed outlier: 3.810A pdb=" N GLY 5 20 " --> pdb=" O THR 5 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '6' and resid 14 through 19 Processing sheet with id=AA4, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.514A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.664A pdb=" N VAL C 184 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG C 270 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS C 183 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE C 268 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 16 removed outlier: 5.417A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE D 177 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLN D 105 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 81 through 84 removed outlier: 4.443A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL D 35 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.304A pdb=" N LEU E 146 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR E 188 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL E 148 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 145 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ARG E 169 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 147 " --> pdb=" O ARG E 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 90 through 91 removed outlier: 6.742A pdb=" N THR F 157 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE F 34 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'G' and resid 16 through 17 Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'G' and resid 122 through 127 removed outlier: 7.127A pdb=" N ASP G 130 " --> pdb=" O PRO G 126 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL G 90 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.808A pdb=" N VAL G 113 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.913A pdb=" N VAL H 19 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL H 3 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.454A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 76 through 77 Processing sheet with id=AC1, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.669A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ALA K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP K 9 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU K 86 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 69 through 70 removed outlier: 6.326A pdb=" N ALA P 59 " --> pdb=" O LYS P 51 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS P 51 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR P 61 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 74 through 78 removed outlier: 3.832A pdb=" N MET L 111 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL L 108 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 121 through 122 Processing sheet with id=AC5, first strand: chain 'Le' and resid 10 through 15 Processing sheet with id=AC6, first strand: chain 'M' and resid 63 through 66 removed outlier: 3.640A pdb=" N GLU M 107 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL M 102 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA M 36 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR M 104 " --> pdb=" O LEU M 34 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 40 through 42 removed outlier: 4.133A pdb=" N TYR M 92 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.216A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 48 through 51 removed outlier: 3.676A pdb=" N TYR O 30 " --> pdb=" O TYR O 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 38 through 45 removed outlier: 3.715A pdb=" N GLU P 35 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER P 84 " --> pdb=" O GLN P 30 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS P 32 " --> pdb=" O VAL P 82 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL P 82 " --> pdb=" O LYS P 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.902A pdb=" N ILE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR R 2 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.830A pdb=" N HIS R 83 " --> pdb=" O LYS R 76 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS R 76 " --> pdb=" O HIS R 83 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS R 85 " --> pdb=" O ILE R 74 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE R 74 " --> pdb=" O LYS R 85 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLN R 87 " --> pdb=" O VAL R 72 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL R 72 " --> pdb=" O GLN R 87 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS R 89 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP R 70 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN R 91 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG R 68 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL R 59 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 3 through 10 removed outlier: 3.560A pdb=" N GLY S 9 " --> pdb=" O CYS S 101 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS S 101 " --> pdb=" O GLY S 9 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR S 104 " --> pdb=" O VAL S 74 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD6, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.123A pdb=" N LYS T 32 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL T 30 " --> pdb=" O PRO T 13 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG T 56 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 66 through 69 Processing sheet with id=AD8, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.771A pdb=" N ARG U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL U 27 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL U 34 " --> pdb=" O LEU U 25 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AE1, first strand: chain 'U' and resid 82 through 86 removed outlier: 4.431A pdb=" N LYS U 85 " --> pdb=" O ILE U 92 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE U 92 " --> pdb=" O LYS U 85 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 5 through 7 removed outlier: 7.040A pdb=" N LEU V 6 " --> pdb=" O ASN V 67 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE V 94 " --> pdb=" O PRO V 30 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL V 32 " --> pdb=" O PHE V 94 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG V 96 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TYR V 34 " --> pdb=" O ARG V 96 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 104 through 107 Processing sheet with id=AE4, first strand: chain 'V' and resid 127 through 129 removed outlier: 6.565A pdb=" N VAL V 160 " --> pdb=" O VAL V 184 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 22 through 23 removed outlier: 6.755A pdb=" N LEU W 59 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 45 through 47 removed outlier: 4.082A pdb=" N ARG W 77 " --> pdb=" O LYS W 72 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 66 through 67 Processing sheet with id=AE8, first strand: chain 'X' and resid 13 through 16 removed outlier: 3.505A pdb=" N VAL X 13 " --> pdb=" O PHE X 29 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 37 through 39 Processing sheet with id=AF1, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.520A pdb=" N VAL Z 37 " --> pdb=" O VAL Z 4 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 31 through 33 Processing sheet with id=AF3, first strand: chain 'b' and resid 68 through 70 removed outlier: 6.422A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU b 161 " --> pdb=" O ILE b 184 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL b 183 " --> pdb=" O TYR b 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'c' and resid 20 through 21 removed outlier: 4.500A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP c 56 " --> pdb=" O THR c 67 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU c 104 " --> pdb=" O ILE c 68 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR c 70 " --> pdb=" O GLU c 104 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 165 through 166 removed outlier: 3.519A pdb=" N VAL c 153 " --> pdb=" O GLU c 166 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 165 through 166 removed outlier: 3.519A pdb=" N VAL c 153 " --> pdb=" O GLU c 166 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL c 198 " --> pdb=" O TYR c 187 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR c 187 " --> pdb=" O VAL c 198 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL c 200 " --> pdb=" O ALA c 185 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA c 185 " --> pdb=" O VAL c 200 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 123 through 124 Processing sheet with id=AF8, first strand: chain 'd' and resid 171 through 172 Processing sheet with id=AF9, first strand: chain 'e' and resid 13 through 25 removed outlier: 5.405A pdb=" N GLU e 14 " --> pdb=" O GLY e 41 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY e 41 " --> pdb=" O GLU e 14 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU e 16 " --> pdb=" O VAL e 39 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL e 39 " --> pdb=" O LEU e 16 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN e 18 " --> pdb=" O LEU e 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR e 35 " --> pdb=" O ASN e 20 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 86 through 89 Processing sheet with id=AG2, first strand: chain 'f' and resid 35 through 46 removed outlier: 6.022A pdb=" N ILE f 36 " --> pdb=" O GLU f 65 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU f 65 " --> pdb=" O ILE f 36 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG f 44 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA f 57 " --> pdb=" O ARG f 44 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS f 58 " --> pdb=" O VAL f 10 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 73 through 74 Processing sheet with id=AG4, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.587A pdb=" N MET h 27 " --> pdb=" O LEU h 59 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER h 60 " --> pdb=" O PHE h 49 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE h 49 " --> pdb=" O SER h 60 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU h 62 " --> pdb=" O ALA h 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'h' and resid 86 through 87 removed outlier: 6.040A pdb=" N VAL h 125 " --> pdb=" O SER h 105 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER h 105 " --> pdb=" O VAL h 125 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS h 127 " --> pdb=" O ILE h 103 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'i' and resid 6 through 11 removed outlier: 6.240A pdb=" N SER i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL i 67 " --> pdb=" O SER i 29 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'j' and resid 40 through 41 Processing sheet with id=AG8, first strand: chain 'j' and resid 45 through 47 removed outlier: 3.594A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR j 69 " --> pdb=" O ARG j 45 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 50 through 51 removed outlier: 3.825A pdb=" N ASP j 63 " --> pdb=" O VAL j 51 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'k' and resid 43 through 46 removed outlier: 3.536A pdb=" N SER k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU k 82 " --> pdb=" O ALA k 108 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE k 110 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL k 84 " --> pdb=" O ILE k 110 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASP k 112 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL k 86 " --> pdb=" O ASP k 112 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'l' and resid 62 through 66 removed outlier: 3.671A pdb=" N CYS l 53 " --> pdb=" O SER l 65 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'p' and resid 9 through 11 removed outlier: 3.665A pdb=" N SER p 11 " --> pdb=" O ARG p 14 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR p 17 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE p 38 " --> pdb=" O TYR p 17 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU p 19 " --> pdb=" O ILE p 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU p 34 " --> pdb=" O VAL p 21 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'p' and resid 9 through 11 removed outlier: 3.665A pdb=" N SER p 11 " --> pdb=" O ARG p 14 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL p 2 " --> pdb=" O GLN p 66 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'q' and resid 11 through 17 removed outlier: 6.659A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LYS q 74 " --> pdb=" O LYS q 46 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N HIS q 48 " --> pdb=" O LYS q 74 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TRP q 76 " --> pdb=" O HIS q 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU q 78 " --> pdb=" O HIS q 50 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALA q 75 " --> pdb=" O THR q 67 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR q 63 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE q 81 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU q 61 " --> pdb=" O ILE q 81 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 's' and resid 31 through 33 removed outlier: 6.411A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR s 33 " --> pdb=" O HIS s 52 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'v' and resid 100 through 102 removed outlier: 6.709A pdb=" N VAL v 84 " --> pdb=" O VAL v 75 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL v 75 " --> pdb=" O VAL v 84 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE v 86 " --> pdb=" O LEU v 73 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR v 41 " --> pdb=" O VAL v 72 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG v 42 " --> pdb=" O VAL v 110 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY v 108 " --> pdb=" O ILE v 44 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU v 46 " --> pdb=" O CYS v 106 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N CYS v 106 " --> pdb=" O GLU v 46 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'v' and resid 141 through 144 removed outlier: 4.092A pdb=" N VAL v 171 " --> pdb=" O TRP v 144 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'v' and resid 181 through 184 removed outlier: 7.625A pdb=" N SER v 236 " --> pdb=" O LEU v 232 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU v 232 " --> pdb=" O SER v 236 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'v' and resid 209 through 210 removed outlier: 4.564A pdb=" N LEU v 209 " --> pdb=" O THR v 259 " (cutoff:3.500A) 1573 hydrogen bonds defined for protein. 4407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3455 hydrogen bonds 5614 hydrogen bond angles 0 basepair planarities 1359 basepair parallelities 2200 stacking parallelities Total time for adding SS restraints: 229.46 Time building geometry restraints manager: 60.60 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: 14489 1.32 - 1.44: 69065 1.44 - 1.56: 64099 1.56 - 1.69: 9202 1.69 - 1.81: 247 Bond restraints: 157102 Sorted by residual: bond pdb=" C ARG r 12 " pdb=" N PHE r 13 " ideal model delta sigma weight residual 1.332 1.379 -0.047 1.40e-02 5.10e+03 1.13e+01 bond pdb=" O4' G A1897 " pdb=" C1' G A1897 " ideal model delta sigma weight residual 1.412 1.365 0.047 1.50e-02 4.44e+03 9.80e+00 bond pdb=" C8 G A1897 " pdb=" N7 G A1897 " ideal model delta sigma weight residual 1.305 1.249 0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" CA ARG Y 6 " pdb=" C ARG Y 6 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.45e-02 4.76e+03 7.91e+00 bond pdb=" N GLN Y 12 " pdb=" CA GLN Y 12 " ideal model delta sigma weight residual 1.459 1.428 0.031 1.20e-02 6.94e+03 6.56e+00 ... (remaining 157097 not shown) Histogram of bond angle deviations from ideal: 31.82 - 53.13: 1 53.13 - 74.44: 0 74.44 - 95.75: 1 95.75 - 117.06: 142201 117.06 - 138.37: 92737 Bond angle restraints: 234940 Sorted by residual: angle pdb=" O ARG r 12 " pdb=" C ARG r 12 " pdb=" N PHE r 13 " ideal model delta sigma weight residual 123.00 31.82 91.18 1.60e+00 3.91e-01 3.25e+03 angle pdb=" C ARG r 12 " pdb=" N PHE r 13 " pdb=" CA PHE r 13 " ideal model delta sigma weight residual 121.54 104.98 16.56 1.91e+00 2.74e-01 7.51e+01 angle pdb=" O2' C A1895 " pdb=" C2' C A1895 " pdb=" C1' C A1895 " ideal model delta sigma weight residual 108.40 118.60 -10.20 1.50e+00 4.44e-01 4.62e+01 angle pdb=" C3' C A1895 " pdb=" C2' C A1895 " pdb=" O2' C A1895 " ideal model delta sigma weight residual 110.70 120.73 -10.03 1.50e+00 4.44e-01 4.48e+01 angle pdb=" N GLU Y 15 " pdb=" CA GLU Y 15 " pdb=" C GLU Y 15 " ideal model delta sigma weight residual 113.88 106.56 7.32 1.23e+00 6.61e-01 3.54e+01 ... (remaining 234935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 88631 35.97 - 71.94: 10495 71.94 - 107.90: 1224 107.90 - 143.87: 50 143.87 - 179.84: 83 Dihedral angle restraints: 100483 sinusoidal: 83692 harmonic: 16791 Sorted by residual: dihedral pdb=" C4' A B 34 " pdb=" C3' A B 34 " pdb=" C2' A B 34 " pdb=" C1' A B 34 " ideal model delta sinusoidal sigma weight residual -35.00 33.49 -68.49 1 8.00e+00 1.56e-02 9.50e+01 dihedral pdb=" C5' A B 34 " pdb=" C4' A B 34 " pdb=" C3' A B 34 " pdb=" O3' A B 34 " ideal model delta sinusoidal sigma weight residual 147.00 78.54 68.46 1 8.00e+00 1.56e-02 9.49e+01 dihedral pdb=" CA THR D 151 " pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual 180.00 132.82 47.18 0 5.00e+00 4.00e-02 8.91e+01 ... (remaining 100480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.907: 29984 0.907 - 1.814: 5 1.814 - 2.721: 0 2.721 - 3.628: 0 3.628 - 4.534: 1 Chirality restraints: 29990 Sorted by residual: chirality pdb=" C1' G A1897 " pdb=" O4' G A1897 " pdb=" C2' G A1897 " pdb=" N9 G A1897 " both_signs ideal model delta sigma weight residual False 2.46 -2.08 4.53 2.00e-01 2.50e+01 5.14e+02 chirality pdb=" CB VAL e 47 " pdb=" CA VAL e 47 " pdb=" CG1 VAL e 47 " pdb=" CG2 VAL e 47 " both_signs ideal model delta sigma weight residual False -2.63 -1.21 -1.42 2.00e-01 2.50e+01 5.03e+01 chirality pdb=" P UDt 47 " pdb=" OP1 UDt 47 " pdb=" OP2 UDt 47 " pdb=" O5' UDt 47 " both_signs ideal model delta sigma weight residual True 2.41 -1.29 1.12 2.00e-01 2.50e+01 3.16e+01 ... (remaining 29987 not shown) Planarity restraints: 12685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG r 12 " 0.083 2.00e-02 2.50e+03 2.31e-01 5.33e+02 pdb=" C ARG r 12 " -0.200 2.00e-02 2.50e+03 pdb=" O ARG r 12 " 0.341 2.00e-02 2.50e+03 pdb=" N PHE r 13 " -0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A2239 " 0.067 2.00e-02 2.50e+03 2.86e-02 2.45e+01 pdb=" N9 G A2239 " -0.065 2.00e-02 2.50e+03 pdb=" C8 G A2239 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A2239 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A2239 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A2239 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G A2239 " 0.021 2.00e-02 2.50e+03 pdb=" N1 G A2239 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G A2239 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G A2239 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A2239 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G A2239 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU Y 5 " 0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C LEU Y 5 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU Y 5 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG Y 6 " 0.023 2.00e-02 2.50e+03 ... (remaining 12682 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 45 1.99 - 2.72: 13725 2.72 - 3.45: 183975 3.45 - 4.17: 455404 4.17 - 4.90: 636975 Nonbonded interactions: 1290124 Sorted by model distance: nonbonded pdb=" C PHE r 10 " pdb=" N ARG r 12 " model vdw 1.265 3.350 nonbonded pdb=" O ARG r 12 " pdb=" CA PHE r 13 " model vdw 1.293 2.776 nonbonded pdb=" CA PHE r 10 " pdb=" N ARG r 12 " model vdw 1.360 3.550 nonbonded pdb=" O LYS r 9 " pdb=" CB ARG r 12 " model vdw 1.665 3.440 nonbonded pdb=" O PHE r 10 " pdb=" N ARG r 12 " model vdw 1.731 2.520 ... (remaining 1290119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 27.360 Check model and map are aligned: 1.380 Set scattering table: 0.900 Process input model: 481.330 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 531.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 157102 Z= 0.164 Angle : 0.662 91.184 234940 Z= 0.352 Chirality : 0.045 4.534 29990 Planarity : 0.005 0.231 12685 Dihedral : 23.382 179.841 89676 Min Nonbonded Distance : 1.265 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.29 % Rotamer: Outliers : 1.65 % Allowed : 5.05 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.11), residues: 5796 helix: -0.34 (0.12), residues: 1783 sheet: -1.27 (0.17), residues: 999 loop : -1.73 (0.11), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 213 HIS 0.010 0.001 HIS 5 30 PHE 0.012 0.001 PHE D 156 TYR 0.013 0.001 TYRLe 44 ARG 0.004 0.000 ARG M 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1835 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1757 time to evaluate : 6.054 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 2 35 GLU cc_start: 0.8219 (tt0) cc_final: 0.7591 (tt0) REVERT: 6 22 ILE cc_start: 0.8958 (mm) cc_final: 0.8706 (mp) REVERT: C 98 ASP cc_start: 0.6572 (p0) cc_final: 0.6228 (p0) REVERT: D 131 ASP cc_start: 0.8191 (m-30) cc_final: 0.7990 (m-30) REVERT: D 184 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7288 (mtp180) REVERT: E 155 ASN cc_start: 0.8925 (m-40) cc_final: 0.8718 (m-40) REVERT: E 175 ASP cc_start: 0.8426 (p0) cc_final: 0.8221 (p0) REVERT: F 24 ASN cc_start: 0.5540 (m-40) cc_final: 0.4764 (t0) REVERT: F 64 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8333 (tttt) REVERT: F 96 MET cc_start: 0.7826 (ttm) cc_final: 0.7484 (ttm) REVERT: J 45 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8832 (p) REVERT: J 73 MET cc_start: 0.8684 (mmm) cc_final: 0.8265 (mmm) REVERT: K 80 ASP cc_start: 0.8026 (p0) cc_final: 0.7754 (p0) REVERT: K 99 PHE cc_start: 0.8752 (m-10) cc_final: 0.8503 (m-10) REVERT: L 59 ARG cc_start: 0.8382 (mtp180) cc_final: 0.8043 (mmm-85) REVERT: Le 22 ILE cc_start: 0.7018 (mt) cc_final: 0.6478 (mt) REVERT: Le 25 ARG cc_start: 0.6872 (ttt-90) cc_final: 0.6508 (ttp80) REVERT: Le 27 THR cc_start: 0.7164 (p) cc_final: 0.6776 (p) REVERT: M 2 LEU cc_start: 0.8846 (mt) cc_final: 0.8557 (mt) REVERT: M 31 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6984 (tp30) REVERT: N 73 LYS cc_start: 0.7261 (mmtt) cc_final: 0.6165 (tmtt) REVERT: Q 9 ILE cc_start: 0.9117 (pp) cc_final: 0.8866 (mm) REVERT: Q 49 ASP cc_start: 0.8548 (m-30) cc_final: 0.8069 (m-30) REVERT: S 31 GLU cc_start: 0.7446 (pm20) cc_final: 0.7132 (pm20) REVERT: U 2 GLN cc_start: 0.8472 (pt0) cc_final: 0.8243 (pm20) REVERT: U 8 ASP cc_start: 0.7649 (m-30) cc_final: 0.7424 (m-30) REVERT: U 80 ASP cc_start: 0.8073 (t0) cc_final: 0.7836 (t0) REVERT: V 93 ASP cc_start: 0.7892 (t70) cc_final: 0.7647 (t0) REVERT: V 94 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7120 (p90) REVERT: V 146 PHE cc_start: 0.8264 (p90) cc_final: 0.7951 (p90) REVERT: W 11 ARG cc_start: 0.7202 (mmt180) cc_final: 0.6588 (mmm-85) REVERT: X 22 HIS cc_start: 0.8272 (m-70) cc_final: 0.8056 (t70) REVERT: Y 3 ASN cc_start: 0.8233 (p0) cc_final: 0.7286 (p0) REVERT: Y 9 SER cc_start: 0.6783 (OUTLIER) cc_final: 0.5980 (p) REVERT: Y 20 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7589 (tp) REVERT: b 65 ASN cc_start: 0.7686 (p0) cc_final: 0.7278 (m-40) REVERT: b 215 ASN cc_start: 0.7528 (m110) cc_final: 0.7172 (m-40) REVERT: d 206 LYS cc_start: 0.5814 (mttt) cc_final: 0.5201 (mmtt) REVERT: e 40 VAL cc_start: 0.8191 (t) cc_final: 0.7792 (p) REVERT: e 132 THR cc_start: 0.9258 (m) cc_final: 0.8904 (p) REVERT: e 148 MET cc_start: 0.8437 (mmt) cc_final: 0.8145 (mmm) REVERT: f 21 MET cc_start: 0.7218 (mtp) cc_final: 0.6915 (mtp) REVERT: f 77 ASN cc_start: 0.7876 (m-40) cc_final: 0.7594 (m110) REVERT: g 15 ASP cc_start: 0.5058 (t0) cc_final: 0.4349 (t0) REVERT: h 9 ASP cc_start: 0.8363 (t70) cc_final: 0.8016 (t0) REVERT: h 43 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7129 (mm-30) REVERT: i 47 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7220 (m) REVERT: j 49 PHE cc_start: 0.6494 (m-80) cc_final: 0.5851 (m-80) REVERT: m 54 ASP cc_start: 0.7631 (p0) cc_final: 0.7369 (p0) REVERT: m 83 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7631 (tp) REVERT: o 26 GLU cc_start: 0.8780 (mp0) cc_final: 0.8570 (mp0) REVERT: o 68 ASP cc_start: 0.8403 (m-30) cc_final: 0.8197 (m-30) REVERT: s 17 LYS cc_start: 0.8055 (pttt) cc_final: 0.7750 (tmmt) REVERT: s 18 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7733 (mtmm) REVERT: s 40 ILE cc_start: 0.8362 (pt) cc_final: 0.8149 (mp) REVERT: s 41 LEU cc_start: 0.8793 (mt) cc_final: 0.8516 (mm) REVERT: s 49 ILE cc_start: 0.8164 (mm) cc_final: 0.7804 (mp) REVERT: s 66 MET cc_start: 0.7552 (mtp) cc_final: 0.6874 (mtp) outliers start: 78 outliers final: 16 residues processed: 1797 average time/residue: 2.2579 time to fit residues: 5712.5057 Evaluate side-chains 965 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 942 time to evaluate : 5.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain d residue 157 GLN Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain m residue 71 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 259 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 865 optimal weight: 9.9990 chunk 776 optimal weight: 9.9990 chunk 431 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 chunk 524 optimal weight: 10.0000 chunk 415 optimal weight: 4.9990 chunk 803 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 10.0000 chunk 597 optimal weight: 10.0000 chunk 930 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 41 HIS 4 16 HIS 4 26 ASN ** 5 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 13 ASN 6 35 GLN C 153 GLN C 163 GLN C 261 ASN D 33 ASN D 65 GLN D 68 HIS D 89 GLN D 126 ASN D 130 GLN E 45 GLN E 61 GLN F 127 ASN G 7 ASN G 23 GLN G 111 HIS ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN J 58 ASN J 76 HIS J 77 HIS ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN L 2 GLN L 4 ASN L 54 GLN L 102 ASN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 HIS N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN P 8 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 HIS Q 37 GLN Q 44 GLN Q 66 ASN Q 72 ASN R 11 GLN R 66 HIS S 102 HIS U 44 HIS ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN ** V 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS V 129 HIS V 161 HIS Y 16 GLN Y 57 ASN Z 33 HIS ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 211 GLN c 6 HIS c 18 HIS c 44 GLN c 69 HIS c 122 GLN d 120 HIS e 98 GLN ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN f 81 ASN h 85 GLN i 126 GLN j 64 GLN k 85 ASN m 55 GLN m 91 HIS n 33 ASN n 45 GLN p 54 GLN p 73 GLN q 34 HIS ** r 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 52 HIS t 13 GLN t 68 HIS v 30 GLN v 98 ASN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.171 157102 Z= 0.641 Angle : 0.977 14.244 234940 Z= 0.492 Chirality : 0.058 4.092 29990 Planarity : 0.008 0.096 12685 Dihedral : 24.798 179.951 78383 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 7.99 % Allowed : 18.74 % Favored : 73.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.10), residues: 5796 helix: -0.40 (0.12), residues: 1847 sheet: -1.50 (0.16), residues: 1016 loop : -1.77 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP b 23 HIS 0.019 0.003 HIS N 16 PHE 0.045 0.004 PHE E 18 TYR 0.041 0.003 TYRLe 44 ARG 0.018 0.002 ARG E 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 977 time to evaluate : 6.190 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: 4 22 MET cc_start: 0.9173 (mmm) cc_final: 0.8790 (tpp) REVERT: 6 20 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7931 (t70) REVERT: 6 24 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8024 (mmm160) REVERT: C 199 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: D 165 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8917 (tt) REVERT: E 15 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6055 (tp30) REVERT: F 24 ASN cc_start: 0.6747 (m-40) cc_final: 0.6133 (t0) REVERT: G 34 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7309 (mt-10) REVERT: G 88 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: J 91 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8728 (mttp) REVERT: J 98 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: J 138 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: L 51 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: L 93 GLN cc_start: 0.8912 (tp40) cc_final: 0.8316 (tp-100) REVERT: L 143 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7529 (pp20) REVERT: Le 59 ARG cc_start: 0.7457 (tpm170) cc_final: 0.7109 (tpm170) REVERT: M 31 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7296 (tp30) REVERT: M 98 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8601 (mp10) REVERT: N 73 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7322 (tmtt) REVERT: O 107 ASP cc_start: 0.8916 (m-30) cc_final: 0.8256 (m-30) REVERT: P 14 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8089 (mtp) REVERT: Q 49 ASP cc_start: 0.8750 (m-30) cc_final: 0.8462 (m-30) REVERT: Q 51 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.6499 (mtm-85) REVERT: R 34 ASP cc_start: 0.8337 (t0) cc_final: 0.7719 (t0) REVERT: R 37 ARG cc_start: 0.8850 (mmm160) cc_final: 0.8494 (tpt-90) REVERT: R 58 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8746 (ttmm) REVERT: R 79 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8559 (ptp-170) REVERT: S 95 ARG cc_start: 0.8568 (ttm110) cc_final: 0.8363 (tpp-160) REVERT: U 8 ASP cc_start: 0.8282 (m-30) cc_final: 0.8004 (m-30) REVERT: U 50 MET cc_start: 0.4430 (OUTLIER) cc_final: 0.4162 (ppp) REVERT: V 91 HIS cc_start: 0.8883 (OUTLIER) cc_final: 0.8271 (t70) REVERT: V 93 ASP cc_start: 0.8322 (t70) cc_final: 0.8050 (t0) REVERT: V 101 HIS cc_start: 0.8309 (m90) cc_final: 0.7828 (m90) REVERT: W 11 ARG cc_start: 0.7611 (mmt180) cc_final: 0.6872 (mmm-85) REVERT: W 12 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8772 (p0) REVERT: W 17 GLU cc_start: 0.8383 (tp30) cc_final: 0.8182 (tp30) REVERT: X 72 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8161 (mtm-85) REVERT: Z 10 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7662 (mptp) REVERT: Z 36 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8051 (mm-30) REVERT: b 138 SER cc_start: 0.9496 (t) cc_final: 0.9160 (p) REVERT: b 226 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: c 83 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: d 206 LYS cc_start: 0.7002 (mttt) cc_final: 0.6448 (mptt) REVERT: e 148 MET cc_start: 0.8828 (mmt) cc_final: 0.8488 (mmm) REVERT: h 43 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7940 (mm-30) REVERT: i 96 SER cc_start: 0.8877 (p) cc_final: 0.8234 (p) REVERT: j 11 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6097 (mmtm) REVERT: k 122 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7745 (ptp-170) REVERT: l 54 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7323 (ttm110) REVERT: m 17 ILE cc_start: 0.9162 (mm) cc_final: 0.8938 (mp) REVERT: m 46 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7934 (mppt) REVERT: m 72 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: n 10 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8129 (tp30) REVERT: o 16 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8282 (ttpp) REVERT: p 13 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9075 (mmtm) REVERT: p 49 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7245 (ttm110) REVERT: q 31 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8597 (mtp-110) REVERT: q 46 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8806 (mtpt) outliers start: 378 outliers final: 149 residues processed: 1197 average time/residue: 2.1899 time to fit residues: 3806.8726 Evaluate side-chains 982 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 801 time to evaluate : 5.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 33 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 29 SER Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 20 ASP Chi-restraints excluded: chain 6 residue 24 ARG Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 90 LYS Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain Le residue 17 SER Chi-restraints excluded: chain Le residue 21 VAL Chi-restraints excluded: chain Le residue 33 HIS Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 20 ARG Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 50 MET Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 130 THR Chi-restraints excluded: chain V residue 186 ASN Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 52 SER Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 72 ARG Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 159 ASP Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain b residue 226 GLN Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 5 ARG Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 111 MET Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 54 ARG Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 46 LYS Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 71 ARG Chi-restraints excluded: chain m residue 72 GLU Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 49 ARG Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 28 ILE Chi-restraints excluded: chain q residue 31 ARG Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 46 LYS Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 59 ASP Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 110 VAL Chi-restraints excluded: chain v residue 168 VAL Chi-restraints excluded: chain v residue 259 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 517 optimal weight: 3.9990 chunk 288 optimal weight: 0.8980 chunk 774 optimal weight: 8.9990 chunk 633 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 932 optimal weight: 10.0000 chunk 1007 optimal weight: 5.9990 chunk 830 optimal weight: 6.9990 chunk 924 optimal weight: 0.8980 chunk 317 optimal weight: 8.9990 chunk 748 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 16 HIS 5 25 HIS 5 42 GLN ** 6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 244 HIS C 261 ASN D 126 ASN E 6 ASN E 45 GLN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN G 128 GLN H 14 ASN J 135 GLN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Le 20 ASN Le 62 GLN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN R 11 GLN U 48 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 HIS ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 GLN c 122 GLN e 74 GLN f 37 HIS f 46 GLN ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN l 77 HIS m 31 GLN m 58 ASN o 42 HIS o 46 ASN ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN v 102 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 157102 Z= 0.278 Angle : 0.636 13.114 234940 Z= 0.331 Chirality : 0.046 4.221 29990 Planarity : 0.005 0.095 12685 Dihedral : 24.470 179.978 78357 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 6.85 % Allowed : 21.96 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5796 helix: 0.20 (0.12), residues: 1834 sheet: -1.25 (0.16), residues: 1039 loop : -1.67 (0.11), residues: 2923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 23 HIS 0.009 0.001 HIS l 77 PHE 0.021 0.002 PHE b 56 TYR 0.019 0.002 TYR H 25 ARG 0.023 0.001 ARG m 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 921 time to evaluate : 5.587 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: 2 27 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9075 (mp) REVERT: 6 24 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7488 (mmm160) REVERT: C 18 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9080 (mtpt) REVERT: C 199 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: C 220 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.8965 (t) REVERT: D 165 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8844 (tt) REVERT: F 24 ASN cc_start: 0.7009 (m-40) cc_final: 0.6421 (t0) REVERT: G 34 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7227 (mt-10) REVERT: G 164 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7596 (p90) REVERT: J 91 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8852 (mttp) REVERT: J 138 GLN cc_start: 0.8454 (pm20) cc_final: 0.8182 (pm20) REVERT: K 91 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7601 (mm-40) REVERT: K 92 GLU cc_start: 0.7981 (mp0) cc_final: 0.7670 (mp0) REVERT: L 51 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: L 111 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.7624 (pmt) REVERT: L 143 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7742 (pp20) REVERT: Le 23 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8066 (mmmt) REVERT: Le 52 ASP cc_start: 0.3593 (OUTLIER) cc_final: 0.3171 (t70) REVERT: Le 59 ARG cc_start: 0.7469 (tpm170) cc_final: 0.7121 (tpm170) REVERT: M 31 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7333 (tp30) REVERT: M 98 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8514 (mp10) REVERT: N 73 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7107 (tmtt) REVERT: O 79 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7540 (pt0) REVERT: O 107 ASP cc_start: 0.8869 (m-30) cc_final: 0.8102 (m-30) REVERT: P 72 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7913 (mt-10) REVERT: Q 49 ASP cc_start: 0.8763 (m-30) cc_final: 0.8440 (m-30) REVERT: Q 51 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.6507 (mtm-85) REVERT: R 34 ASP cc_start: 0.8358 (t0) cc_final: 0.7676 (t0) REVERT: R 37 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8384 (tpt-90) REVERT: R 46 ASP cc_start: 0.8722 (t70) cc_final: 0.8453 (t70) REVERT: R 58 LYS cc_start: 0.9104 (mtpt) cc_final: 0.8768 (ttmm) REVERT: R 62 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8192 (pp20) REVERT: R 71 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8482 (tppp) REVERT: R 79 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8227 (ptp-170) REVERT: R 101 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9083 (mm) REVERT: S 59 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: U 8 ASP cc_start: 0.8113 (m-30) cc_final: 0.7777 (m-30) REVERT: V 93 ASP cc_start: 0.8122 (t70) cc_final: 0.7692 (t0) REVERT: V 94 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7552 (p90) REVERT: V 101 HIS cc_start: 0.8332 (m90) cc_final: 0.7807 (m90) REVERT: W 11 ARG cc_start: 0.7561 (mmt180) cc_final: 0.6781 (mmm-85) REVERT: W 70 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: X 22 HIS cc_start: 0.8491 (m-70) cc_final: 0.7738 (t70) REVERT: Z 10 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7537 (mptp) REVERT: b 6 MET cc_start: 0.7151 (mmm) cc_final: 0.6879 (mmt) REVERT: b 138 SER cc_start: 0.9476 (t) cc_final: 0.9121 (p) REVERT: b 226 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: c 83 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: c 131 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7780 (ttm110) REVERT: c 168 TYR cc_start: 0.7877 (m-80) cc_final: 0.7569 (m-80) REVERT: c 169 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8039 (tmt170) REVERT: d 206 LYS cc_start: 0.7001 (mttt) cc_final: 0.6389 (mptt) REVERT: e 142 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: e 148 MET cc_start: 0.8642 (mmt) cc_final: 0.8427 (mmm) REVERT: f 14 GLN cc_start: 0.9136 (mp10) cc_final: 0.8847 (mp10) REVERT: g 74 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7921 (pt0) REVERT: g 86 GLN cc_start: 0.7633 (mt0) cc_final: 0.7307 (mt0) REVERT: h 43 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7844 (mm-30) REVERT: h 96 ARG cc_start: 0.8575 (mtt90) cc_final: 0.8184 (mtt90) REVERT: i 62 ASP cc_start: 0.7686 (t70) cc_final: 0.7478 (t70) REVERT: i 96 SER cc_start: 0.8895 (p) cc_final: 0.8296 (p) REVERT: j 11 LYS cc_start: 0.6579 (mppt) cc_final: 0.6192 (mmtp) REVERT: j 15 HIS cc_start: 0.5313 (p-80) cc_final: 0.4338 (p90) REVERT: k 122 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.7971 (ptp-170) REVERT: m 91 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.7933 (t70) REVERT: p 49 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.6906 (ttm110) REVERT: q 14 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8359 (tpt-90) REVERT: q 19 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.8818 (mmmm) REVERT: s 13 LEU cc_start: 0.8630 (mm) cc_final: 0.8059 (pp) REVERT: s 17 LYS cc_start: 0.8415 (tmmt) cc_final: 0.8070 (pptt) REVERT: t 48 GLN cc_start: 0.8938 (mt0) cc_final: 0.8719 (mt0) outliers start: 324 outliers final: 132 residues processed: 1104 average time/residue: 2.0205 time to fit residues: 3246.0602 Evaluate side-chains 997 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 830 time to evaluate : 5.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 27 LEU Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 29 SER Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 24 ARG Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain Le residue 17 SER Chi-restraints excluded: chain Le residue 21 VAL Chi-restraints excluded: chain Le residue 23 LYS Chi-restraints excluded: chain Le residue 33 HIS Chi-restraints excluded: chain Le residue 52 ASP Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 52 SER Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain b residue 226 GLN Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 196 ASN Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 71 ARG Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 49 ARG Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 19 LYS Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 110 VAL Chi-restraints excluded: chain v residue 125 THR Chi-restraints excluded: chain v residue 158 TRP Chi-restraints excluded: chain v residue 259 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 921 optimal weight: 2.9990 chunk 701 optimal weight: 10.0000 chunk 483 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 445 optimal weight: 6.9990 chunk 626 optimal weight: 10.0000 chunk 935 optimal weight: 6.9990 chunk 990 optimal weight: 0.6980 chunk 488 optimal weight: 6.9990 chunk 886 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN D 126 ASN E 45 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN Le 20 ASN Le 62 GLN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN S 61 ASN T 14 HIS ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN b 51 ASN ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 74 GLN e 122 GLN f 46 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 4 GLN l 59 ASN l 75 GLN m 8 ASN m 31 GLN p 54 GLN r 54 GLN ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN v 56 ASN v 98 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 157102 Z= 0.361 Angle : 0.682 14.188 234940 Z= 0.354 Chirality : 0.047 4.152 29990 Planarity : 0.005 0.102 12685 Dihedral : 24.459 179.744 78354 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.27 % Favored : 92.63 % Rotamer: Outliers : 7.21 % Allowed : 22.95 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.11), residues: 5796 helix: 0.38 (0.12), residues: 1839 sheet: -1.23 (0.16), residues: 1018 loop : -1.65 (0.11), residues: 2939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP c 167 HIS 0.009 0.002 HIS 5 30 PHE 0.022 0.002 PHE c 130 TYR 0.020 0.002 TYR H 25 ARG 0.010 0.001 ARG r 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 883 time to evaluate : 6.123 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: 2 27 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9053 (mp) REVERT: 4 22 MET cc_start: 0.9121 (mmm) cc_final: 0.8851 (tpp) REVERT: 6 24 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7383 (mmm160) REVERT: C 18 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9075 (mtpt) REVERT: C 115 GLN cc_start: 0.8847 (pt0) cc_final: 0.8539 (pt0) REVERT: C 171 TYR cc_start: 0.8854 (m-80) cc_final: 0.8513 (m-80) REVERT: C 199 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: D 165 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8852 (tt) REVERT: G 34 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7516 (mt-10) REVERT: G 164 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7721 (p90) REVERT: J 10 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8869 (p) REVERT: J 91 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8745 (mttm) REVERT: J 118 MET cc_start: 0.8882 (mtt) cc_final: 0.8644 (mtt) REVERT: J 138 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: K 12 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: K 90 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8457 (ptmm) REVERT: K 92 GLU cc_start: 0.8040 (mp0) cc_final: 0.7718 (mp0) REVERT: L 51 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: L 59 ARG cc_start: 0.8499 (mtm180) cc_final: 0.8257 (mmm-85) REVERT: L 111 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.7441 (pmt) REVERT: Le 59 ARG cc_start: 0.7444 (tpm170) cc_final: 0.7207 (tpm170) REVERT: M 31 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7315 (tp30) REVERT: M 48 GLU cc_start: 0.8687 (tp30) cc_final: 0.8348 (tp30) REVERT: M 98 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8511 (mp10) REVERT: M 101 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8590 (tttp) REVERT: N 73 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7212 (tmtt) REVERT: O 35 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.8058 (p-80) REVERT: P 14 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7093 (mpp) REVERT: P 90 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7951 (ptm-80) REVERT: P 114 LYS cc_start: 0.2127 (OUTLIER) cc_final: 0.1238 (pttt) REVERT: Q 49 ASP cc_start: 0.8748 (m-30) cc_final: 0.8372 (m-30) REVERT: Q 51 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.6494 (mtm-85) REVERT: R 34 ASP cc_start: 0.8350 (t0) cc_final: 0.7421 (t0) REVERT: R 37 ARG cc_start: 0.8705 (mmm160) cc_final: 0.8405 (tpt-90) REVERT: R 46 ASP cc_start: 0.8678 (t70) cc_final: 0.8394 (t70) REVERT: R 58 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8834 (tttm) REVERT: R 71 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8615 (tppp) REVERT: R 79 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8273 (ptp-170) REVERT: R 101 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9174 (mm) REVERT: S 59 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: T 4 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: U 8 ASP cc_start: 0.8185 (m-30) cc_final: 0.7802 (m-30) REVERT: U 50 MET cc_start: 0.4975 (pp-130) cc_final: 0.4728 (ppp) REVERT: V 93 ASP cc_start: 0.8105 (t70) cc_final: 0.7693 (t0) REVERT: V 94 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7582 (p90) REVERT: V 101 HIS cc_start: 0.8302 (m90) cc_final: 0.7772 (m90) REVERT: W 11 ARG cc_start: 0.7652 (mmt180) cc_final: 0.6893 (mmm-85) REVERT: W 17 GLU cc_start: 0.8337 (tp30) cc_final: 0.8086 (tp30) REVERT: W 18 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8198 (p) REVERT: X 22 HIS cc_start: 0.8540 (m-70) cc_final: 0.7944 (m-70) REVERT: X 78 PHE cc_start: 0.6961 (m-80) cc_final: 0.6562 (m-80) REVERT: Z 10 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7648 (mptp) REVERT: b 138 SER cc_start: 0.9433 (t) cc_final: 0.9106 (p) REVERT: b 154 MET cc_start: 0.5077 (tpt) cc_final: 0.3418 (tpt) REVERT: b 226 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: c 83 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: c 94 GLN cc_start: 0.8096 (mt0) cc_final: 0.7718 (mm-40) REVERT: c 131 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.8028 (ttm110) REVERT: c 162 ILE cc_start: 0.8365 (mm) cc_final: 0.7775 (tt) REVERT: c 168 TYR cc_start: 0.7816 (m-80) cc_final: 0.7488 (m-80) REVERT: c 183 ASP cc_start: 0.8725 (t0) cc_final: 0.8463 (t70) REVERT: d 206 LYS cc_start: 0.6937 (mttt) cc_final: 0.6387 (mptt) REVERT: e 13 ILE cc_start: 0.8486 (mp) cc_final: 0.8239 (mt) REVERT: e 16 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8853 (tp) REVERT: e 142 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: g 74 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: h 43 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7877 (mm-30) REVERT: h 91 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8081 (mm-40) REVERT: i 96 SER cc_start: 0.8844 (p) cc_final: 0.8434 (p) REVERT: j 68 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6161 (mtm180) REVERT: k 122 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.7979 (ptp-170) REVERT: m 72 GLU cc_start: 0.8270 (pt0) cc_final: 0.8021 (pt0) REVERT: m 91 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.8146 (t70) REVERT: o 58 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8541 (ttt180) REVERT: p 49 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.6843 (ttm110) REVERT: q 14 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8423 (tpt-90) REVERT: q 29 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7941 (mm-30) REVERT: s 13 LEU cc_start: 0.8743 (mm) cc_final: 0.8194 (pp) outliers start: 341 outliers final: 161 residues processed: 1087 average time/residue: 2.0604 time to fit residues: 3252.3610 Evaluate side-chains 1021 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 819 time to evaluate : 6.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 27 LEU Chi-restraints excluded: chain 2 residue 33 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 29 SER Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 24 ARG Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 LYS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain Le residue 8 THR Chi-restraints excluded: chain Le residue 17 SER Chi-restraints excluded: chain Le residue 21 VAL Chi-restraints excluded: chain Le residue 33 HIS Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 20 ARG Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain P residue 114 LYS Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 4 GLU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 5 ARG Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 52 SER Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 49 MET Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain b residue 226 GLN Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 71 ARG Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 29 ASP Chi-restraints excluded: chain p residue 49 ARG Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 59 ASP Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 158 TRP Chi-restraints excluded: chain v residue 168 VAL Chi-restraints excluded: chain v residue 259 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 825 optimal weight: 2.9990 chunk 562 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 737 optimal weight: 10.0000 chunk 408 optimal weight: 5.9990 chunk 845 optimal weight: 10.0000 chunk 684 optimal weight: 10.0000 chunk 1 optimal weight: 0.2980 chunk 505 optimal weight: 5.9990 chunk 889 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 37 HIS ** 6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN E 45 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN L 55 GLN Le 20 ASN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN R 11 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN h 4 GLN l 59 ASN m 12 ASN m 31 GLN t 3 ASN t 48 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 157102 Z= 0.318 Angle : 0.640 12.679 234940 Z= 0.333 Chirality : 0.046 4.174 29990 Planarity : 0.005 0.101 12685 Dihedral : 24.399 179.705 78354 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.85 % Favored : 93.06 % Rotamer: Outliers : 7.23 % Allowed : 23.99 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.11), residues: 5796 helix: 0.53 (0.12), residues: 1844 sheet: -1.11 (0.16), residues: 985 loop : -1.65 (0.11), residues: 2967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP c 167 HIS 0.009 0.001 HIS 5 30 PHE 0.019 0.002 PHE v 162 TYR 0.019 0.002 TYR i 127 ARG 0.014 0.001 ARGLe 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 874 time to evaluate : 6.270 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: 2 27 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9068 (mp) REVERT: 6 24 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7485 (mmm160) REVERT: C 115 GLN cc_start: 0.8862 (pt0) cc_final: 0.8613 (pt0) REVERT: C 171 TYR cc_start: 0.8857 (m-80) cc_final: 0.8562 (m-80) REVERT: C 199 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: C 220 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8898 (t) REVERT: D 88 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8512 (pm20) REVERT: D 165 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8882 (tt) REVERT: E 39 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8311 (ptm160) REVERT: F 118 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8229 (p0) REVERT: G 34 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7772 (mt-10) REVERT: G 49 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6612 (pp20) REVERT: G 164 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7680 (p90) REVERT: J 10 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8902 (p) REVERT: J 91 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8760 (mttm) REVERT: J 118 MET cc_start: 0.8893 (mtt) cc_final: 0.8652 (mtt) REVERT: J 138 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: K 90 LYS cc_start: 0.8777 (ptmm) cc_final: 0.8254 (ptpp) REVERT: K 92 GLU cc_start: 0.8001 (mp0) cc_final: 0.7731 (mp0) REVERT: L 51 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: L 111 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.7426 (pmt) REVERT: Le 1 MET cc_start: 0.8815 (mmt) cc_final: 0.8395 (mmt) REVERT: M 31 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: M 79 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8379 (tp) REVERT: M 98 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8741 (pm20) REVERT: N 73 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7138 (tmtt) REVERT: P 14 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.6771 (mpp) REVERT: P 90 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7921 (ptm-80) REVERT: Q 49 ASP cc_start: 0.8768 (m-30) cc_final: 0.8476 (m-30) REVERT: Q 51 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.6500 (UNCLASSIFIED) REVERT: R 34 ASP cc_start: 0.8335 (t0) cc_final: 0.7428 (t0) REVERT: R 46 ASP cc_start: 0.8670 (t70) cc_final: 0.8375 (t70) REVERT: R 58 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8803 (tttm) REVERT: R 62 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8208 (pp20) REVERT: R 71 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8573 (tppp) REVERT: R 79 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8189 (ptp-170) REVERT: R 101 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9129 (mm) REVERT: S 59 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: T 4 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8249 (mt-10) REVERT: U 8 ASP cc_start: 0.8244 (m-30) cc_final: 0.7879 (m-30) REVERT: U 50 MET cc_start: 0.5120 (pp-130) cc_final: 0.4785 (ppp) REVERT: V 93 ASP cc_start: 0.8068 (t70) cc_final: 0.7631 (t0) REVERT: V 94 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7523 (p90) REVERT: W 11 ARG cc_start: 0.7626 (mmt180) cc_final: 0.6844 (mmm-85) REVERT: W 17 GLU cc_start: 0.8249 (tp30) cc_final: 0.7973 (tp30) REVERT: W 70 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8110 (pt0) REVERT: X 22 HIS cc_start: 0.8585 (m-70) cc_final: 0.7976 (m-70) REVERT: X 78 PHE cc_start: 0.6992 (m-80) cc_final: 0.6617 (m-80) REVERT: Z 10 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.7635 (mptp) REVERT: b 154 MET cc_start: 0.3702 (tpt) cc_final: 0.3111 (tpt) REVERT: b 226 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: c 83 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6840 (m-30) REVERT: c 94 GLN cc_start: 0.8096 (mt0) cc_final: 0.7821 (mm-40) REVERT: c 130 PHE cc_start: 0.8385 (p90) cc_final: 0.8062 (p90) REVERT: c 162 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7650 (tt) REVERT: c 169 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8123 (tmt170) REVERT: c 193 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7789 (p90) REVERT: d 206 LYS cc_start: 0.6953 (mttt) cc_final: 0.6407 (mptt) REVERT: e 16 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8930 (tp) REVERT: e 66 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: e 73 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8336 (pt) REVERT: e 142 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: f 27 LYS cc_start: 0.9026 (mptt) cc_final: 0.8567 (mmtt) REVERT: g 15 ASP cc_start: 0.5833 (t0) cc_final: 0.5244 (t70) REVERT: g 52 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7955 (pp20) REVERT: g 53 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7590 (mpp-170) REVERT: g 74 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: h 4 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7218 (mt0) REVERT: h 43 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7755 (mm-30) REVERT: h 91 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8112 (mm-40) REVERT: h 96 ARG cc_start: 0.8588 (mtt90) cc_final: 0.8379 (mtt90) REVERT: i 96 SER cc_start: 0.8795 (p) cc_final: 0.8441 (p) REVERT: j 15 HIS cc_start: 0.5432 (OUTLIER) cc_final: 0.4731 (p90) REVERT: k 18 ASP cc_start: 0.7044 (t70) cc_final: 0.6790 (t0) REVERT: k 37 ARG cc_start: 0.8586 (mmm160) cc_final: 0.8362 (mmm160) REVERT: k 122 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8025 (ptp-170) REVERT: l 103 ASP cc_start: 0.8846 (m-30) cc_final: 0.8605 (m-30) REVERT: m 91 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8150 (t70) REVERT: m 92 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6857 (ttp80) REVERT: o 7 GLU cc_start: 0.8370 (mp0) cc_final: 0.7975 (mp0) REVERT: o 58 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8530 (ttt180) REVERT: p 13 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.9031 (mmtm) REVERT: p 49 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.6794 (ttm110) REVERT: q 14 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8400 (tpt-90) REVERT: q 29 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7951 (mm-30) REVERT: q 43 ARG cc_start: 0.8232 (mmp80) cc_final: 0.8013 (mmp80) REVERT: q 58 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9026 (mp) REVERT: s 13 LEU cc_start: 0.8700 (mm) cc_final: 0.8195 (pp) REVERT: s 64 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6969 (tm-30) REVERT: t 4 THR cc_start: 0.8786 (p) cc_final: 0.8514 (t) REVERT: u 47 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: v 97 ARG cc_start: 0.6890 (tpp-160) cc_final: 0.6394 (tpp-160) outliers start: 342 outliers final: 166 residues processed: 1076 average time/residue: 1.9636 time to fit residues: 3074.0331 Evaluate side-chains 1047 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 827 time to evaluate : 6.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 27 LEU Chi-restraints excluded: chain 2 residue 33 THR Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 29 SER Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 24 ARG Chi-restraints excluded: chain 6 residue 37 GLN Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain Le residue 8 THR Chi-restraints excluded: chain Le residue 17 SER Chi-restraints excluded: chain Le residue 21 VAL Chi-restraints excluded: chain Le residue 33 HIS Chi-restraints excluded: chain Le residue 34 LEU Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 4 GLU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 5 ARG Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 52 SER Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain b residue 226 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain c residue 193 TYR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 66 GLU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 18 TYR Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 53 ARG Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 75 GLN Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 71 ARG Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 29 ASP Chi-restraints excluded: chain p residue 49 ARG Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 59 ASP Chi-restraints excluded: chain u residue 47 ARG Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 168 VAL Chi-restraints excluded: chain v residue 259 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 333 optimal weight: 10.0000 chunk 892 optimal weight: 0.2980 chunk 195 optimal weight: 6.9990 chunk 581 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 991 optimal weight: 8.9990 chunk 823 optimal weight: 6.9990 chunk 459 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 328 optimal weight: 2.9990 chunk 520 optimal weight: 4.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN E 45 GLN F 24 ASN F 63 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN L 55 GLN Le 20 ASN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 161 HIS Y 35 GLN Z 38 GLN b 5 ASN ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 72 GLN m 12 ASN m 31 GLN m 58 ASN n 14 GLN t 3 ASN t 48 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 157102 Z= 0.279 Angle : 0.622 13.737 234940 Z= 0.324 Chirality : 0.045 4.173 29990 Planarity : 0.005 0.101 12685 Dihedral : 24.355 179.961 78354 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.66 % Rotamer: Outliers : 7.10 % Allowed : 24.54 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 5796 helix: 0.67 (0.12), residues: 1844 sheet: -1.02 (0.16), residues: 979 loop : -1.61 (0.11), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 167 HIS 0.008 0.001 HIS 5 30 PHE 0.022 0.002 PHE v 162 TYR 0.016 0.002 TYR i 127 ARG 0.010 0.001 ARG c 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 867 time to evaluate : 6.124 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: 2 27 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9068 (mp) REVERT: 4 22 MET cc_start: 0.9060 (mmm) cc_final: 0.8793 (tpp) REVERT: 6 24 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7414 (mmm160) REVERT: C 115 GLN cc_start: 0.8854 (pt0) cc_final: 0.8529 (pt0) REVERT: C 171 TYR cc_start: 0.8840 (m-80) cc_final: 0.8577 (m-80) REVERT: C 199 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: C 219 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8487 (p) REVERT: C 220 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8957 (t) REVERT: C 271 ARG cc_start: 0.8714 (mmm160) cc_final: 0.8506 (tpt-90) REVERT: D 165 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8834 (tt) REVERT: E 4 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8299 (p0) REVERT: E 39 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8337 (ptm160) REVERT: F 118 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8248 (p0) REVERT: G 34 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7857 (mt-10) REVERT: G 115 TYR cc_start: 0.8821 (t80) cc_final: 0.8619 (t80) REVERT: G 164 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7664 (p90) REVERT: J 10 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8899 (p) REVERT: J 91 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8761 (mttm) REVERT: J 118 MET cc_start: 0.8935 (mtt) cc_final: 0.8637 (mtp) REVERT: J 138 GLN cc_start: 0.8424 (pm20) cc_final: 0.8083 (pm20) REVERT: L 51 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: L 59 ARG cc_start: 0.8555 (mtm180) cc_final: 0.8279 (mmm-85) REVERT: L 111 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.7451 (pmt) REVERT: L 136 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: Le 1 MET cc_start: 0.8805 (mmt) cc_final: 0.8417 (mmt) REVERT: M 31 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: M 48 GLU cc_start: 0.8594 (tp30) cc_final: 0.8288 (tp30) REVERT: M 98 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8579 (mp10) REVERT: N 73 LYS cc_start: 0.8423 (mmtt) cc_final: 0.7049 (tmtt) REVERT: P 90 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7898 (ptm-80) REVERT: Q 49 ASP cc_start: 0.8762 (m-30) cc_final: 0.8438 (m-30) REVERT: Q 51 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.6492 (UNCLASSIFIED) REVERT: R 34 ASP cc_start: 0.8375 (t0) cc_final: 0.7488 (t0) REVERT: R 46 ASP cc_start: 0.8681 (t70) cc_final: 0.8371 (t70) REVERT: R 58 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8829 (tttm) REVERT: R 62 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8219 (pp20) REVERT: R 71 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8592 (tppp) REVERT: R 79 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8193 (ptp-170) REVERT: S 59 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: T 56 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8540 (ptp90) REVERT: U 8 ASP cc_start: 0.8262 (m-30) cc_final: 0.7899 (m-30) REVERT: U 50 MET cc_start: 0.5083 (pp-130) cc_final: 0.4784 (ppp) REVERT: V 93 ASP cc_start: 0.8021 (t70) cc_final: 0.7566 (t0) REVERT: V 94 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7440 (p90) REVERT: W 11 ARG cc_start: 0.7629 (mmt180) cc_final: 0.6841 (mmm-85) REVERT: W 17 GLU cc_start: 0.8273 (tp30) cc_final: 0.7851 (tp30) REVERT: W 18 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8195 (p) REVERT: W 70 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: X 22 HIS cc_start: 0.8584 (m-70) cc_final: 0.7968 (m-70) REVERT: X 78 PHE cc_start: 0.6943 (m-80) cc_final: 0.6600 (m-80) REVERT: Z 10 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.7668 (mptp) REVERT: b 154 MET cc_start: 0.3893 (tpt) cc_final: 0.3161 (tpt) REVERT: b 226 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: c 83 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6738 (m-30) REVERT: c 94 GLN cc_start: 0.8056 (mt0) cc_final: 0.7786 (mm-40) REVERT: c 162 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.7969 (tt) REVERT: c 169 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8162 (tmt170) REVERT: c 193 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7840 (p90) REVERT: d 181 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8608 (p) REVERT: d 206 LYS cc_start: 0.6976 (mttt) cc_final: 0.6429 (mptt) REVERT: e 16 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8902 (tp) REVERT: e 73 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8285 (pt) REVERT: e 142 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: f 27 LYS cc_start: 0.9013 (mptt) cc_final: 0.8547 (mmtt) REVERT: g 15 ASP cc_start: 0.5793 (t0) cc_final: 0.4963 (t70) REVERT: g 53 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7747 (mtt180) REVERT: g 86 GLN cc_start: 0.8000 (mm110) cc_final: 0.7495 (mm-40) REVERT: h 43 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7722 (mm-30) REVERT: h 91 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8102 (mm-40) REVERT: h 96 ARG cc_start: 0.8515 (mtt90) cc_final: 0.8145 (mtt90) REVERT: i 62 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6912 (t70) REVERT: i 96 SER cc_start: 0.8707 (p) cc_final: 0.8417 (p) REVERT: j 15 HIS cc_start: 0.5237 (p90) cc_final: 0.4609 (p90) REVERT: j 68 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6276 (mmm160) REVERT: k 122 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8020 (ptp-170) REVERT: l 103 ASP cc_start: 0.8818 (m-30) cc_final: 0.8597 (m-30) REVERT: m 91 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8070 (t70) REVERT: m 92 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6815 (ttp80) REVERT: o 7 GLU cc_start: 0.8371 (mp0) cc_final: 0.7981 (mp0) REVERT: o 58 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8530 (ttt180) REVERT: p 49 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.6803 (ttm110) REVERT: q 14 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8379 (tpt-90) REVERT: q 29 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7960 (mm-30) REVERT: q 58 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.9004 (mp) REVERT: s 13 LEU cc_start: 0.8697 (mm) cc_final: 0.8212 (pp) REVERT: s 25 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7997 (pmtt) REVERT: s 56 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: t 4 THR cc_start: 0.8818 (p) cc_final: 0.8510 (t) outliers start: 336 outliers final: 174 residues processed: 1058 average time/residue: 1.8828 time to fit residues: 2906.8028 Evaluate side-chains 1048 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 825 time to evaluate : 5.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 27 LEU Chi-restraints excluded: chain 2 residue 33 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 29 SER Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 24 ARG Chi-restraints excluded: chain 6 residue 37 GLN Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 LYS Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain Le residue 8 THR Chi-restraints excluded: chain Le residue 17 SER Chi-restraints excluded: chain Le residue 21 VAL Chi-restraints excluded: chain Le residue 33 HIS Chi-restraints excluded: chain Le residue 34 LEU Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 5 ARG Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 52 SER Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 38 GLN Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 49 MET Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain b residue 226 GLN Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain c residue 193 TYR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 196 ASN Chi-restraints excluded: chain e residue 12 TYR Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 18 TYR Chi-restraints excluded: chain g residue 53 ARG Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 71 ARG Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 29 ASP Chi-restraints excluded: chain p residue 49 ARG Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 53 SER Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 25 LYS Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 56 GLN Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 110 VAL Chi-restraints excluded: chain v residue 168 VAL Chi-restraints excluded: chain v residue 259 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 956 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 565 optimal weight: 0.0000 chunk 724 optimal weight: 10.0000 chunk 561 optimal weight: 9.9990 chunk 834 optimal weight: 8.9990 chunk 553 optimal weight: 0.7980 chunk 987 optimal weight: 4.9990 chunk 618 optimal weight: 8.9990 chunk 602 optimal weight: 1.9990 chunk 456 optimal weight: 0.0870 overall best weight: 1.5766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN F 21 GLN F 24 ASN F 52 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN K 82 ASN L 55 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN U 2 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN Y 35 GLN Z 38 GLN ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 ASN ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 72 GLN l 59 ASN m 31 GLN n 14 GLN t 3 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 157102 Z= 0.164 Angle : 0.558 15.625 234940 Z= 0.290 Chirality : 0.042 4.140 29990 Planarity : 0.004 0.101 12685 Dihedral : 24.259 179.654 78354 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.42 % Favored : 93.53 % Rotamer: Outliers : 5.16 % Allowed : 27.05 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.11), residues: 5796 helix: 0.89 (0.12), residues: 1845 sheet: -0.80 (0.16), residues: 980 loop : -1.49 (0.11), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP c 167 HIS 0.008 0.001 HIS 5 30 PHE 0.025 0.001 PHE v 162 TYR 0.040 0.001 TYR i 90 ARG 0.011 0.000 ARG K 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 901 time to evaluate : 6.145 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 115 GLN cc_start: 0.8834 (pt0) cc_final: 0.8467 (pt0) REVERT: C 171 TYR cc_start: 0.8816 (m-80) cc_final: 0.8557 (m-80) REVERT: C 199 GLU cc_start: 0.8520 (pt0) cc_final: 0.8117 (pm20) REVERT: C 219 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8484 (p) REVERT: C 271 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8381 (tpt-90) REVERT: D 165 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8772 (tt) REVERT: F 118 ASN cc_start: 0.8648 (p0) cc_final: 0.8319 (p0) REVERT: G 34 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7757 (mt-10) REVERT: G 164 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7495 (p90) REVERT: J 118 MET cc_start: 0.8972 (mtt) cc_final: 0.8746 (mtp) REVERT: J 138 GLN cc_start: 0.8447 (pm20) cc_final: 0.8116 (pm20) REVERT: K 51 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8676 (mttt) REVERT: L 51 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: L 59 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8211 (mmm-85) REVERT: L 111 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.7589 (pmt) REVERT: Le 1 MET cc_start: 0.8783 (mmt) cc_final: 0.8401 (mmt) REVERT: M 31 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7251 (tp30) REVERT: M 48 GLU cc_start: 0.8561 (tp30) cc_final: 0.8241 (tp30) REVERT: M 98 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8394 (mp10) REVERT: N 73 LYS cc_start: 0.8389 (mmtt) cc_final: 0.6967 (tmtt) REVERT: O 75 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8135 (tm-30) REVERT: Q 49 ASP cc_start: 0.8740 (m-30) cc_final: 0.8447 (m-30) REVERT: R 34 ASP cc_start: 0.8386 (t0) cc_final: 0.8054 (t0) REVERT: R 58 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8854 (ttmm) REVERT: R 62 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: R 71 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8387 (tppp) REVERT: R 79 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7967 (ptp-170) REVERT: S 59 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: T 56 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8550 (ptp90) REVERT: U 8 ASP cc_start: 0.8147 (m-30) cc_final: 0.7877 (m-30) REVERT: U 41 ILE cc_start: 0.8281 (tp) cc_final: 0.8061 (pp) REVERT: U 50 MET cc_start: 0.5251 (OUTLIER) cc_final: 0.4962 (ppp) REVERT: V 93 ASP cc_start: 0.7934 (t70) cc_final: 0.7486 (t0) REVERT: V 94 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7599 (p90) REVERT: W 11 ARG cc_start: 0.7466 (mmt180) cc_final: 0.6912 (mmm-85) REVERT: W 17 GLU cc_start: 0.8202 (tp30) cc_final: 0.7719 (tp30) REVERT: W 70 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: X 22 HIS cc_start: 0.8523 (m-70) cc_final: 0.7885 (m-70) REVERT: X 78 PHE cc_start: 0.6865 (m-80) cc_final: 0.6586 (m-80) REVERT: Z 10 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.7561 (mptp) REVERT: b 154 MET cc_start: 0.3942 (tpt) cc_final: 0.3140 (tpt) REVERT: b 226 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7152 (mp10) REVERT: c 83 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: c 94 GLN cc_start: 0.8012 (mt0) cc_final: 0.7718 (mm-40) REVERT: c 162 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7883 (tt) REVERT: c 169 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8077 (tmt170) REVERT: d 181 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8599 (p) REVERT: d 206 LYS cc_start: 0.6847 (mttt) cc_final: 0.6284 (mptt) REVERT: e 16 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8962 (tp) REVERT: e 66 GLU cc_start: 0.8088 (mp0) cc_final: 0.7833 (mp0) REVERT: e 73 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8259 (pt) REVERT: e 142 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: g 15 ASP cc_start: 0.6191 (t0) cc_final: 0.5433 (t0) REVERT: g 53 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7754 (mtt180) REVERT: g 86 GLN cc_start: 0.8190 (mm110) cc_final: 0.7701 (mm-40) REVERT: h 91 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8088 (mm-40) REVERT: h 96 ARG cc_start: 0.8457 (mtt90) cc_final: 0.8105 (mtt90) REVERT: j 15 HIS cc_start: 0.5027 (p90) cc_final: 0.4347 (p90) REVERT: j 48 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7913 (mmt90) REVERT: j 68 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.6120 (mtm180) REVERT: j 71 LYS cc_start: 0.6468 (tmmm) cc_final: 0.5888 (pttt) REVERT: k 122 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8181 (ptp-170) REVERT: l 103 ASP cc_start: 0.8778 (m-30) cc_final: 0.8532 (m-30) REVERT: m 81 MET cc_start: 0.7601 (mtp) cc_final: 0.7369 (mtp) REVERT: m 91 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7973 (t70) REVERT: m 92 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6923 (ttt90) REVERT: o 7 GLU cc_start: 0.8419 (mp0) cc_final: 0.8004 (mp0) REVERT: o 58 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8519 (ttt180) REVERT: p 49 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.6753 (ttm110) REVERT: q 14 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8385 (tpt-90) REVERT: q 29 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7929 (mm-30) REVERT: q 43 ARG cc_start: 0.8250 (mmp80) cc_final: 0.7958 (mmp80) REVERT: q 84 ARG cc_start: 0.8088 (tmm160) cc_final: 0.7818 (tmm160) REVERT: r 25 ASP cc_start: 0.8664 (t0) cc_final: 0.8429 (t0) REVERT: s 13 LEU cc_start: 0.8670 (mm) cc_final: 0.8160 (pp) REVERT: s 25 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7972 (pmtt) REVERT: s 64 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6993 (tm-30) REVERT: t 4 THR cc_start: 0.8798 (p) cc_final: 0.8508 (t) outliers start: 244 outliers final: 122 residues processed: 1040 average time/residue: 1.9239 time to fit residues: 2927.2763 Evaluate side-chains 975 residues out of total 4829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 820 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 29 SER Chi-restraints excluded: chain 6 residue 37 GLN Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain Le residue 8 THR Chi-restraints excluded: chain Le residue 17 SER Chi-restraints excluded: chain Le residue 21 VAL Chi-restraints excluded: chain Le residue 33 HIS Chi-restraints excluded: chain Le residue 34 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 50 MET Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain b residue 226 GLN Chi-restraints excluded: chain c residue 56 ASP Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain e residue 12 TYR Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 53 ARG Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 71 ARG Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 49 ARG Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 25 LYS Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 41 LEU Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1025 random chunks: chunk 611 optimal weight: 2.9990 chunk 394 optimal weight: 9.9990 chunk 590 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 628 optimal weight: 10.0000 chunk 673 optimal weight: 8.9990 chunk 488 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 776 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: