Starting phenix.real_space_refine on Wed Mar 20 03:00:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spg_10285/03_2024/6spg_10285.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spg_10285/03_2024/6spg_10285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spg_10285/03_2024/6spg_10285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spg_10285/03_2024/6spg_10285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spg_10285/03_2024/6spg_10285.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spg_10285/03_2024/6spg_10285.pdb" } resolution = 3.34 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= 0.002 sd= 0.015 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 4524 5.49 5 Mg 172 5.21 5 S 137 5.16 5 C 71243 2.51 5 N 26435 2.21 5 O 39452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 38": "NH1" <-> "NH2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "g ARG 5": "NH1" <-> "NH2" Residue "k ARG 127": "NH1" <-> "NH2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "p ARG 5": "NH1" <-> "NH2" Residue "p ARG 31": "NH1" <-> "NH2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "r ARG 8": "NH1" <-> "NH2" Residue "u ARG 35": "NH1" <-> "NH2" Residue "u ARG 66": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 110": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "T ARG 76": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V ARG 21": "NH1" <-> "NH2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ARG 14": "NH1" <-> "NH2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 39": "NH1" <-> "NH2" Residue "W ARG 41": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 48": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "2 ARG 10": "NH1" <-> "NH2" Residue "2 ARG 16": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 51": "NH1" <-> "NH2" Residue "4 ARG 3": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 14": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "4 ARG 21": "NH1" <-> "NH2" Residue "4 ARG 33": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 ARG 41": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 141963 Number of models: 1 Model: "" Number of chains: 58 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: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1822 Classifications: {'peptide': 234} Modifications used: {'COO': 1} 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: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} 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: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 778 Classifications: {'peptide': 98} Modifications used: {'COO': 1} 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: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 556 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 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: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 655 Classifications: {'peptide': 85} Modifications used: {'COO': 1} 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} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain breaks: 1 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': 276, 'rna2p_pyr': 166, 'rna3p_pur': 1377, 'rna3p_pyr': 1064} Link IDs: {'rna2p': 442, 'rna3p': 2440} Chain breaks: 2 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2495 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 50} Link IDs: {'rna2p': 12, 'rna3p': 104} 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: "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: "I" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1026 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 130} 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: "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: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "V" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1397 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: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 574 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: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 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: "1" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} 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: "3" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 418 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' MG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 152 Unusual residues: {' MG': 152} Classifications: {'undetermined': 152} Link IDs: {None: 151} Chain: "B" 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} 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: 51.40, per 1000 atoms: 0.36 Number of scatterers: 141963 At special positions: 0 Unit cell: (270.6, 226.6, 253, 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 137 16.00 P 4524 15.00 Mg 172 11.99 O 39452 8.00 N 26435 7.00 C 71243 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: 52.16 Conformation dependent library (CDL) restraints added in 8.5 seconds 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10568 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 70 sheets defined 30.7% alpha, 15.2% beta 1189 base pairs and 2493 stacking pairs defined. Time for finding SS restraints: 47.87 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.823A pdb=" N MET b 9 " --> pdb=" O ASN b 5 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 34 through 38 removed outlier: 3.660A pdb=" N LYS b 37 " --> pdb=" O ALA b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 62 removed outlier: 3.882A pdb=" N MET b 49 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU b 54 " --> pdb=" O PHE b 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE b 56 " --> pdb=" O GLU b 52 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA b 62 " --> pdb=" O GLU b 58 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 83 Processing helix chain 'b' and resid 103 through 111 removed outlier: 3.562A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 121 removed outlier: 4.280A pdb=" N GLU b 118 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR b 119 " --> pdb=" O ARG b 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER b 121 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 139 removed outlier: 3.828A pdb=" N LEU b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 148 removed outlier: 3.974A pdb=" N LYS b 143 " --> pdb=" O ARG b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 178 Processing helix chain 'b' and resid 206 through 213 Processing helix chain 'b' and resid 214 through 232 removed outlier: 3.510A pdb=" N GLU b 219 " --> pdb=" O ASN b 215 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 47 removed outlier: 3.566A pdb=" N LEU c 33 " --> pdb=" O TYR c 29 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE c 34 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA c 35 " --> pdb=" O ASP c 31 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS c 38 " --> pdb=" O PHE c 34 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG c 40 " --> pdb=" O ASP c 36 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU c 41 " --> pdb=" O LEU c 37 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR c 42 " --> pdb=" O LYS c 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP c 45 " --> pdb=" O GLU c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 4.189A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 92 removed outlier: 3.719A pdb=" N ASP c 90 " --> pdb=" O LYS c 86 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR c 92 " --> pdb=" O ARG c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 111 Processing helix chain 'c' and resid 112 through 124 removed outlier: 3.795A pdb=" N SER c 119 " --> pdb=" O LEU c 115 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA c 121 " --> pdb=" O ALA c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 144 removed outlier: 4.031A pdb=" N ARG c 136 " --> pdb=" O ARG c 132 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN c 139 " --> pdb=" O LYS c 135 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA c 141 " --> pdb=" O ALA c 137 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 3.802A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.772A pdb=" N GLN d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY d 66 " --> pdb=" O ARG d 62 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 82 removed outlier: 3.615A pdb=" N GLY d 74 " --> pdb=" O ARG d 70 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG d 82 " --> pdb=" O GLU d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 96 removed outlier: 3.591A pdb=" N LEU d 94 " --> pdb=" O LEU d 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 106 removed outlier: 3.670A pdb=" N TYR d 103 " --> pdb=" O ASP d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 120 removed outlier: 3.791A pdb=" N SER d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN d 116 " --> pdb=" O SER d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 150 removed outlier: 3.848A pdb=" N LYS d 150 " --> pdb=" O GLU d 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 147 through 150' Processing helix chain 'd' and resid 152 through 159 removed outlier: 3.740A pdb=" N ALA d 158 " --> pdb=" O ARG d 154 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU d 159 " --> pdb=" O ILE d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 204 removed outlier: 3.541A pdb=" N TYR d 204 " --> pdb=" O ILE d 200 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 69 removed outlier: 4.143A pdb=" N GLN e 62 " --> pdb=" O PRO e 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG e 69 " --> pdb=" O MET e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 119 removed outlier: 3.846A pdb=" N VAL e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 146 removed outlier: 3.589A pdb=" N ALA e 140 " --> pdb=" O ASN e 136 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY e 144 " --> pdb=" O ALA e 140 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 16 removed outlier: 3.703A pdb=" N SER f 15 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 12 through 16' Processing helix chain 'f' and resid 17 through 33 removed outlier: 3.535A pdb=" N MET f 21 " --> pdb=" O GLN f 17 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU f 23 " --> pdb=" O GLY f 19 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR f 25 " --> pdb=" O MET f 21 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 78 removed outlier: 3.545A pdb=" N LEU f 71 " --> pdb=" O SER f 67 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA f 72 " --> pdb=" O ALA f 68 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP f 76 " --> pdb=" O ALA f 72 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 106 Processing helix chain 'g' and resid 21 through 29 removed outlier: 3.668A pdb=" N LYS g 25 " --> pdb=" O GLN g 21 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS g 29 " --> pdb=" O LYS g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 44 removed outlier: 3.675A pdb=" N ARG g 41 " --> pdb=" O ALA g 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE g 42 " --> pdb=" O VAL g 38 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 54 Processing helix chain 'g' and resid 57 through 67 removed outlier: 3.726A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 109 removed outlier: 3.565A pdb=" N LEU g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA g 100 " --> pdb=" O ARG g 96 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL g 105 " --> pdb=" O MET g 101 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP g 106 " --> pdb=" O ARG g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 127 removed outlier: 3.633A pdb=" N LEU g 120 " --> pdb=" O MET g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.744A pdb=" N VAL g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA g 145 " --> pdb=" O VAL g 141 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 152 Processing helix chain 'h' and resid 6 through 18 removed outlier: 3.535A pdb=" N LEU h 11 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR h 12 " --> pdb=" O ALA h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 32 through 44 removed outlier: 4.119A pdb=" N LYS h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 113 through 120 removed outlier: 3.693A pdb=" N ALA h 118 " --> pdb=" O ARG h 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 39 removed outlier: 3.572A pdb=" N PHE i 39 " --> pdb=" O LEU i 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 35 through 39' Processing helix chain 'i' and resid 43 through 48 removed outlier: 3.706A pdb=" N VAL i 47 " --> pdb=" O THR i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 55 Processing helix chain 'i' and resid 71 through 88 removed outlier: 3.798A pdb=" N ALA i 76 " --> pdb=" O VAL i 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY i 77 " --> pdb=" O SER i 73 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR i 84 " --> pdb=" O ARG i 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG i 85 " --> pdb=" O HIS i 81 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE i 88 " --> pdb=" O THR i 84 " (cutoff:3.500A) Processing helix chain 'i' and resid 95 through 100 Processing helix chain 'j' and resid 17 through 21 removed outlier: 3.614A pdb=" N SER j 21 " --> pdb=" O ILE j 18 " (cutoff:3.500A) Processing helix chain 'j' and resid 22 through 31 removed outlier: 4.327A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 87 removed outlier: 3.506A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 92 removed outlier: 3.650A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 59 removed outlier: 3.678A pdb=" N SER k 58 " --> pdb=" O SER k 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR k 59 " --> pdb=" O ARG k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 55 through 59' Processing helix chain 'k' and resid 61 through 71 removed outlier: 3.922A pdb=" N ALA k 67 " --> pdb=" O ALA k 63 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 removed outlier: 3.517A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 20 through 23 removed outlier: 3.726A pdb=" N TYR m 23 " --> pdb=" O THR m 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 20 through 23' Processing helix chain 'm' and resid 28 through 38 removed outlier: 3.612A pdb=" N SER m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS m 34 " --> pdb=" O ALA m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 52 through 61 removed outlier: 3.503A pdb=" N GLU m 59 " --> pdb=" O GLN m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 4.435A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.738A pdb=" N HIS m 91 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 10 removed outlier: 3.682A pdb=" N ARG n 9 " --> pdb=" O SER n 5 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 21 removed outlier: 3.506A pdb=" N LEU n 15 " --> pdb=" O LEU n 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR n 20 " --> pdb=" O THR n 16 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 32 removed outlier: 3.625A pdb=" N ILE n 31 " --> pdb=" O LEU n 27 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA n 32 " --> pdb=" O LYS n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 50 removed outlier: 3.651A pdb=" N ASN n 43 " --> pdb=" O GLU n 39 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA n 44 " --> pdb=" O GLU n 40 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA n 47 " --> pdb=" O ASN n 43 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN n 49 " --> pdb=" O GLN n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 60 Processing helix chain 'n' and resid 83 through 89 Processing helix chain 'o' and resid 4 through 15 removed outlier: 3.545A pdb=" N LYS o 8 " --> pdb=" O SER o 4 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE o 11 " --> pdb=" O GLU o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 40 removed outlier: 3.925A pdb=" N ALA o 30 " --> pdb=" O GLU o 26 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN o 35 " --> pdb=" O LEU o 31 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN o 37 " --> pdb=" O SER o 33 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS o 38 " --> pdb=" O ALA o 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU o 39 " --> pdb=" O ASN o 35 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 46 removed outlier: 3.610A pdb=" N ALA o 45 " --> pdb=" O ASP o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 72 removed outlier: 3.794A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE o 57 " --> pdb=" O ARG o 53 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG o 58 " --> pdb=" O ARG o 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP o 68 " --> pdb=" O ARG o 64 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.563A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG o 84 " --> pdb=" O ALA o 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 62 removed outlier: 3.800A pdb=" N ALA p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU p 61 " --> pdb=" O ALA p 57 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY p 62 " --> pdb=" O THR p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 75 Processing helix chain 'r' and resid 5 through 9 removed outlier: 3.568A pdb=" N ARG r 9 " --> pdb=" O PHE r 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 5 through 9' Processing helix chain 'r' and resid 10 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 48 through 65 removed outlier: 3.723A pdb=" N ARG r 53 " --> pdb=" O ALA r 49 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR r 57 " --> pdb=" O ARG r 53 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA r 58 " --> pdb=" O GLN r 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR r 64 " --> pdb=" O LYS r 60 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 25 removed outlier: 3.650A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 74 removed outlier: 3.626A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 40 removed outlier: 3.629A pdb=" N LYS t 12 " --> pdb=" O LYS t 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA t 14 " --> pdb=" O ARG t 10 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU t 15 " --> pdb=" O ALA t 11 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS t 16 " --> pdb=" O LYS t 12 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG t 17 " --> pdb=" O GLN t 13 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS t 20 " --> pdb=" O LYS t 16 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL t 28 " --> pdb=" O LEU t 24 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG t 29 " --> pdb=" O ARG t 25 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 4.431A pdb=" N VAL t 35 " --> pdb=" O TYR t 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP t 40 " --> pdb=" O VAL t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 53 removed outlier: 3.866A pdb=" N ALA t 47 " --> pdb=" O ASP t 43 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA t 53 " --> pdb=" O ALA t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 54 through 64 removed outlier: 3.606A pdb=" N ASP t 63 " --> pdb=" O ASP t 59 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS t 64 " --> pdb=" O ARG t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 84 removed outlier: 3.673A pdb=" N ARG t 74 " --> pdb=" O ASN t 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS t 75 " --> pdb=" O LYS t 71 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS t 76 " --> pdb=" O ALA t 72 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER t 77 " --> pdb=" O ALA t 73 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 4.033A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG u 21 " --> pdb=" O ARG u 17 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER u 22 " --> pdb=" O ARG u 18 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU u 24 " --> pdb=" O LYS u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 29 through 34 removed outlier: 3.686A pdb=" N ARG u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 57 removed outlier: 3.693A pdb=" N ARG u 47 " --> pdb=" O ALA u 43 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS u 48 " --> pdb=" O GLU u 44 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA u 52 " --> pdb=" O LYS u 48 " (cutoff:3.500A) Processing helix chain 'u' and resid 57 through 66 removed outlier: 4.278A pdb=" N GLU u 63 " --> pdb=" O LYS u 59 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN u 64 " --> pdb=" O VAL u 60 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG u 65 " --> pdb=" O GLN u 61 " (cutoff:3.500A) 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 207 through 211 removed outlier: 3.631A pdb=" N THR C 211 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.664A pdb=" N ILE C 268 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.732A pdb=" N ASP D 44 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.818A 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: 4.390A pdb=" N LEU D 100 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.550A pdb=" N TRP D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 37 removed outlier: 3.876A pdb=" N VAL E 27 " --> pdb=" O ASN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 114 removed outlier: 3.588A pdb=" N ARG E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 103 " --> pdb=" O MET E 99 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 104 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.689A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 159 removed outlier: 3.534A pdb=" N ALA E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.547A pdb=" N TYR E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 193 removed outlier: 4.091A pdb=" N LYS E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 189 through 193' Processing helix chain 'E' and resid 193 through 199 removed outlier: 4.073A pdb=" N GLU E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 removed outlier: 3.961A pdb=" N LYS F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 20 removed outlier: 3.638A pdb=" N LYS F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 removed outlier: 4.110A pdb=" N GLU F 27 " --> pdb=" O ASN F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.658A pdb=" N ASP F 46 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS F 47 " --> pdb=" O VAL F 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 43 through 47' Processing helix chain 'F' and resid 49 through 62 removed outlier: 4.006A pdb=" N LYS F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 100 removed outlier: 3.516A pdb=" N PHE F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 171 Processing helix chain 'G' and resid 60 through 79 removed outlier: 4.141A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.849A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 50 removed outlier: 3.697A pdb=" N PHE H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.530A 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 62 removed outlier: 3.966A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 37 removed outlier: 3.662A pdb=" N GLU I 37 " --> pdb=" O ASN I 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 34 through 37' Processing helix chain 'I' and resid 38 through 43 Processing helix chain 'I' and resid 80 through 85 removed outlier: 4.185A pdb=" N ALA I 84 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY I 85 " --> pdb=" O LYS I 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 80 through 85' Processing helix chain 'I' and resid 108 through 113 removed outlier: 3.778A pdb=" N LYS I 111 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR I 112 " --> pdb=" O ILE I 109 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS I 113 " --> pdb=" O ALA I 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 108 through 113' Processing helix chain 'I' and resid 122 through 130 Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.694A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 71 removed outlier: 3.602A pdb=" N THR J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP J 71 " --> pdb=" O LYS J 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 71' Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.951A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS J 95 " --> pdb=" O LYS J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 107 removed outlier: 3.625A pdb=" N THR J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL J 105 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 111 through 117 removed outlier: 3.996A pdb=" N VAL K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER K 116 " --> pdb=" O MET K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.915A pdb=" N SER L 40 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG L 41 " --> pdb=" O LEU L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 41' Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 80 through 85 removed outlier: 3.914A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 98 removed outlier: 3.995A pdb=" N LEU L 95 " --> pdb=" O SER L 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 136 Processing helix chain 'M' and resid 45 through 55 removed outlier: 3.611A pdb=" N ALA M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 123 removed outlier: 3.544A pdb=" N ALA M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.584A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL N 26 " --> pdb=" O GLN N 22 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU N 30 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 42 Processing helix chain 'N' and resid 43 through 47 removed outlier: 3.783A pdb=" N ARG N 46 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 55 removed outlier: 3.619A pdb=" N LEU N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 68 Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.532A pdb=" N VAL N 76 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 23 removed outlier: 3.613A pdb=" N THR O 7 " --> pdb=" O VAL O 3 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG O 13 " --> pdb=" O LEU O 9 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA O 15 " --> pdb=" O ARG O 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 82 removed outlier: 4.242A pdb=" N LYS O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA O 78 " --> pdb=" O GLY O 74 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU O 79 " --> pdb=" O GLN O 75 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 112 removed outlier: 3.501A pdb=" N LEU O 105 " --> pdb=" O ARG O 101 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 14 removed outlier: 3.557A pdb=" N ILE P 9 " --> pdb=" O ILE P 5 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU P 10 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU P 12 " --> pdb=" O GLN P 8 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET P 14 " --> pdb=" O GLU P 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 5 through 14' Processing helix chain 'P' and resid 98 through 102 removed outlier: 3.920A pdb=" N LEU P 101 " --> pdb=" O LEU P 98 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG P 102 " --> pdb=" O TYR P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 98 through 102' Processing helix chain 'Q' and resid 8 through 21 removed outlier: 3.824A pdb=" N ARG Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 removed outlier: 3.805A pdb=" N SER Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 Processing helix chain 'Q' and resid 36 through 71 removed outlier: 4.127A pdb=" N ALA Q 42 " --> pdb=" O ALA Q 38 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE Q 57 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU Q 60 " --> pdb=" O GLN Q 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA Q 67 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 84 removed outlier: 3.524A pdb=" N ALA Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 4.214A pdb=" N LYS Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 16 No H-bonds generated for 'chain 'S' and resid 14 through 16' Processing helix chain 'S' and resid 17 through 25 removed outlier: 3.722A pdb=" N ALA S 21 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 36 removed outlier: 3.547A pdb=" N LEU S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.966A pdb=" N GLU S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS S 49 " --> pdb=" O GLU S 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 21 removed outlier: 3.710A pdb=" N GLY T 21 " --> pdb=" O GLU T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 26 removed outlier: 3.521A pdb=" N GLY T 25 " --> pdb=" O GLY T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 50 removed outlier: 3.599A pdb=" N GLU T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 25 removed outlier: 3.768A pdb=" N LEU V 22 " --> pdb=" O ALA V 18 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG V 23 " --> pdb=" O SER V 19 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG V 24 " --> pdb=" O ARG V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 56 removed outlier: 3.553A pdb=" N LYS V 52 " --> pdb=" O ARG V 48 " (cutoff:3.500A) removed outlier: 3.674A 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: 3.802A 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 removed outlier: 3.639A pdb=" N ILE X 58 " --> pdb=" O LYS X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 73 removed outlier: 3.550A pdb=" N VAL X 67 " --> pdb=" O GLY X 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 removed outlier: 3.610A pdb=" N GLU Y 7 " --> pdb=" O ASN Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 34 removed outlier: 4.390A pdb=" N SER Y 19 " --> pdb=" O GLY Y 15 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU Y 21 " --> pdb=" O ASN Y 17 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG Y 23 " --> pdb=" O SER Y 19 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP Y 24 " --> pdb=" O HIS Y 20 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU Y 28 " --> pdb=" O ASP Y 24 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS Y 32 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 44 removed outlier: 4.065A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 39 through 44' Processing helix chain 'Y' and resid 46 through 57 removed outlier: 3.647A pdb=" N ALA Y 51 " --> pdb=" O LYS Y 47 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 27 removed outlier: 3.863A pdb=" N LYS Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 50 removed outlier: 3.694A pdb=" N ASN Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 13 Processing helix chain '2' and resid 9 through 15 Processing helix chain '2' and resid 16 through 19 removed outlier: 4.120A pdb=" N HIS 2 19 " --> pdb=" O ARG 2 16 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 16 through 19' Processing helix chain '4' and resid 9 through 17 removed outlier: 3.652A pdb=" N ARG 4 14 " --> pdb=" O LEU 4 10 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL 4 15 " --> pdb=" O LYS 4 11 " (cutoff:3.500A) Processing helix chain '4' and resid 17 through 22 Processing helix chain '4' and resid 26 through 38 removed outlier: 3.566A pdb=" N SER 4 32 " --> pdb=" O ARG 4 28 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY 4 38 " --> pdb=" O ARG 4 34 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 14 Processing helix chain '5' and resid 36 through 41 Processing helix chain '5' and resid 53 through 61 removed outlier: 4.060A pdb=" N ARG 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 34 removed outlier: 3.615A pdb=" N HIS 6 33 " --> pdb=" O GLU 6 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 31 through 33 removed outlier: 6.539A pdb=" N ILE b 40 " --> pdb=" O PHE b 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 68 through 69 removed outlier: 6.441A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU b 161 " --> pdb=" O ILE b 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'c' and resid 20 through 21 removed outlier: 4.434A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE c 66 " --> pdb=" O ASN c 102 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLU c 104 " --> pdb=" O ILE c 66 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE c 68 " --> pdb=" O GLU c 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 165 through 166 Processing sheet with id=AA5, first strand: chain 'c' and resid 165 through 166 removed outlier: 3.531A pdb=" N TYR c 187 " --> pdb=" O VAL c 198 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA c 185 " --> pdb=" O VAL c 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 123 through 124 Processing sheet with id=AA7, first strand: chain 'e' and resid 13 through 19 removed outlier: 6.736A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL e 19 " --> pdb=" O THR e 35 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR e 35 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 13 through 19 removed outlier: 6.736A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL e 19 " --> pdb=" O THR e 35 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR e 35 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'f' and resid 36 through 43 removed outlier: 3.825A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS f 58 " --> pdb=" O VAL f 10 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 73 through 74 Processing sheet with id=AB3, first strand: chain 'h' and resid 24 through 28 removed outlier: 6.335A pdb=" N SER h 60 " --> pdb=" O PHE h 49 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE h 49 " --> pdb=" O SER h 60 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU h 62 " --> pdb=" O ALA h 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 86 through 87 removed outlier: 6.109A pdb=" N VAL h 125 " --> pdb=" O SER h 105 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER h 105 " --> pdb=" O VAL h 125 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS h 127 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY h 109 " --> pdb=" O THR h 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 6 through 10 removed outlier: 3.657A pdb=" N GLY i 10 " --> pdb=" O ALA i 17 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL i 67 " --> pdb=" O SER i 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 40 through 41 Processing sheet with id=AB7, first strand: chain 'j' and resid 45 through 52 Processing sheet with id=AB8, first strand: chain 'k' and resid 41 through 46 removed outlier: 8.114A pdb=" N LEU k 82 " --> pdb=" O ALA k 108 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE k 110 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL k 84 " --> pdb=" O ILE k 110 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP k 112 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL k 86 " --> pdb=" O ASP k 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 62 through 66 removed outlier: 3.526A pdb=" N CYS l 53 " --> pdb=" O SER l 65 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG l 83 " --> pdb=" O HIS l 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'p' and resid 34 through 35 removed outlier: 3.693A pdb=" N GLU p 34 " --> pdb=" O VAL p 21 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL p 2 " --> pdb=" O GLN p 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'q' and resid 46 through 47 removed outlier: 3.619A pdb=" N LEU q 47 " --> pdb=" O VAL q 26 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL q 26 " --> pdb=" O LEU q 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU q 61 " --> pdb=" O ILE q 81 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE q 81 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR q 63 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG q 65 " --> pdb=" O THR q 77 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ALA q 75 " --> pdb=" O THR q 67 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU q 78 " --> pdb=" O HIS q 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 's' and resid 31 through 33 removed outlier: 6.523A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR s 33 " --> pdb=" O HIS s 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AC5, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AC6, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.930A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.625A pdb=" N VAL C 184 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 5 through 16 removed outlier: 5.889A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE D 177 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLN D 105 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AD1, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.455A pdb=" N LEU E 146 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N THR E 188 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N VAL E 148 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL E 145 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG E 169 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE E 147 " --> pdb=" O ARG E 169 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.735A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD4, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AD5, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AD6, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AD7, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AD9, first strand: chain 'I' and resid 12 through 14 removed outlier: 3.585A pdb=" N VAL I 13 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.699A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 76 through 77 Processing sheet with id=AE3, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.691A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ALA K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP K 9 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU K 86 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.675A pdb=" N ILE K 76 " --> pdb=" O THR P 74 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA P 59 " --> pdb=" O LYS P 51 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS P 51 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR P 61 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE P 65 " --> pdb=" O GLU P 45 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N GLU P 45 " --> pdb=" O ILE P 65 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG P 38 " --> pdb=" O GLU P 35 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU P 35 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN P 30 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER P 84 " --> pdb=" O GLN P 30 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS P 32 " --> pdb=" O VAL P 82 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL P 82 " --> pdb=" O LYS P 32 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 74 through 78 removed outlier: 6.486A pdb=" N VAL L 108 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 121 through 122 Processing sheet with id=AE7, first strand: chain 'M' and resid 63 through 66 removed outlier: 3.630A pdb=" N GLU M 107 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU M 34 " --> pdb=" O LEU M 103 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU M 105 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR M 32 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 40 through 42 removed outlier: 6.164A pdb=" N VAL M 90 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS M 76 " --> pdb=" O VAL M 90 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR M 92 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.236A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 48 through 52 removed outlier: 3.640A pdb=" N ALA O 50 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR O 30 " --> pdb=" O TYR O 37 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL O 25 " --> pdb=" O ALA O 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 2 through 5 removed outlier: 6.945A pdb=" N TYR R 2 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 19 through 22 removed outlier: 4.785A pdb=" N HIS R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN R 91 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP R 70 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE R 93 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG R 68 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU R 95 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N HIS R 66 " --> pdb=" O GLU R 95 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS R 97 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL R 64 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR R 99 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N GLU R 62 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE R 101 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR R 60 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.592A pdb=" N PHE S 75 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL S 71 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AF6, first strand: chain 'T' and resid 10 through 13 removed outlier: 4.322A pdb=" N GLY T 12 " --> pdb=" O LYS T 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL T 33 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG T 56 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 66 through 68 Processing sheet with id=AF8, first strand: chain 'U' and resid 10 through 12 removed outlier: 4.023A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 24 through 27 removed outlier: 3.614A pdb=" N LYS U 26 " --> pdb=" O VAL U 34 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 40 through 44 removed outlier: 3.710A pdb=" N VAL U 58 " --> pdb=" O ARG U 43 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 82 through 83 Processing sheet with id=AG3, first strand: chain 'V' and resid 5 through 7 removed outlier: 7.211A pdb=" N VAL V 6 " --> pdb=" O ASN V 67 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE V 94 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR V 34 " --> pdb=" O PHE V 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'V' and resid 104 through 107 Processing sheet with id=AG5, first strand: chain 'V' and resid 126 through 129 removed outlier: 3.667A pdb=" N ALA V 185 " --> pdb=" O VAL V 160 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 22 through 23 removed outlier: 3.830A pdb=" N GLY W 22 " --> pdb=" O ARG W 39 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU W 59 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 46 through 47 removed outlier: 3.679A pdb=" N ARG W 77 " --> pdb=" O LYS W 72 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 66 through 67 Processing sheet with id=AG9, first strand: chain 'X' and resid 13 through 16 removed outlier: 3.516A pdb=" N GLY X 15 " --> pdb=" O ARG X 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'X' and resid 37 through 39 Processing sheet with id=AH2, first strand: chain 'Z' and resid 3 through 7 removed outlier: 3.689A pdb=" N VAL Z 4 " --> pdb=" O VAL Z 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL Z 35 " --> pdb=" O VAL Z 6 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AH4, first strand: chain '3' and resid 3 through 8 Processing sheet with id=AH5, first strand: chain '3' and resid 33 through 36 removed outlier: 3.644A pdb=" N GLN 3 41 " --> pdb=" O ASP 3 36 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '5' and resid 15 through 17 removed outlier: 3.535A pdb=" N LYS 5 15 " --> pdb=" O LYS 5 22 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY 5 20 " --> pdb=" O THR 5 17 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '6' and resid 14 through 19 removed outlier: 3.551A pdb=" N ILE 6 26 " --> pdb=" O LYS 6 15 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2881 hydrogen bonds 4676 hydrogen bond angles 0 basepair planarities 1189 basepair parallelities 2493 stacking parallelities Total time for adding SS restraints: 206.49 Time building geometry restraints manager: 56.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 17948 1.32 - 1.45: 65461 1.45 - 1.57: 61343 1.57 - 1.69: 9046 1.69 - 1.82: 237 Bond restraints: 154035 Sorted by residual: bond pdb=" N LEU l 24 " pdb=" CA LEU l 24 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" N LEU 4 42 " pdb=" CA LEU 4 42 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.29e-02 6.01e+03 7.78e+00 bond pdb=" N LEU W 40 " pdb=" CA LEU W 40 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.54e+00 bond pdb=" N ARG D 154 " pdb=" CA ARG D 154 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.32e-02 5.74e+03 6.14e+00 bond pdb=" N ALA l 23 " pdb=" CA ALA l 23 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.34e-02 5.57e+03 5.36e+00 ... (remaining 154030 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.45: 22876 105.45 - 113.22: 92902 113.22 - 120.99: 70904 120.99 - 128.75: 39109 128.75 - 136.52: 4630 Bond angle restraints: 230421 Sorted by residual: angle pdb=" C LEU R 51 " pdb=" N PRO R 52 " pdb=" CA PRO R 52 " ideal model delta sigma weight residual 119.84 111.21 8.63 1.25e+00 6.40e-01 4.77e+01 angle pdb=" N SER C 196 " pdb=" CA SER C 196 " pdb=" C SER C 196 " ideal model delta sigma weight residual 110.97 118.22 -7.25 1.09e+00 8.42e-01 4.42e+01 angle pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta sigma weight residual 119.84 128.02 -8.18 1.25e+00 6.40e-01 4.28e+01 angle pdb=" N VAL Q 39 " pdb=" CA VAL Q 39 " pdb=" C VAL Q 39 " ideal model delta sigma weight residual 111.90 106.94 4.96 8.10e-01 1.52e+00 3.76e+01 angle pdb=" O3' G A2536 " pdb=" C3' G A2536 " pdb=" C2' G A2536 " ideal model delta sigma weight residual 113.70 121.63 -7.93 1.50e+00 4.44e-01 2.80e+01 ... (remaining 230416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 86847 35.89 - 71.78: 10362 71.78 - 107.68: 1220 107.68 - 143.57: 46 143.57 - 179.46: 74 Dihedral angle restraints: 98549 sinusoidal: 82122 harmonic: 16427 Sorted by residual: 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 49.90 130.10 0 5.00e+00 4.00e-02 6.77e+02 dihedral pdb=" CA LEU R 51 " pdb=" C LEU R 51 " pdb=" N PRO R 52 " pdb=" CA PRO R 52 " ideal model delta harmonic sigma weight residual 180.00 132.78 47.22 0 5.00e+00 4.00e-02 8.92e+01 dihedral pdb=" O4' U A1009 " pdb=" C1' U A1009 " pdb=" N1 U A1009 " pdb=" C2 U A1009 " ideal model delta sinusoidal sigma weight residual -160.00 13.79 -173.79 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 98546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 27340 0.086 - 0.173: 1951 0.173 - 0.259: 125 0.259 - 0.345: 30 0.345 - 0.432: 16 Chirality restraints: 29462 Sorted by residual: chirality pdb=" C3' C A2703 " pdb=" C4' C A2703 " pdb=" O3' C A2703 " pdb=" C2' C A2703 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" C1' G A 774 " pdb=" O4' G A 774 " pdb=" C2' G A 774 " pdb=" N9 G A 774 " both_signs ideal model delta sigma weight residual False 2.46 2.03 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C3' U A 953 " pdb=" C4' U A 953 " pdb=" O3' U A 953 " pdb=" C2' U A 953 " both_signs ideal model delta sigma weight residual False -2.48 -2.06 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 29459 not shown) Planarity restraints: 12404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 51 " 0.077 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO R 52 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO R 52 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO R 52 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE c 106 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ILE c 106 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE c 106 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG c 107 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO I 22 " 0.055 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO I 23 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO I 23 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO I 23 " 0.046 5.00e-02 4.00e+02 ... (remaining 12401 not shown) Histogram of nonbonded interaction distances: 0.51 - 1.39: 30 1.39 - 2.27: 215 2.27 - 3.15: 97726 3.15 - 4.02: 418878 4.02 - 4.90: 713615 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1230464 Sorted by model distance: nonbonded pdb=" N2 G A1897 " pdb=" C4 G A1909 " model vdw 0.514 3.340 nonbonded pdb=" C2 C A1896 " pdb=" C1' G A1897 " model vdw 0.610 3.690 nonbonded pdb=" CG ARG m 92 " pdb=" N3 C A 877 " model vdw 0.649 3.520 nonbonded pdb=" N1 G A1897 " pdb=" N1 G A1909 " model vdw 0.652 2.560 nonbonded pdb=" N3 A A 499 " pdb=" NH2 ARG S 80 " model vdw 0.717 2.600 ... (remaining 1230459 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: 2.740 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: 0.110 Extract box with map and model: 16.270 Check model and map are aligned: 1.360 Set scattering table: 0.860 Process input model: 454.420 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 481.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.007 0.075 154035 Z= 0.450 Angle : 0.908 13.427 230421 Z= 0.460 Chirality : 0.048 0.432 29462 Planarity : 0.006 0.118 12404 Dihedral : 23.439 179.462 87978 Min Nonbonded Distance : 0.514 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.58 % Favored : 91.38 % Rotamer: Outliers : 0.30 % Allowed : 3.41 % Favored : 96.29 % 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: -5.03 (0.08), residues: 5678 helix: -4.46 (0.06), residues: 1542 sheet: -2.54 (0.15), residues: 992 loop : -3.06 (0.09), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP C 213 HIS 0.018 0.003 HIS N 16 PHE 0.042 0.003 PHE 5 27 TYR 0.029 0.003 TYR P 99 ARG 0.021 0.001 ARG V 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1690 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1676 time to evaluate : 6.019 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 111 ILE cc_start: 0.7119 (tt) cc_final: 0.6810 (mm) REVERT: c 68 ILE cc_start: 0.8336 (mt) cc_final: 0.8108 (tt) REVERT: c 140 ASN cc_start: 0.6047 (m-40) cc_final: 0.5735 (t0) REVERT: e 69 ARG cc_start: 0.7238 (ptp90) cc_final: 0.6941 (ptp-170) REVERT: e 78 ASN cc_start: 0.7999 (t0) cc_final: 0.7689 (t0) REVERT: f 13 ASP cc_start: 0.7896 (m-30) cc_final: 0.7157 (p0) REVERT: f 36 ILE cc_start: 0.8486 (mp) cc_final: 0.8057 (mp) REVERT: f 42 TRP cc_start: 0.8097 (m-10) cc_final: 0.7783 (m-10) REVERT: i 46 MET cc_start: 0.3856 (mpp) cc_final: 0.3314 (mpp) REVERT: i 80 ARG cc_start: 0.7096 (ttp80) cc_final: 0.6582 (ttp-170) REVERT: k 47 SER cc_start: 0.9130 (m) cc_final: 0.8810 (m) REVERT: l 14 ARG cc_start: 0.7667 (tmt90) cc_final: 0.7418 (ttm170) REVERT: l 67 ILE cc_start: 0.8586 (mt) cc_final: 0.8337 (mt) REVERT: n 49 GLN cc_start: 0.6822 (mt0) cc_final: 0.6600 (mm-40) REVERT: o 12 VAL cc_start: 0.6883 (t) cc_final: 0.6651 (m) REVERT: t 20 HIS cc_start: 0.8343 (t70) cc_final: 0.8024 (t-170) REVERT: t 44 LEU cc_start: 0.6448 (tp) cc_final: 0.5574 (tt) REVERT: t 55 VAL cc_start: 0.8806 (t) cc_final: 0.8513 (m) REVERT: C 171 TYR cc_start: 0.7806 (m-10) cc_final: 0.7321 (m-80) REVERT: D 190 LYS cc_start: 0.8770 (tmtp) cc_final: 0.8430 (ttpt) REVERT: E 155 ASN cc_start: 0.8414 (m-40) cc_final: 0.7981 (m-40) REVERT: E 162 ASN cc_start: 0.8476 (t0) cc_final: 0.8177 (t0) REVERT: F 121 SER cc_start: 0.6556 (p) cc_final: 0.6337 (t) REVERT: F 146 ILE cc_start: 0.5903 (tp) cc_final: 0.5165 (tp) REVERT: F 149 LEU cc_start: 0.6439 (mp) cc_final: 0.6215 (tt) REVERT: F 155 THR cc_start: 0.7663 (m) cc_final: 0.7363 (p) REVERT: G 59 GLN cc_start: 0.7624 (mp-120) cc_final: 0.7390 (tm-30) REVERT: G 74 ASN cc_start: 0.8115 (m-40) cc_final: 0.7818 (m-40) REVERT: G 115 TYR cc_start: 0.7461 (t80) cc_final: 0.6599 (t80) REVERT: J 100 VAL cc_start: 0.9207 (t) cc_final: 0.8979 (m) REVERT: J 117 ASP cc_start: 0.7115 (m-30) cc_final: 0.6913 (m-30) REVERT: J 126 LYS cc_start: 0.8203 (ptmm) cc_final: 0.7890 (tptp) REVERT: K 38 ILE cc_start: 0.9166 (mm) cc_final: 0.8926 (mm) REVERT: K 47 ILE cc_start: 0.7197 (tp) cc_final: 0.6966 (mt) REVERT: L 142 PHE cc_start: 0.7411 (t80) cc_final: 0.7194 (t80) REVERT: M 13 MET cc_start: 0.8000 (mmt) cc_final: 0.7698 (mmt) REVERT: O 17 LEU cc_start: 0.8769 (tp) cc_final: 0.8295 (tp) REVERT: P 15 ASN cc_start: 0.5721 (m110) cc_final: 0.5183 (p0) REVERT: S 18 ARG cc_start: 0.8379 (mmt90) cc_final: 0.8179 (mmt90) REVERT: S 29 VAL cc_start: 0.8690 (m) cc_final: 0.8422 (t) REVERT: T 77 ASN cc_start: 0.8089 (t0) cc_final: 0.7730 (t0) REVERT: Y 58 ASN cc_start: 0.7723 (m-40) cc_final: 0.7411 (t0) REVERT: Z 40 THR cc_start: 0.8270 (p) cc_final: 0.7830 (p) REVERT: Z 42 GLU cc_start: 0.7827 (pm20) cc_final: 0.7398 (pm20) REVERT: 3 22 ASN cc_start: 0.8180 (t0) cc_final: 0.7934 (t0) outliers start: 14 outliers final: 10 residues processed: 1685 average time/residue: 1.3977 time to fit residues: 3908.8887 Evaluate side-chains 1048 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1038 time to evaluate : 5.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain 4 residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 850 optimal weight: 2.9990 chunk 763 optimal weight: 8.9990 chunk 423 optimal weight: 10.0000 chunk 260 optimal weight: 0.4980 chunk 514 optimal weight: 7.9990 chunk 407 optimal weight: 6.9990 chunk 789 optimal weight: 0.0000 chunk 305 optimal weight: 9.9990 chunk 479 optimal weight: 6.9990 chunk 587 optimal weight: 4.9990 chunk 914 optimal weight: 0.9980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 6 HIS d 100 ASN e 20 ASN e 98 GLN e 133 ASN ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS g 148 ASN j 70 HIS k 64 GLN k 81 ASN l 46 ASN l 77 HIS m 40 ASN ** n 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN q 54 ASN s 52 HIS ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 HIS D 33 ASN D 65 GLN D 132 ASN D 173 GLN E 6 ASN E 40 GLN E 45 GLN E 61 GLN E 91 HIS ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN G 23 GLN I 17 GLN I 19 ASN J 77 HIS J 138 GLN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 GLN U 44 HIS V 83 HIS V 110 HIS W 35 ASN W 46 HIS Y 20 HIS Y 58 ASN Z 43 ASN 4 26 ASN 5 42 GLN 6 13 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 154035 Z= 0.174 Angle : 0.658 22.466 230421 Z= 0.335 Chirality : 0.038 0.401 29462 Planarity : 0.005 0.075 12404 Dihedral : 24.272 179.522 76968 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.91 % Favored : 93.07 % Rotamer: Outliers : 2.80 % Allowed : 12.54 % Favored : 84.66 % 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: -3.95 (0.09), residues: 5678 helix: -2.97 (0.10), residues: 1593 sheet: -1.97 (0.16), residues: 940 loop : -2.68 (0.10), residues: 3145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 213 HIS 0.020 0.001 HIS l 77 PHE 0.019 0.002 PHE b 32 TYR 0.017 0.001 TYR o 69 ARG 0.022 0.001 ARG m 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1164 time to evaluate : 6.057 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 45 LYS cc_start: 0.6666 (tmmt) cc_final: 0.6297 (mtmt) REVERT: b 141 LEU cc_start: 0.5164 (OUTLIER) cc_final: 0.4772 (pt) REVERT: c 90 ASP cc_start: 0.6476 (m-30) cc_final: 0.6088 (m-30) REVERT: c 114 MET cc_start: 0.6705 (tpp) cc_final: 0.6494 (tpp) REVERT: d 123 ILE cc_start: 0.8652 (mm) cc_final: 0.8339 (mm) REVERT: d 178 LYS cc_start: 0.5732 (mmpt) cc_final: 0.5231 (mttm) REVERT: e 83 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7342 (mm110) REVERT: e 107 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.7460 (pt) REVERT: e 149 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8088 (mm-40) REVERT: h 19 MET cc_start: 0.6906 (mtp) cc_final: 0.6675 (mtp) REVERT: i 60 LYS cc_start: 0.6790 (ptmm) cc_final: 0.6575 (ptmm) REVERT: k 52 PHE cc_start: 0.7290 (m-80) cc_final: 0.6680 (m-80) REVERT: t 55 VAL cc_start: 0.8014 (t) cc_final: 0.7720 (t) REVERT: C 171 TYR cc_start: 0.7886 (m-10) cc_final: 0.7372 (m-80) REVERT: D 154 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7047 (ptt90) REVERT: E 60 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7717 (ptm160) REVERT: E 155 ASN cc_start: 0.8489 (m-40) cc_final: 0.8177 (t0) REVERT: E 162 ASN cc_start: 0.8514 (t0) cc_final: 0.8242 (t0) REVERT: F 88 LYS cc_start: 0.8045 (tmmm) cc_final: 0.7472 (ptmt) REVERT: F 94 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.5560 (p0) REVERT: F 146 ILE cc_start: 0.6050 (tp) cc_final: 0.5775 (tp) REVERT: G 59 GLN cc_start: 0.7614 (mp-120) cc_final: 0.7378 (tm-30) REVERT: G 74 ASN cc_start: 0.8084 (m-40) cc_final: 0.7453 (m110) REVERT: I 36 MET cc_start: 0.1438 (pmm) cc_final: 0.1039 (pmm) REVERT: K 47 ILE cc_start: 0.7431 (tp) cc_final: 0.7020 (mt) REVERT: K 90 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6650 (tmmt) REVERT: K 92 GLU cc_start: 0.6710 (pm20) cc_final: 0.6402 (pm20) REVERT: N 87 TYR cc_start: 0.8554 (m-10) cc_final: 0.8269 (m-80) REVERT: O 25 VAL cc_start: 0.7995 (t) cc_final: 0.7741 (m) REVERT: P 15 ASN cc_start: 0.5674 (m110) cc_final: 0.5388 (m110) REVERT: V 102 LYS cc_start: 0.6985 (tptm) cc_final: 0.6750 (tptp) REVERT: V 132 SER cc_start: 0.8186 (t) cc_final: 0.7972 (m) REVERT: W 78 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7613 (mttm) REVERT: W 79 TYR cc_start: 0.8287 (m-80) cc_final: 0.8073 (m-80) REVERT: X 56 MET cc_start: 0.7964 (mmt) cc_final: 0.7561 (mmt) REVERT: X 74 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6931 (mtp-110) REVERT: Y 30 MET cc_start: 0.8156 (mmm) cc_final: 0.7931 (mmt) REVERT: Y 58 ASN cc_start: 0.8089 (m110) cc_final: 0.7807 (t0) REVERT: Z 40 THR cc_start: 0.8089 (p) cc_final: 0.7646 (p) REVERT: Z 42 GLU cc_start: 0.7745 (pm20) cc_final: 0.7271 (pm20) REVERT: 4 43 THR cc_start: 0.7723 (t) cc_final: 0.7509 (t) outliers start: 129 outliers final: 73 residues processed: 1232 average time/residue: 1.3480 time to fit residues: 2866.5695 Evaluate side-chains 1079 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1001 time to evaluate : 6.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain c residue 58 HIS Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 155 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 107 ILE Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain p residue 61 LEU Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 52 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 90 LYS Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain 1 residue 16 CYS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 3 residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 508 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 761 optimal weight: 20.0000 chunk 622 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 916 optimal weight: 5.9990 chunk 989 optimal weight: 1.9990 chunk 815 optimal weight: 2.9990 chunk 908 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 734 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 HIS c 139 GLN e 122 GLN g 148 ASN i 5 GLN j 15 HIS l 5 ASN l 29 GLN l 72 HIS m 14 HIS ** n 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN D 173 GLN E 45 GLN I 12 GLN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 16 ASN Z 43 ASN 5 42 GLN 6 35 GLN 6 37 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 154035 Z= 0.283 Angle : 0.670 21.042 230421 Z= 0.342 Chirality : 0.039 0.318 29462 Planarity : 0.005 0.073 12404 Dihedral : 24.170 179.915 76961 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.36 % Allowed : 14.63 % Favored : 81.01 % 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: -3.43 (0.10), residues: 5678 helix: -2.23 (0.11), residues: 1619 sheet: -1.77 (0.16), residues: 950 loop : -2.51 (0.10), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 213 HIS 0.010 0.002 HIS 5 30 PHE 0.030 0.002 PHE X 78 TYR 0.020 0.002 TYR k 77 ARG 0.021 0.001 ARG S 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1246 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1045 time to evaluate : 6.115 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 45 LYS cc_start: 0.6428 (tmmt) cc_final: 0.5993 (mtmt) REVERT: d 15 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5365 (mp0) REVERT: h 27 MET cc_start: 0.8609 (ptp) cc_final: 0.8146 (ptp) REVERT: i 60 LYS cc_start: 0.6814 (ptmm) cc_final: 0.6450 (ttpp) REVERT: m 17 ILE cc_start: 0.5773 (mp) cc_final: 0.5234 (tt) REVERT: u 40 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7327 (mmtp) REVERT: C 102 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7473 (mtt180) REVERT: C 246 VAL cc_start: 0.9118 (p) cc_final: 0.8775 (m) REVERT: D 168 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: E 34 TYR cc_start: 0.8835 (t80) cc_final: 0.8591 (t80) REVERT: E 162 ASN cc_start: 0.8597 (t0) cc_final: 0.8293 (t0) REVERT: F 145 LYS cc_start: 0.7886 (mmtm) cc_final: 0.7226 (mtpt) REVERT: F 146 ILE cc_start: 0.6658 (tp) cc_final: 0.6159 (tp) REVERT: G 11 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7724 (pp) REVERT: G 74 ASN cc_start: 0.8096 (m-40) cc_final: 0.7541 (m110) REVERT: G 147 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7459 (tm-30) REVERT: I 36 MET cc_start: 0.1667 (pmm) cc_final: 0.1042 (pmm) REVERT: J 12 GLN cc_start: 0.6302 (tm-30) cc_final: 0.5959 (tm-30) REVERT: J 14 ASP cc_start: 0.7431 (m-30) cc_final: 0.7097 (m-30) REVERT: J 52 ASP cc_start: 0.8601 (m-30) cc_final: 0.8375 (m-30) REVERT: K 47 ILE cc_start: 0.7563 (tp) cc_final: 0.6981 (mt) REVERT: M 13 MET cc_start: 0.7908 (mmt) cc_final: 0.7606 (mtt) REVERT: M 98 GLN cc_start: 0.8477 (pt0) cc_final: 0.7896 (mt0) REVERT: Q 18 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9013 (mm) REVERT: Q 103 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7721 (mtpp) REVERT: S 22 ASP cc_start: 0.7776 (p0) cc_final: 0.7568 (p0) REVERT: S 52 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: V 94 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.6695 (p90) REVERT: X 56 MET cc_start: 0.8088 (mmt) cc_final: 0.7761 (mmt) REVERT: X 74 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7253 (mtp-110) REVERT: Y 16 ASN cc_start: 0.8157 (m-40) cc_final: 0.7891 (m110) REVERT: Z 7 THR cc_start: 0.8492 (m) cc_final: 0.8153 (p) REVERT: Z 40 THR cc_start: 0.8272 (p) cc_final: 0.7871 (p) REVERT: Z 42 GLU cc_start: 0.7889 (pm20) cc_final: 0.7432 (pm20) outliers start: 201 outliers final: 137 residues processed: 1166 average time/residue: 1.2465 time to fit residues: 2499.4692 Evaluate side-chains 1105 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 960 time to evaluate : 5.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain c residue 37 LEU Chi-restraints excluded: chain c residue 58 HIS Chi-restraints excluded: chain c residue 66 ILE Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 104 GLU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 15 GLU Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 155 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 61 LEU Chi-restraints excluded: chain q residue 18 ASP Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 61 LEU Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 80 SER Chi-restraints excluded: chain t residue 82 HIS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 204 SER 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 108 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 103 LYS Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain Y residue 34 THR Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain 1 residue 16 CYS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 51 ARG Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 residue 25 THR Chi-restraints excluded: chain 6 residue 8 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 905 optimal weight: 8.9990 chunk 688 optimal weight: 9.9990 chunk 475 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 chunk 437 optimal weight: 6.9990 chunk 615 optimal weight: 10.0000 chunk 919 optimal weight: 6.9990 chunk 973 optimal weight: 9.9990 chunk 480 optimal weight: 8.9990 chunk 871 optimal weight: 0.4980 chunk 262 optimal weight: 10.0000 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 78 ASN e 83 GLN ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN i 5 GLN o 37 ASN D 37 GLN D 68 HIS E 40 GLN E 45 GLN G 59 GLN H 14 ASN J 58 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 35 ASN X 16 ASN Z 33 HIS 2 41 HIS 5 42 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 154035 Z= 0.409 Angle : 0.782 20.326 230421 Z= 0.396 Chirality : 0.045 0.351 29462 Planarity : 0.006 0.079 12404 Dihedral : 24.253 179.777 76960 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.90 % Favored : 90.08 % Rotamer: Outliers : 5.73 % Allowed : 15.99 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.10), residues: 5678 helix: -1.97 (0.11), residues: 1637 sheet: -1.69 (0.16), residues: 963 loop : -2.53 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 213 HIS 0.012 0.002 HIS N 16 PHE 0.026 0.003 PHE S 75 TYR 0.020 0.002 TYR M 92 ARG 0.021 0.001 ARG m 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 999 time to evaluate : 5.537 Fit side-chains 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: symmetry clash revert: symmetry clash REVERT: d 202 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7521 (mm-30) REVERT: e 49 PHE cc_start: 0.8633 (p90) cc_final: 0.8408 (p90) REVERT: e 83 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7501 (mm-40) REVERT: e 122 GLN cc_start: 0.8195 (mp-120) cc_final: 0.7550 (mp-120) REVERT: e 143 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7423 (mtmm) REVERT: f 3 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7829 (m-70) REVERT: f 18 VAL cc_start: 0.7374 (p) cc_final: 0.6924 (p) REVERT: h 27 MET cc_start: 0.8479 (ptp) cc_final: 0.8110 (ptp) REVERT: h 40 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8675 (mp) REVERT: i 28 ILE cc_start: 0.4973 (OUTLIER) cc_final: 0.4700 (mp) REVERT: k 56 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7338 (mtm-85) REVERT: l 89 ASP cc_start: 0.7714 (t0) cc_final: 0.7507 (t0) REVERT: m 17 ILE cc_start: 0.6018 (mp) cc_final: 0.5624 (tt) REVERT: o 15 TYR cc_start: 0.7242 (m-80) cc_final: 0.6871 (m-80) REVERT: o 56 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8721 (tp) REVERT: q 37 TYR cc_start: 0.8442 (m-80) cc_final: 0.8150 (m-80) REVERT: q 55 GLN cc_start: 0.7998 (pp30) cc_final: 0.7479 (pp30) REVERT: u 40 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7365 (mmtp) REVERT: C 102 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7538 (mtt180) REVERT: C 171 TYR cc_start: 0.8172 (m-10) cc_final: 0.7862 (m-10) REVERT: C 246 VAL cc_start: 0.9080 (p) cc_final: 0.8781 (m) REVERT: D 154 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7503 (ptt90) REVERT: D 168 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: E 34 TYR cc_start: 0.8979 (t80) cc_final: 0.8721 (t80) REVERT: E 153 ASP cc_start: 0.7942 (t0) cc_final: 0.7741 (t70) REVERT: G 11 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7760 (pp) REVERT: G 74 ASN cc_start: 0.8092 (m-40) cc_final: 0.7839 (m-40) REVERT: J 12 GLN cc_start: 0.6261 (tm-30) cc_final: 0.5719 (tm-30) REVERT: J 14 ASP cc_start: 0.7786 (m-30) cc_final: 0.7495 (m-30) REVERT: L 76 GLU cc_start: 0.7622 (pp20) cc_final: 0.7376 (pp20) REVERT: O 68 ASP cc_start: 0.7469 (m-30) cc_final: 0.7261 (m-30) REVERT: Q 18 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8975 (mm) REVERT: Q 103 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7902 (mtpp) REVERT: V 90 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.5932 (mtt) REVERT: V 94 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.6999 (p90) REVERT: V 110 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.6409 (m90) REVERT: X 74 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7322 (mtp-110) REVERT: Z 42 GLU cc_start: 0.8160 (pm20) cc_final: 0.7627 (pm20) REVERT: 2 14 ASP cc_start: 0.8241 (m-30) cc_final: 0.8032 (m-30) outliers start: 264 outliers final: 179 residues processed: 1164 average time/residue: 1.1791 time to fit residues: 2372.6262 Evaluate side-chains 1132 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 938 time to evaluate : 5.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 37 LEU Chi-restraints excluded: chain c residue 58 HIS Chi-restraints excluded: chain c residue 66 ILE Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 104 GLU Chi-restraints excluded: chain c residue 130 PHE Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 155 ILE Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 83 GLN Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 143 LYS Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain h residue 127 CYS Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 18 ASP Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 44 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 80 SER Chi-restraints excluded: chain t residue 82 HIS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 253 THR 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 94 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 103 LYS Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 90 MET Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 110 HIS Chi-restraints excluded: chain V residue 156 LEU Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 75 PHE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain 1 residue 16 CYS Chi-restraints excluded: chain 1 residue 22 ILE Chi-restraints excluded: chain 2 residue 20 ASP Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 51 ARG Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 6 residue 8 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 810 optimal weight: 3.9990 chunk 552 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 724 optimal weight: 5.9990 chunk 401 optimal weight: 6.9990 chunk 830 optimal weight: 0.9980 chunk 672 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 497 optimal weight: 10.0000 chunk 873 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 78 ASN e 83 GLN f 63 ASN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 4 GLN l 6 GLN ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN J 138 GLN ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN X 22 HIS 5 42 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 154035 Z= 0.299 Angle : 0.675 20.181 230421 Z= 0.344 Chirality : 0.040 0.337 29462 Planarity : 0.005 0.078 12404 Dihedral : 24.112 179.950 76960 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 5.21 % Allowed : 17.75 % Favored : 77.04 % 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: -3.03 (0.10), residues: 5678 helix: -1.59 (0.12), residues: 1637 sheet: -1.58 (0.16), residues: 956 loop : -2.44 (0.10), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 213 HIS 0.009 0.001 HIS 5 30 PHE 0.022 0.002 PHE f 8 TYR 0.016 0.002 TYR d 103 ARG 0.008 0.001 ARG 2 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 957 time to evaluate : 5.963 Fit side-chains 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: symmetry clash revert: symmetry clash REVERT: c 3 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6541 (mp10) REVERT: c 110 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6448 (pp20) REVERT: d 202 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7554 (mm-30) REVERT: e 16 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8484 (tp) REVERT: e 122 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7511 (mp-120) REVERT: e 139 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: e 143 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7380 (mtmm) REVERT: f 9 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7616 (pp) REVERT: h 27 MET cc_start: 0.8445 (ptp) cc_final: 0.8093 (ptp) REVERT: h 40 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8629 (mp) REVERT: h 117 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6823 (ttp-170) REVERT: i 28 ILE cc_start: 0.5045 (OUTLIER) cc_final: 0.4431 (mp) REVERT: i 115 LYS cc_start: 0.7063 (mmmt) cc_final: 0.6421 (tppt) REVERT: k 56 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7435 (mtm-85) REVERT: l 89 ASP cc_start: 0.7711 (t0) cc_final: 0.7486 (t0) REVERT: m 17 ILE cc_start: 0.6068 (mp) cc_final: 0.5594 (tt) REVERT: o 64 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7438 (tpp-160) REVERT: q 37 TYR cc_start: 0.8414 (m-80) cc_final: 0.8149 (m-80) REVERT: q 55 GLN cc_start: 0.7763 (pp30) cc_final: 0.7299 (pp30) REVERT: u 40 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7191 (mmtp) REVERT: C 102 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7474 (mtt180) REVERT: C 171 TYR cc_start: 0.8124 (m-10) cc_final: 0.7790 (m-10) REVERT: C 246 VAL cc_start: 0.9102 (p) cc_final: 0.8792 (m) REVERT: D 168 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6918 (tt0) REVERT: E 34 TYR cc_start: 0.8920 (t80) cc_final: 0.8646 (t80) REVERT: G 11 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7715 (pp) REVERT: G 74 ASN cc_start: 0.8071 (m-40) cc_final: 0.7832 (m-40) REVERT: J 12 GLN cc_start: 0.6255 (tm-30) cc_final: 0.5837 (tm-30) REVERT: J 14 ASP cc_start: 0.7540 (m-30) cc_final: 0.7299 (m-30) REVERT: M 98 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: O 68 ASP cc_start: 0.7470 (m-30) cc_final: 0.7203 (m-30) REVERT: Q 18 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8914 (mm) REVERT: V 90 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5994 (mtt) REVERT: V 94 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7131 (p90) REVERT: V 110 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.6353 (m90) REVERT: X 74 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7415 (mtp-110) REVERT: Z 42 GLU cc_start: 0.8019 (pm20) cc_final: 0.7618 (pm20) REVERT: 2 14 ASP cc_start: 0.8268 (m-30) cc_final: 0.8060 (m-30) outliers start: 240 outliers final: 178 residues processed: 1099 average time/residue: 1.1984 time to fit residues: 2288.0348 Evaluate side-chains 1111 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 915 time to evaluate : 5.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 37 LEU Chi-restraints excluded: chain c residue 58 HIS Chi-restraints excluded: chain c residue 66 ILE Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 104 GLU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 122 GLN Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 139 TYR Chi-restraints excluded: chain e residue 143 LYS Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 THR Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 46 LYS Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 44 LEU Chi-restraints excluded: chain t residue 82 HIS Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 204 SER 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 108 ASP Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU 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 116 GLU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 90 MET Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 110 HIS Chi-restraints excluded: chain V residue 156 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain 1 residue 16 CYS Chi-restraints excluded: chain 2 residue 20 ASP Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 51 ARG Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 6 residue 8 LYS Chi-restraints excluded: chain 6 residue 37 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 327 optimal weight: 5.9990 chunk 876 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 571 optimal weight: 20.0000 chunk 240 optimal weight: 30.0000 chunk 974 optimal weight: 4.9990 chunk 808 optimal weight: 6.9990 chunk 451 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 511 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 177 ASN f 63 ASN o 10 GLN ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN T 90 GLN ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN 2 37 HIS 5 42 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 154035 Z= 0.422 Angle : 0.784 20.100 230421 Z= 0.396 Chirality : 0.045 0.353 29462 Planarity : 0.006 0.082 12404 Dihedral : 24.220 179.525 76960 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.52 % Favored : 89.46 % Rotamer: Outliers : 6.47 % Allowed : 18.19 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.10), residues: 5678 helix: -1.61 (0.12), residues: 1664 sheet: -1.60 (0.16), residues: 980 loop : -2.48 (0.10), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 213 HIS 0.010 0.002 HIS 5 30 PHE 0.027 0.002 PHE f 78 TYR 0.022 0.002 TYR M 92 ARG 0.008 0.001 ARG 2 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 950 time to evaluate : 6.136 Fit side-chains 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6171 (ttp) REVERT: b 145 GLU cc_start: 0.7486 (pm20) cc_final: 0.7179 (pm20) REVERT: b 225 LYS cc_start: 0.2857 (ptpt) cc_final: 0.2597 (mmmt) REVERT: c 3 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6644 (mp10) REVERT: c 33 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7936 (mp) REVERT: c 110 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6460 (pp20) REVERT: e 16 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8477 (tp) REVERT: e 83 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7665 (mm-40) REVERT: e 122 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7622 (mp-120) REVERT: e 139 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: e 143 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7455 (mtmm) REVERT: f 3 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.7882 (m-70) REVERT: f 9 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7641 (pp) REVERT: f 77 ASN cc_start: 0.8144 (m-40) cc_final: 0.7768 (m-40) REVERT: g 53 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.6097 (mmt90) REVERT: h 27 MET cc_start: 0.8432 (ptp) cc_final: 0.8070 (ptp) REVERT: h 40 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8675 (mp) REVERT: h 117 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6829 (ttp-170) REVERT: i 28 ILE cc_start: 0.5205 (OUTLIER) cc_final: 0.4581 (mp) REVERT: i 115 LYS cc_start: 0.7174 (mmmt) cc_final: 0.6664 (tppt) REVERT: m 17 ILE cc_start: 0.5983 (mp) cc_final: 0.5718 (tt) REVERT: o 26 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: o 64 ARG cc_start: 0.7887 (tpp-160) cc_final: 0.7654 (tpp-160) REVERT: q 37 TYR cc_start: 0.8479 (m-80) cc_final: 0.8226 (m-80) REVERT: q 55 GLN cc_start: 0.7937 (pp30) cc_final: 0.7121 (pp30) REVERT: s 43 HIS cc_start: 0.5011 (OUTLIER) cc_final: 0.4686 (t-90) REVERT: u 40 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7275 (mmtp) REVERT: C 59 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8266 (ttmp) REVERT: C 246 VAL cc_start: 0.9075 (p) cc_final: 0.8766 (m) REVERT: D 168 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: E 34 TYR cc_start: 0.8979 (t80) cc_final: 0.8727 (t80) REVERT: G 11 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7722 (pp) REVERT: J 12 GLN cc_start: 0.6437 (tm-30) cc_final: 0.5914 (tm-30) REVERT: J 14 ASP cc_start: 0.7590 (m-30) cc_final: 0.7363 (m-30) REVERT: J 45 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8687 (p) REVERT: J 71 ASP cc_start: 0.8223 (m-30) cc_final: 0.8021 (m-30) REVERT: L 5 ASP cc_start: 0.7605 (t0) cc_final: 0.7350 (t0) REVERT: L 7 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6973 (pmm150) REVERT: M 98 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: O 68 ASP cc_start: 0.7584 (m-30) cc_final: 0.7345 (m-30) REVERT: O 114 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7129 (tt) REVERT: V 90 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.6052 (mtt) REVERT: V 94 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7441 (p90) REVERT: V 110 HIS cc_start: 0.6979 (OUTLIER) cc_final: 0.6503 (m90) REVERT: Z 42 GLU cc_start: 0.8119 (pm20) cc_final: 0.7914 (pm20) REVERT: 2 14 ASP cc_start: 0.8242 (m-30) cc_final: 0.8011 (m-30) outliers start: 298 outliers final: 219 residues processed: 1143 average time/residue: 1.2114 time to fit residues: 2403.8799 Evaluate side-chains 1172 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 926 time to evaluate : 5.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 37 LEU Chi-restraints excluded: chain c residue 58 HIS Chi-restraints excluded: chain c residue 66 ILE Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 104 GLU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 130 PHE Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 122 GLN Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 139 TYR Chi-restraints excluded: chain e residue 143 LYS Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 53 ARG Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain h residue 127 CYS Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 26 GLU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 20 MET Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 THR Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 46 LYS Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 81 ILE Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 43 HIS Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 44 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 82 HIS Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 219 THR 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 122 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 95 LYS Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 90 MET Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 110 HIS Chi-restraints excluded: chain V residue 156 LEU Chi-restraints excluded: chain V residue 165 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 75 PHE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 1 residue 16 CYS Chi-restraints excluded: chain 1 residue 22 ILE Chi-restraints excluded: chain 2 residue 20 ASP Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 51 ARG Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 8 LYS Chi-restraints excluded: chain 6 residue 37 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 939 optimal weight: 0.0170 chunk 109 optimal weight: 10.0000 chunk 555 optimal weight: 8.9990 chunk 711 optimal weight: 5.9990 chunk 551 optimal weight: 10.0000 chunk 820 optimal weight: 6.9990 chunk 544 optimal weight: 7.9990 chunk 970 optimal weight: 0.9990 chunk 607 optimal weight: 7.9990 chunk 591 optimal weight: 50.0000 chunk 448 optimal weight: 4.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS g 148 ASN ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 188 HIS X 16 ASN 5 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 154035 Z= 0.253 Angle : 0.650 20.574 230421 Z= 0.333 Chirality : 0.039 0.329 29462 Planarity : 0.005 0.079 12404 Dihedral : 24.083 179.870 76960 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 5.38 % Allowed : 19.84 % Favored : 74.78 % 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: -2.80 (0.10), residues: 5678 helix: -1.31 (0.12), residues: 1659 sheet: -1.40 (0.16), residues: 963 loop : -2.36 (0.10), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 213 HIS 0.006 0.001 HIS N 16 PHE 0.023 0.002 PHE f 8 TYR 0.015 0.002 TYR d 103 ARG 0.007 0.000 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 946 time to evaluate : 6.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 225 LYS cc_start: 0.2781 (ptpt) cc_final: 0.2528 (mmmt) REVERT: c 3 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6488 (mp10) REVERT: c 33 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7943 (mp) REVERT: e 16 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8477 (tp) REVERT: e 83 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7742 (mm-40) REVERT: e 122 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7575 (mp-120) REVERT: e 139 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: e 143 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7355 (mtmm) REVERT: f 3 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7828 (m-70) REVERT: f 9 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7558 (pp) REVERT: h 27 MET cc_start: 0.8389 (ptp) cc_final: 0.8054 (ptp) REVERT: h 40 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8632 (mp) REVERT: h 117 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6891 (ttp-170) REVERT: i 28 ILE cc_start: 0.5164 (OUTLIER) cc_final: 0.4514 (mp) REVERT: i 97 SER cc_start: 0.7257 (m) cc_final: 0.7037 (p) REVERT: i 115 LYS cc_start: 0.6980 (mmmt) cc_final: 0.6644 (tppt) REVERT: k 56 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7683 (mtm-85) REVERT: o 64 ARG cc_start: 0.7919 (tpp-160) cc_final: 0.7680 (tpp-160) REVERT: q 37 TYR cc_start: 0.8351 (m-80) cc_final: 0.8133 (m-80) REVERT: q 55 GLN cc_start: 0.7855 (pp30) cc_final: 0.7059 (pp30) REVERT: u 40 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7179 (mmtp) REVERT: C 171 TYR cc_start: 0.8066 (m-10) cc_final: 0.7709 (m-10) REVERT: C 246 VAL cc_start: 0.9100 (p) cc_final: 0.8812 (m) REVERT: D 168 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: E 34 TYR cc_start: 0.8878 (t80) cc_final: 0.8648 (t80) REVERT: F 111 VAL cc_start: 0.7546 (t) cc_final: 0.7296 (t) REVERT: F 145 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7326 (pttt) REVERT: G 11 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7709 (pp) REVERT: J 12 GLN cc_start: 0.6424 (tm-30) cc_final: 0.6001 (tm-30) REVERT: J 45 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8642 (p) REVERT: M 98 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: O 68 ASP cc_start: 0.7432 (m-30) cc_final: 0.7193 (m-30) REVERT: O 88 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: O 114 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7123 (tt) REVERT: Q 18 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8995 (mm) REVERT: V 90 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5930 (mtt) REVERT: V 94 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7137 (p90) REVERT: V 110 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6445 (m90) REVERT: 2 14 ASP cc_start: 0.8241 (m-30) cc_final: 0.8012 (m-30) outliers start: 248 outliers final: 195 residues processed: 1111 average time/residue: 1.2166 time to fit residues: 2348.3478 Evaluate side-chains 1132 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 915 time to evaluate : 5.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 37 LEU Chi-restraints excluded: chain c residue 58 HIS Chi-restraints excluded: chain c residue 66 ILE Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 155 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 122 GLN Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 139 TYR Chi-restraints excluded: chain e residue 143 LYS Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain h residue 127 CYS Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 46 LYS Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 44 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 82 HIS Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 219 THR 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 108 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 95 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 90 MET Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 110 HIS Chi-restraints excluded: chain V residue 156 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 75 PHE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 16 LEU Chi-restraints excluded: chain 1 residue 16 CYS Chi-restraints excluded: chain 1 residue 22 ILE Chi-restraints excluded: chain 2 residue 20 ASP Chi-restraints excluded: chain 2 residue 51 ARG Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 6 residue 2 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 600 optimal weight: 10.0000 chunk 387 optimal weight: 8.9990 chunk 579 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 188 optimal weight: 0.0570 chunk 617 optimal weight: 10.0000 chunk 661 optimal weight: 10.0000 chunk 479 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 762 optimal weight: 6.9990 overall best weight: 5.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 177 ASN ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 215 ASN ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN j 15 HIS m 14 HIS p 54 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN 5 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 154035 Z= 0.371 Angle : 0.736 20.436 230421 Z= 0.373 Chirality : 0.043 0.348 29462 Planarity : 0.006 0.079 12404 Dihedral : 24.131 179.959 76960 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 6.10 % Allowed : 19.53 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.10), residues: 5678 helix: -1.35 (0.12), residues: 1663 sheet: -1.49 (0.16), residues: 979 loop : -2.40 (0.10), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 167 HIS 0.007 0.002 HIS D 164 PHE 0.025 0.002 PHE f 78 TYR 0.021 0.002 TYR c 184 ARG 0.015 0.001 ARG b 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 934 time to evaluate : 6.069 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 3 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6670 (mp10) REVERT: c 33 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7944 (mp) REVERT: c 36 ASP cc_start: 0.7816 (m-30) cc_final: 0.7542 (m-30) REVERT: e 16 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8461 (tp) REVERT: e 83 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7692 (mm-40) REVERT: e 122 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7650 (mp-120) REVERT: e 139 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: e 143 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7528 (mtmm) REVERT: f 3 HIS cc_start: 0.8265 (OUTLIER) cc_final: 0.7875 (m-70) REVERT: f 9 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7630 (pp) REVERT: g 53 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5924 (mmt90) REVERT: h 27 MET cc_start: 0.8407 (ptp) cc_final: 0.8058 (ptp) REVERT: h 40 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8623 (mp) REVERT: h 117 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6806 (ttp-170) REVERT: i 28 ILE cc_start: 0.5560 (OUTLIER) cc_final: 0.4756 (mp) REVERT: i 97 SER cc_start: 0.7365 (m) cc_final: 0.7143 (t) REVERT: i 115 LYS cc_start: 0.7070 (mmmt) cc_final: 0.6758 (tppt) REVERT: o 64 ARG cc_start: 0.7893 (tpp-160) cc_final: 0.7676 (tpp-160) REVERT: q 55 GLN cc_start: 0.7828 (pp30) cc_final: 0.6807 (pp30) REVERT: s 38 SER cc_start: 0.5383 (t) cc_final: 0.5107 (t) REVERT: u 40 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7260 (mmtp) REVERT: C 59 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8256 (ttmp) REVERT: C 246 VAL cc_start: 0.9081 (p) cc_final: 0.8770 (m) REVERT: D 168 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6956 (tt0) REVERT: E 34 TYR cc_start: 0.8922 (t80) cc_final: 0.8682 (t80) REVERT: F 130 MET cc_start: 0.6100 (tmm) cc_final: 0.5503 (ppp) REVERT: G 11 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7668 (pp) REVERT: G 147 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7758 (tm-30) REVERT: J 45 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8666 (p) REVERT: K 47 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7262 (mt) REVERT: L 7 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.6903 (pmm150) REVERT: M 98 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: O 68 ASP cc_start: 0.7585 (m-30) cc_final: 0.7340 (m-30) REVERT: O 88 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: O 114 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7254 (tt) REVERT: Q 18 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8952 (mm) REVERT: S 109 ASP cc_start: 0.6361 (OUTLIER) cc_final: 0.5683 (m-30) REVERT: V 90 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.6040 (mtt) REVERT: V 94 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7400 (p90) REVERT: V 110 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6504 (m90) REVERT: X 74 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7942 (ttp80) REVERT: 2 14 ASP cc_start: 0.8233 (m-30) cc_final: 0.7994 (m-30) outliers start: 281 outliers final: 222 residues processed: 1119 average time/residue: 1.3412 time to fit residues: 2632.0786 Evaluate side-chains 1163 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 914 time to evaluate : 6.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 37 LEU Chi-restraints excluded: chain c residue 58 HIS Chi-restraints excluded: chain c residue 66 ILE Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 155 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 65 MET Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 122 GLN Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 139 TYR Chi-restraints excluded: chain e residue 143 LYS Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 53 ARG Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain h residue 127 CYS Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 54 GLN Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 81 ILE Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 44 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 82 HIS Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 253 THR 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 110 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 95 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 90 MET Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain V residue 110 HIS Chi-restraints excluded: chain V residue 156 LEU Chi-restraints excluded: chain V residue 165 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 75 PHE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 16 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain 1 residue 16 CYS Chi-restraints excluded: chain 1 residue 22 ILE Chi-restraints excluded: chain 2 residue 20 ASP Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 51 ARG Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 37 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 882 optimal weight: 6.9990 chunk 929 optimal weight: 9.9990 chunk 848 optimal weight: 10.0000 chunk 904 optimal weight: 0.0970 chunk 544 optimal weight: 8.9990 chunk 394 optimal weight: 8.9990 chunk 710 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 817 optimal weight: 6.9990 chunk 855 optimal weight: 7.9990 chunk 901 optimal weight: 0.7980 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 177 ASN ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN o 42 HIS p 54 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN 5 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 154035 Z= 0.258 Angle : 0.668 20.741 230421 Z= 0.342 Chirality : 0.039 0.332 29462 Planarity : 0.005 0.079 12404 Dihedral : 24.094 179.850 76960 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.36 % Allowed : 20.75 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 5678 helix: -1.23 (0.12), residues: 1661 sheet: -1.41 (0.17), residues: 970 loop : -2.31 (0.10), residues: 3047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP c 167 HIS 0.006 0.001 HIS N 16 PHE 0.028 0.002 PHE f 78 TYR 0.022 0.002 TYR M 92 ARG 0.007 0.001 ARG b 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 932 time to evaluate : 6.068 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 3 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: c 33 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7929 (mp) REVERT: c 36 ASP cc_start: 0.7887 (m-30) cc_final: 0.7613 (m-30) REVERT: e 16 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8467 (tp) REVERT: e 122 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7627 (mp-120) REVERT: e 139 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: e 143 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7523 (mtmm) REVERT: f 3 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7866 (m-70) REVERT: f 9 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7636 (pp) REVERT: g 53 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.6018 (mmt90) REVERT: h 27 MET cc_start: 0.8387 (ptp) cc_final: 0.8062 (ptp) REVERT: h 40 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8644 (mp) REVERT: h 117 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6888 (ttp-170) REVERT: i 28 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.4644 (mp) REVERT: i 115 LYS cc_start: 0.6986 (mmmt) cc_final: 0.6724 (tppt) REVERT: l 89 ASP cc_start: 0.7403 (t0) cc_final: 0.7182 (t0) REVERT: q 55 GLN cc_start: 0.7907 (pp30) cc_final: 0.6905 (pp30) REVERT: s 38 SER cc_start: 0.5345 (t) cc_final: 0.5056 (t) REVERT: u 40 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7174 (mmtp) REVERT: C 59 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8276 (ttmp) REVERT: C 102 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7377 (mtt180) REVERT: C 171 TYR cc_start: 0.8092 (m-10) cc_final: 0.7703 (m-10) REVERT: C 246 VAL cc_start: 0.9093 (p) cc_final: 0.8786 (m) REVERT: D 168 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: E 34 TYR cc_start: 0.8886 (t80) cc_final: 0.8654 (t80) REVERT: F 130 MET cc_start: 0.6123 (tmm) cc_final: 0.5494 (ppp) REVERT: G 11 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7712 (pp) REVERT: J 45 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8634 (p) REVERT: K 47 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7205 (mt) REVERT: L 7 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6892 (pmm150) REVERT: M 98 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: O 68 ASP cc_start: 0.7492 (m-30) cc_final: 0.7249 (m-30) REVERT: O 88 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: O 114 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7284 (tt) REVERT: P 51 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8311 (mtmt) REVERT: Q 18 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8961 (mm) REVERT: S 23 GLN cc_start: 0.8312 (tt0) cc_final: 0.7956 (tp-100) REVERT: V 90 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5952 (mtt) REVERT: V 94 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7366 (p90) REVERT: V 110 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6508 (m90) REVERT: X 74 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7870 (ttp80) REVERT: 2 14 ASP cc_start: 0.8236 (m-30) cc_final: 0.8007 (m-30) outliers start: 247 outliers final: 204 residues processed: 1087 average time/residue: 1.2253 time to fit residues: 2306.9229 Evaluate side-chains 1147 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 916 time to evaluate : 7.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 37 LEU Chi-restraints excluded: chain c residue 58 HIS Chi-restraints excluded: chain c residue 66 ILE Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 155 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain e residue 12 TYR Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 122 GLN Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 139 TYR Chi-restraints excluded: chain e residue 143 LYS Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 53 ARG Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain h residue 127 CYS Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 61 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 81 ILE Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 44 LEU Chi-restraints excluded: chain t residue 82 HIS Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 253 THR 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 108 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 95 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 90 MET Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain V residue 110 HIS Chi-restraints excluded: chain V residue 156 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 75 PHE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 16 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain 1 residue 16 CYS Chi-restraints excluded: chain 1 residue 22 ILE Chi-restraints excluded: chain 2 residue 20 ASP Chi-restraints excluded: chain 2 residue 51 ARG Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 6 residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 593 optimal weight: 40.0000 chunk 956 optimal weight: 6.9990 chunk 583 optimal weight: 8.9990 chunk 453 optimal weight: 8.9990 chunk 664 optimal weight: 10.0000 chunk 1003 optimal weight: 5.9990 chunk 923 optimal weight: 8.9990 chunk 798 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 617 optimal weight: 10.0000 chunk 489 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 177 ASN ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 78 ASN ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN p 54 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 25 ASN ** V 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN 5 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 154035 Z= 0.420 Angle : 0.774 20.512 230421 Z= 0.390 Chirality : 0.044 0.357 29462 Planarity : 0.006 0.077 12404 Dihedral : 24.165 179.755 76960 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 5.47 % Allowed : 20.81 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.10), residues: 5678 helix: -1.37 (0.12), residues: 1666 sheet: -1.50 (0.16), residues: 971 loop : -2.40 (0.10), residues: 3041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP c 167 HIS 0.009 0.002 HIS k 118 PHE 0.028 0.002 PHE f 78 TYR 0.016 0.002 TYR O 37 ARG 0.007 0.001 ARG 2 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11356 Ramachandran restraints generated. 5678 Oldfield, 0 Emsley, 5678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 934 time to evaluate : 6.135 Fit side-chains 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: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6218 (ttp) REVERT: c 3 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6636 (mp10) REVERT: c 33 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7972 (mp) REVERT: c 36 ASP cc_start: 0.7827 (m-30) cc_final: 0.7530 (m-30) REVERT: e 122 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7685 (mp-120) REVERT: e 139 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: e 143 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7551 (mtmm) REVERT: f 3 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7837 (m-70) REVERT: f 9 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7648 (pp) REVERT: g 53 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6164 (mmt90) REVERT: h 27 MET cc_start: 0.8403 (ptp) cc_final: 0.8083 (ptp) REVERT: h 40 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8650 (mp) REVERT: h 117 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6832 (ttp-170) REVERT: i 28 ILE cc_start: 0.5556 (OUTLIER) cc_final: 0.4729 (mp) REVERT: i 115 LYS cc_start: 0.7146 (mmmt) cc_final: 0.6836 (tppt) REVERT: j 74 LEU cc_start: 0.5185 (pp) cc_final: 0.4663 (tp) REVERT: q 55 GLN cc_start: 0.8016 (pp30) cc_final: 0.6774 (pp30) REVERT: s 38 SER cc_start: 0.5503 (t) cc_final: 0.5218 (t) REVERT: u 40 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7266 (mmtp) REVERT: C 59 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8266 (ttmp) REVERT: C 246 VAL cc_start: 0.9077 (p) cc_final: 0.8763 (m) REVERT: D 151 THR cc_start: 0.8912 (p) cc_final: 0.8419 (m) REVERT: D 168 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: E 34 TYR cc_start: 0.8924 (t80) cc_final: 0.8667 (t80) REVERT: G 11 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7762 (pp) REVERT: J 45 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8681 (p) REVERT: K 47 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7320 (mt) REVERT: L 7 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6894 (pmm150) REVERT: M 98 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: O 68 ASP cc_start: 0.7618 (m-30) cc_final: 0.7371 (m-30) REVERT: O 88 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7553 (mp10) REVERT: O 114 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7669 (tt) REVERT: P 51 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8283 (mtmt) REVERT: Q 18 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8975 (mm) REVERT: S 109 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5631 (m-30) REVERT: U 50 MET cc_start: 0.3199 (ptp) cc_final: 0.2450 (mtm) REVERT: V 90 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6267 (mtt) REVERT: V 94 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7559 (p90) REVERT: V 110 HIS cc_start: 0.7119 (OUTLIER) cc_final: 0.6557 (m90) REVERT: X 74 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.7803 (ttp80) REVERT: 2 14 ASP cc_start: 0.8301 (m-30) cc_final: 0.8089 (m-30) outliers start: 252 outliers final: 209 residues processed: 1099 average time/residue: 1.2256 time to fit residues: 2339.9764 Evaluate side-chains 1161 residues out of total 4706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 924 time to evaluate : 5.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 37 LEU Chi-restraints excluded: chain c residue 58 HIS Chi-restraints excluded: chain c residue 66 ILE Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 193 TYR Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 155 ILE Chi-restraints excluded: chain e residue 12 TYR Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 122 GLN Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 139 TYR Chi-restraints excluded: chain e residue 143 LYS Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 53 ARG Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain h residue 127 CYS Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 81 ILE Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 44 LEU Chi-restraints excluded: chain t residue 82 HIS Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 253 THR 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 110 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 95 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 90 MET Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain V residue 110 HIS Chi-restraints excluded: chain V residue 156 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 75 PHE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 16 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain 1 residue 16 CYS Chi-restraints excluded: chain 1 residue 22 ILE Chi-restraints excluded: chain 2 residue 20 ASP Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 51 ARG Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 6 residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1007 random chunks: chunk 634 optimal weight: 6.9990 chunk 850 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 736 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 800 optimal weight: 0.9990 chunk 334 optimal weight: 1.9990 chunk 821 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 147 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 177 ASN e 78 ASN ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN i 5 GLN ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 14 GLN ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Z 43 ASN 5 42 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.116070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094511 restraints weight = 352564.575| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.18 r_work: 0.3140 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 154035 Z= 0.231 Angle : 0.647 21.004 230421 Z= 0.331 Chirality : 0.038 0.326 29462 Planarity : 0.005 0.076 12404 Dihedral : 24.038 179.951 76960 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.32 % Allowed : 21.35 % Favored : 73.33 % 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: -2.62 (0.10), residues: 5678 helix: -1.15 (0.12), residues: 1659 sheet: -1.35 (0.17), residues: 955 loop : -2.25 (0.10), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP c 167 HIS 0.005 0.001 HIS D 140 PHE 0.028 0.002 PHE f 78 TYR 0.018 0.002 TYR M 92 ARG 0.010 0.000 ARG K 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36105.58 seconds wall clock time: 629 minutes 30.19 seconds (37770.19 seconds total)