Starting phenix.real_space_refine on Sat Feb 17 01:25:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qt0_4630/02_2024/6qt0_4630.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qt0_4630/02_2024/6qt0_4630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qt0_4630/02_2024/6qt0_4630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qt0_4630/02_2024/6qt0_4630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qt0_4630/02_2024/6qt0_4630.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qt0_4630/02_2024/6qt0_4630.pdb" } resolution = 3.4 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= 0.018 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 Zn 5 6.06 5 P 3437 5.49 5 S 105 5.16 5 C 64826 2.51 5 N 22892 2.21 5 O 32800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 166": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ARG 185": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "q ARG 4": "NH1" <-> "NH2" Residue "q ARG 24": "NH1" <-> "NH2" Residue "q GLU 66": "OE1" <-> "OE2" Residue "q PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 110": "NH1" <-> "NH2" Residue "q ARG 139": "NH1" <-> "NH2" Residue "q GLU 180": "OE1" <-> "OE2" Residue "q ARG 185": "NH1" <-> "NH2" Residue "q GLU 215": "OE1" <-> "OE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K ARG 128": "NH1" <-> "NH2" Residue "K GLU 136": "OE1" <-> "OE2" Residue "K ARG 157": "NH1" <-> "NH2" Residue "K ARG 171": "NH1" <-> "NH2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K ARG 180": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O GLU 29": "OE1" <-> "OE2" Residue "O ARG 49": "NH1" <-> "NH2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 104": "OE1" <-> "OE2" Residue "P GLU 124": "OE1" <-> "OE2" Residue "P GLU 133": "OE1" <-> "OE2" Residue "P ARG 140": "NH1" <-> "NH2" Residue "P ARG 158": "NH1" <-> "NH2" Residue "P GLU 186": "OE1" <-> "OE2" Residue "P GLU 188": "OE1" <-> "OE2" Residue "P ARG 196": "NH1" <-> "NH2" Residue "P ARG 273": "NH1" <-> "NH2" Residue "P ARG 282": "NH1" <-> "NH2" Residue "P ARG 285": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q GLU 148": "OE1" <-> "OE2" Residue "Q GLU 173": "OE1" <-> "OE2" Residue "Q ARG 176": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "S GLU 21": "OE1" <-> "OE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S GLU 34": "OE1" <-> "OE2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "T GLU 137": "OE1" <-> "OE2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "U ARG 3": "NH1" <-> "NH2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U ARG 128": "NH1" <-> "NH2" Residue "U ARG 135": "NH1" <-> "NH2" Residue "V GLU 102": "OE1" <-> "OE2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W ARG 56": "NH1" <-> "NH2" Residue "W ARG 125": "NH1" <-> "NH2" Residue "W ARG 138": "NH1" <-> "NH2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Z GLU 15": "OE1" <-> "OE2" Residue "Z ARG 38": "NH1" <-> "NH2" Residue "Z TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b GLU 125": "OE1" <-> "OE2" Residue "b GLU 170": "OE1" <-> "OE2" Residue "b GLU 233": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 76": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "g ARG 16": "NH1" <-> "NH2" Residue "h GLU 46": "OE1" <-> "OE2" Residue "h ARG 99": "NH1" <-> "NH2" Residue "i ARG 63": "NH1" <-> "NH2" Residue "j GLU 13": "OE1" <-> "OE2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "k ARG 28": "NH1" <-> "NH2" Residue "l ARG 8": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 45": "NH1" <-> "NH2" Residue "l ARG 71": "NH1" <-> "NH2" Residue "m GLU 30": "OE1" <-> "OE2" Residue "m ARG 36": "NH1" <-> "NH2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "m GLU 91": "OE1" <-> "OE2" Residue "n GLU 98": "OE1" <-> "OE2" Residue "n ARG 100": "NH1" <-> "NH2" Residue "n GLU 124": "OE1" <-> "OE2" Residue "n GLU 126": "OE1" <-> "OE2" Residue "n GLU 127": "OE1" <-> "OE2" Residue "n GLU 172": "OE1" <-> "OE2" Residue "n ARG 188": "NH1" <-> "NH2" Residue "n GLU 219": "OE1" <-> "OE2" Residue "v ARG 17": "NH1" <-> "NH2" Residue "z GLU 416": "OE1" <-> "OE2" Residue "z ARG 419": "NH1" <-> "NH2" Residue "z ARG 427": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 124065 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 67663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3164, 67663 Inner-chain residues flagged as termini: ['pdbres=" G A 494 "', 'pdbres=" A A2093 "', 'pdbres=" G A3264 "'] Classifications: {'RNA': 3164} Modifications used: {'5*END': 4, 'rna2p_pur': 321, 'rna2p_pyr': 197, 'rna3p_pur': 1434, 'rna3p_pyr': 1212} Link IDs: {'rna2p': 518, 'rna3p': 2645} Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1878 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain: "C" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3039 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 14, 'TRANS': 366} Chain: "D" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1352 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1502 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "G" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1399 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1742 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "q" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1754 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 10, 'TRANS': 205} Chain: "J" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1563 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1486 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1002 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1058 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1172 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1719 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2298 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 275} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1440 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1209 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1444 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1275 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1222 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "V" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 786 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Y" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1091 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 968 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 430 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "b" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1760 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "c" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 741 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "d" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 872 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "e" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 976 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "f" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 849 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "g" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 812 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "h" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 763 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "i" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "j" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 611 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "k" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 435 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "l" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 756 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "m" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 693 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "n" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1691 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "t" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "v" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 500 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "z" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 445 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "x" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 51} Link IDs: {'rna2p': 14, 'rna3p': 106} Chain: "y" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3313 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 14, 'rna3p_pur': 62, 'rna3p_pyr': 64} Link IDs: {'rna2p': 30, 'rna3p': 125} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A08A2 SG CYS g 44 122.872 118.040 201.196 1.00 47.32 S ATOM A08I5 SG CYS g 84 121.383 115.437 203.168 1.00 52.64 S ATOM A09BV SG CYS i 19 145.823 134.355 150.526 1.00 25.73 S ATOM A09CK SG CYS i 22 146.387 135.768 147.159 1.00 28.58 S ATOM A09FC SG CYS i 34 143.486 132.636 148.251 1.00 29.14 S ATOM A09FU SG CYS i 37 148.028 132.606 146.873 1.00 30.87 S ATOM A0AM4 SG CYS l 12 140.911 62.027 87.951 1.00 56.18 S ATOM A0AN3 SG CYS l 17 142.542 58.619 86.264 1.00 63.36 S ATOM A0AZZ SG CYS l 74 139.761 58.659 88.967 1.00 57.19 S ATOM A0BD8 SG CYS m 39 107.420 106.162 197.732 1.00 58.95 S ATOM A0BGW SG CYS m 57 106.696 109.854 197.197 1.00 54.46 S ATOM A0D30 SG CYS t 96 53.758 132.044 80.669 1.00 94.36 S ATOM A0D3Q SG CYS t 99 54.819 135.187 82.253 1.00 91.86 S ATOM A0D65 SG CYS t 110 53.590 136.231 78.886 1.00 91.10 S ATOM A0D7F SG CYS t 115 56.947 134.991 79.347 1.00 91.00 S Time building chain proxies: 45.03, per 1000 atoms: 0.36 Number of scatterers: 124065 At special positions: 0 Unit cell: (230.04, 230.04, 249.21, 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) Zn 5 29.99 S 105 16.00 P 3437 15.00 O 32800 8.00 N 22892 7.00 C 64826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 43.96 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " pdb=" ZN i 101 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 19 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 34 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 22 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 37 " pdb=" ZN l 201 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 12 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 74 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 17 " pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 57 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 39 " pdb=" ZN t 201 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 110 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 99 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 115 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 96 " Number of angles added : 12 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11846 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 72 sheets defined 32.6% alpha, 14.3% beta 924 base pairs and 1881 stacking pairs defined. Time for finding SS restraints: 41.52 Creating SS restraints... Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.815A pdb=" N ASP B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 177 " --> pdb=" O ARG B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 173 through 177' Processing helix chain 'B' and resid 181 through 190 removed outlier: 3.835A pdb=" N HIS B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'C' and resid 13 through 17 removed outlier: 3.545A pdb=" N PHE C 16 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 17 " --> pdb=" O LEU C 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 13 through 17' Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 141 through 155 removed outlier: 4.456A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 187 through 198 removed outlier: 3.513A pdb=" N TRP C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.591A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.629A pdb=" N SER D 27 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 40 Processing helix chain 'D' and resid 114 through 128 removed outlier: 3.572A pdb=" N ALA D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 162 through 170 removed outlier: 3.842A pdb=" N ALA D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 183 removed outlier: 3.644A pdb=" N LYS D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 195 removed outlier: 4.203A pdb=" N GLY D 192 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR D 194 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.512A pdb=" N LEU D 219 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 240 through 243 removed outlier: 3.523A pdb=" N HIS D 243 " --> pdb=" O PRO D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.533A pdb=" N ILE D 289 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 320 through 328 removed outlier: 3.889A pdb=" N ARG D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 352 through 358 Processing helix chain 'E' and resid 27 through 42 removed outlier: 3.809A pdb=" N SER E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.893A pdb=" N ILE E 79 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.770A pdb=" N LEU E 112 " --> pdb=" O HIS E 109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 113 " --> pdb=" O ILE E 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 109 through 113' Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.591A pdb=" N LYS E 166 " --> pdb=" O TRP E 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 84 removed outlier: 3.767A pdb=" N ARG F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 150 through 165 removed outlier: 3.569A pdb=" N VAL F 154 " --> pdb=" O SER F 150 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU F 161 " --> pdb=" O ASN F 157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 107 removed outlier: 4.012A pdb=" N ALA G 107 " --> pdb=" O GLU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 119 removed outlier: 3.625A pdb=" N GLU G 118 " --> pdb=" O GLU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 150 removed outlier: 3.777A pdb=" N ASP G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA G 147 " --> pdb=" O LYS G 143 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 160 removed outlier: 3.557A pdb=" N SER G 160 " --> pdb=" O LYS G 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 4.030A pdb=" N VAL H 50 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 69 removed outlier: 4.355A pdb=" N LYS H 63 " --> pdb=" O GLN H 59 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 69 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 removed outlier: 3.700A pdb=" N GLN H 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR H 80 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 97 removed outlier: 3.757A pdb=" N GLU H 89 " --> pdb=" O ASN H 85 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS H 96 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 114 removed outlier: 3.548A pdb=" N THR H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 145 removed outlier: 3.512A pdb=" N ASN H 145 " --> pdb=" O ALA H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 165 through 173 Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.516A pdb=" N THR H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'H' and resid 207 through 220 removed outlier: 3.655A pdb=" N SER H 216 " --> pdb=" O ALA H 212 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR H 217 " --> pdb=" O LYS H 213 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA H 220 " --> pdb=" O SER H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 232 removed outlier: 4.020A pdb=" N LYS H 231 " --> pdb=" O ASP H 227 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 247 removed outlier: 3.613A pdb=" N MET H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 80 removed outlier: 3.636A pdb=" N TYR q 75 " --> pdb=" O CYS q 71 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET q 76 " --> pdb=" O ALA q 72 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR q 77 " --> pdb=" O ASN q 73 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR q 78 " --> pdb=" O LYS q 74 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 84 removed outlier: 3.616A pdb=" N ALA q 84 " --> pdb=" O GLY q 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 81 through 84' Processing helix chain 'q' and resid 144 through 157 removed outlier: 4.208A pdb=" N VAL q 148 " --> pdb=" O ASN q 144 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU q 150 " --> pdb=" O ASP q 146 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR q 157 " --> pdb=" O ARG q 153 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 187 removed outlier: 3.520A pdb=" N LYS q 183 " --> pdb=" O PRO q 179 " (cutoff:3.500A) Processing helix chain 'q' and resid 207 through 212 Processing helix chain 'J' and resid 14 through 19 Processing helix chain 'J' and resid 19 through 27 removed outlier: 3.547A pdb=" N LYS J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN J 25 " --> pdb=" O THR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 39 Processing helix chain 'J' and resid 45 through 55 Processing helix chain 'J' and resid 74 through 86 removed outlier: 3.699A pdb=" N MET J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 97 Processing helix chain 'J' and resid 119 through 122 Processing helix chain 'J' and resid 123 through 128 removed outlier: 3.511A pdb=" N ARG J 127 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 142 Processing helix chain 'J' and resid 148 through 182 removed outlier: 3.661A pdb=" N VAL J 161 " --> pdb=" O ASP J 157 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG J 162 " --> pdb=" O LYS J 158 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU J 165 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS J 169 " --> pdb=" O GLU J 165 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA J 182 " --> pdb=" O SER J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 194 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'K' and resid 26 through 46 removed outlier: 4.627A pdb=" N GLY K 30 " --> pdb=" O PHE K 26 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS K 32 " --> pdb=" O GLN K 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL K 33 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA K 38 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA K 40 " --> pdb=" O ARG K 36 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 67 removed outlier: 4.633A pdb=" N ARG K 67 " --> pdb=" O LYS K 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 64 through 67' Processing helix chain 'K' and resid 76 through 82 Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 105 through 122 removed outlier: 3.521A pdb=" N ALA K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 179 removed outlier: 3.564A pdb=" N SER K 175 " --> pdb=" O ARG K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 187 Processing helix chain 'L' and resid 119 through 124 Processing helix chain 'M' and resid 59 through 61 No H-bonds generated for 'chain 'M' and resid 59 through 61' Processing helix chain 'M' and resid 77 through 88 removed outlier: 4.008A pdb=" N LYS M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 97 removed outlier: 3.616A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA M 96 " --> pdb=" O GLU M 92 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 109 Processing helix chain 'M' and resid 110 through 112 No H-bonds generated for 'chain 'M' and resid 110 through 112' Processing helix chain 'M' and resid 114 through 135 removed outlier: 4.266A pdb=" N VAL M 120 " --> pdb=" O GLU M 116 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN M 126 " --> pdb=" O VAL M 122 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL M 131 " --> pdb=" O LYS M 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS M 132 " --> pdb=" O ARG M 128 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS M 133 " --> pdb=" O TYR M 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 removed outlier: 3.572A pdb=" N MET N 45 " --> pdb=" O HIS N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 82 removed outlier: 4.939A pdb=" N TRP N 79 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE N 82 " --> pdb=" O TRP N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 94 removed outlier: 3.901A pdb=" N ASP N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLN N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR N 90 " --> pdb=" O LYS N 86 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU N 91 " --> pdb=" O ARG N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 108 Processing helix chain 'N' and resid 131 through 140 removed outlier: 3.982A pdb=" N ILE N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 12 Processing helix chain 'O' and resid 16 through 31 removed outlier: 3.950A pdb=" N TRP O 28 " --> pdb=" O ARG O 24 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU O 29 " --> pdb=" O VAL O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 50 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 97 through 110 removed outlier: 3.667A pdb=" N ARG O 109 " --> pdb=" O ARG O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 158 through 163 removed outlier: 3.764A pdb=" N ARG O 162 " --> pdb=" O HIS O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 172 removed outlier: 3.573A pdb=" N SER O 171 " --> pdb=" O THR O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 194 removed outlier: 3.582A pdb=" N TRP O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS O 192 " --> pdb=" O ARG O 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 14 removed outlier: 3.660A pdb=" N SER P 13 " --> pdb=" O SER P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 29 through 38 removed outlier: 4.254A pdb=" N ARG P 35 " --> pdb=" O TYR P 31 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR P 38 " --> pdb=" O LYS P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 86 Proline residue: P 84 - end of helix No H-bonds generated for 'chain 'P' and resid 81 through 86' Processing helix chain 'P' and resid 94 through 114 Processing helix chain 'P' and resid 158 through 170 removed outlier: 3.552A pdb=" N ALA P 162 " --> pdb=" O ARG P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 200 removed outlier: 3.724A pdb=" N ARG P 196 " --> pdb=" O PRO P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 215 removed outlier: 3.507A pdb=" N SER P 205 " --> pdb=" O GLY P 201 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR P 207 " --> pdb=" O HIS P 203 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU P 209 " --> pdb=" O SER P 205 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP P 213 " --> pdb=" O GLU P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 223 removed outlier: 3.528A pdb=" N PHE P 219 " --> pdb=" O ASP P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 228 removed outlier: 3.688A pdb=" N LEU P 227 " --> pdb=" O PHE P 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 235 through 250 removed outlier: 3.707A pdb=" N ARG P 248 " --> pdb=" O HIS P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 268 removed outlier: 3.682A pdb=" N ALA P 267 " --> pdb=" O GLU P 263 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU P 268 " --> pdb=" O GLN P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 291 removed outlier: 3.575A pdb=" N ALA P 283 " --> pdb=" O LYS P 279 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA P 284 " --> pdb=" O GLU P 280 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG P 285 " --> pdb=" O GLU P 281 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA P 287 " --> pdb=" O ALA P 283 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA P 288 " --> pdb=" O ALA P 284 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 39 removed outlier: 4.378A pdb=" N LEU Q 29 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 52 removed outlier: 3.648A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 20 No H-bonds generated for 'chain 'R' and resid 18 through 20' Processing helix chain 'R' and resid 28 through 35 removed outlier: 3.943A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 47 removed outlier: 3.629A pdb=" N ARG R 42 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 72 removed outlier: 3.866A pdb=" N GLU R 72 " --> pdb=" O GLN R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 111 removed outlier: 3.918A pdb=" N VAL R 101 " --> pdb=" O ARG R 97 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU R 105 " --> pdb=" O VAL R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 124 removed outlier: 4.154A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 134 through 147 removed outlier: 3.524A pdb=" N LEU R 138 " --> pdb=" O HIS R 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 45 removed outlier: 3.732A pdb=" N TRP S 42 " --> pdb=" O LYS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.518A pdb=" N ARG S 113 " --> pdb=" O ASP S 109 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 142 removed outlier: 3.640A pdb=" N GLN S 142 " --> pdb=" O GLN S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'T' and resid 26 through 30 removed outlier: 3.801A pdb=" N TYR T 30 " --> pdb=" O LEU T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 110 removed outlier: 4.270A pdb=" N ARG T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 123 removed outlier: 4.085A pdb=" N ALA T 117 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS T 120 " --> pdb=" O ARG T 116 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 12 No H-bonds generated for 'chain 'U' and resid 10 through 12' Processing helix chain 'U' and resid 25 through 34 removed outlier: 4.040A pdb=" N GLU U 31 " --> pdb=" O LYS U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 49 removed outlier: 3.613A pdb=" N LYS U 46 " --> pdb=" O THR U 42 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU U 49 " --> pdb=" O GLN U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 54 Processing helix chain 'U' and resid 73 through 77 Processing helix chain 'U' and resid 84 through 99 removed outlier: 3.516A pdb=" N PHE U 90 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY U 93 " --> pdb=" O LYS U 89 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU U 94 " --> pdb=" O PHE U 90 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN U 97 " --> pdb=" O GLY U 93 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 105 removed outlier: 3.620A pdb=" N ALA U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 134 No H-bonds generated for 'chain 'U' and resid 132 through 134' Processing helix chain 'V' and resid 19 through 25 removed outlier: 3.636A pdb=" N THR V 23 " --> pdb=" O VAL V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 41 Processing helix chain 'V' and resid 72 through 87 Processing helix chain 'W' and resid 58 through 62 Processing helix chain 'W' and resid 71 through 78 removed outlier: 3.674A pdb=" N LYS W 75 " --> pdb=" O THR W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 104 Processing helix chain 'W' and resid 131 through 140 Processing helix chain 'X' and resid 11 through 21 removed outlier: 3.633A pdb=" N TYR X 19 " --> pdb=" O ALA X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 31 removed outlier: 3.799A pdb=" N LEU X 30 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU X 31 " --> pdb=" O ARG X 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 26 through 31' Processing helix chain 'X' and resid 38 through 43 Processing helix chain 'X' and resid 100 through 102 No H-bonds generated for 'chain 'X' and resid 100 through 102' Processing helix chain 'X' and resid 115 through 122 Processing helix chain 'Y' and resid 59 through 64 removed outlier: 3.782A pdb=" N ALA Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS Y 64 " --> pdb=" O LYS Y 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 59 through 64' Processing helix chain 'Y' and resid 99 through 103 removed outlier: 3.588A pdb=" N GLU Y 102 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN Y 103 " --> pdb=" O THR Y 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 99 through 103' Processing helix chain 'Y' and resid 105 through 120 removed outlier: 3.680A pdb=" N GLU Y 109 " --> pdb=" O SER Y 105 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL Y 113 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL Y 114 " --> pdb=" O ALA Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 132 removed outlier: 3.525A pdb=" N SER Y 132 " --> pdb=" O TRP Y 129 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 9 Processing helix chain 'Z' and resid 13 through 38 removed outlier: 3.602A pdb=" N SER Z 19 " --> pdb=" O GLU Z 15 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU Z 36 " --> pdb=" O LYS Z 32 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER Z 37 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 49 Processing helix chain 'Z' and resid 49 through 68 Processing helix chain 'Z' and resid 85 through 90 Processing helix chain 'Z' and resid 101 through 111 removed outlier: 3.760A pdb=" N GLN Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE Z 109 " --> pdb=" O ARG Z 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 17 Processing helix chain 'a' and resid 36 through 56 removed outlier: 3.573A pdb=" N HIS a 45 " --> pdb=" O ARG a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 57 removed outlier: 4.586A pdb=" N ALA b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU b 39 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS b 40 " --> pdb=" O ALA b 36 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA b 50 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU b 56 " --> pdb=" O GLN b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 72 removed outlier: 3.828A pdb=" N ILE b 62 " --> pdb=" O ALA b 58 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS b 66 " --> pdb=" O ILE b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 106 removed outlier: 3.592A pdb=" N GLN b 104 " --> pdb=" O ARG b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 128 removed outlier: 3.811A pdb=" N GLU b 125 " --> pdb=" O LYS b 121 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU b 126 " --> pdb=" O ALA b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 132 No H-bonds generated for 'chain 'b' and resid 130 through 132' Processing helix chain 'b' and resid 141 through 151 Processing helix chain 'b' and resid 165 through 174 removed outlier: 4.217A pdb=" N ILE b 169 " --> pdb=" O ASP b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 177 No H-bonds generated for 'chain 'b' and resid 175 through 177' Processing helix chain 'b' and resid 180 through 190 Processing helix chain 'b' and resid 194 through 200 Processing helix chain 'b' and resid 235 through 243 removed outlier: 3.539A pdb=" N LEU b 239 " --> pdb=" O PHE b 235 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS b 241 " --> pdb=" O ASN b 237 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER b 242 " --> pdb=" O LYS b 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 17 Processing helix chain 'c' and resid 27 through 36 removed outlier: 3.512A pdb=" N LYS c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG c 35 " --> pdb=" O VAL c 31 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 64 removed outlier: 3.639A pdb=" N LEU c 56 " --> pdb=" O ARG c 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR c 58 " --> pdb=" O SER c 54 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET c 61 " --> pdb=" O GLU c 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER c 63 " --> pdb=" O TYR c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 82 removed outlier: 3.719A pdb=" N GLY c 78 " --> pdb=" O ASN c 74 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR c 79 " --> pdb=" O ASN c 75 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA c 80 " --> pdb=" O GLU c 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 43 removed outlier: 3.561A pdb=" N ARG d 31 " --> pdb=" O LYS d 27 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL d 33 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS d 41 " --> pdb=" O LYS d 37 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS d 43 " --> pdb=" O PHE d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 61 through 63 No H-bonds generated for 'chain 'd' and resid 61 through 63' Processing helix chain 'e' and resid 54 through 58 removed outlier: 3.527A pdb=" N TYR e 57 " --> pdb=" O LYS e 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 83 Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.679A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE e 108 " --> pdb=" O ASN e 104 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA e 110 " --> pdb=" O VAL e 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS e 113 " --> pdb=" O LEU e 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 65 removed outlier: 4.264A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 60 through 65' Processing helix chain 'g' and resid 66 through 70 removed outlier: 3.768A pdb=" N HIS g 69 " --> pdb=" O SER g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 102 removed outlier: 3.965A pdb=" N ARG g 88 " --> pdb=" O CYS g 84 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG g 91 " --> pdb=" O GLU g 87 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN g 98 " --> pdb=" O LEU g 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 49 removed outlier: 3.571A pdb=" N GLU h 46 " --> pdb=" O SER h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 62 removed outlier: 3.811A pdb=" N ARG h 56 " --> pdb=" O PRO h 52 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU h 57 " --> pdb=" O TYR h 53 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE h 58 " --> pdb=" O GLU h 54 " (cutoff:3.500A) Processing helix chain 'h' and resid 64 through 77 removed outlier: 4.093A pdb=" N ARG h 68 " --> pdb=" O SER h 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA h 69 " --> pdb=" O GLY h 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG h 70 " --> pdb=" O GLU h 66 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL h 72 " --> pdb=" O ARG h 68 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS h 75 " --> pdb=" O LYS h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 98 removed outlier: 3.637A pdb=" N ASN h 92 " --> pdb=" O GLU h 88 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA h 96 " --> pdb=" O ASN h 92 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 55 removed outlier: 3.571A pdb=" N LYS i 54 " --> pdb=" O ALA i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 68 No H-bonds generated for 'chain 'i' and resid 66 through 68' Processing helix chain 'i' and resid 69 through 77 removed outlier: 3.631A pdb=" N LYS i 75 " --> pdb=" O SER i 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN i 76 " --> pdb=" O ARG i 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 16 removed outlier: 3.666A pdb=" N GLU j 13 " --> pdb=" O LYS j 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG j 16 " --> pdb=" O LEU j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 68 removed outlier: 4.624A pdb=" N LYS j 64 " --> pdb=" O GLY j 60 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER j 68 " --> pdb=" O LYS j 64 " (cutoff:3.500A) Processing helix chain 'k' and resid 6 through 19 removed outlier: 4.355A pdb=" N LYS k 12 " --> pdb=" O ARG k 8 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS k 15 " --> pdb=" O GLN k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 30 removed outlier: 3.670A pdb=" N LEU k 29 " --> pdb=" O TRP k 26 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 48 removed outlier: 3.625A pdb=" N TYR l 43 " --> pdb=" O GLY l 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 13 removed outlier: 3.801A pdb=" N GLY m 12 " --> pdb=" O GLY m 9 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS m 13 " --> pdb=" O ILE m 10 " (cutoff:3.500A) Processing helix chain 'm' and resid 21 through 35 removed outlier: 3.666A pdb=" N LYS m 27 " --> pdb=" O ARG m 23 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS m 28 " --> pdb=" O ARG m 24 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN m 33 " --> pdb=" O LEU m 29 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS m 34 " --> pdb=" O GLU m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 73 through 83 removed outlier: 3.702A pdb=" N ALA m 77 " --> pdb=" O THR m 73 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR m 78 " --> pdb=" O ALA m 74 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL m 79 " --> pdb=" O ALA m 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 35 through 40 removed outlier: 3.801A pdb=" N GLU n 39 " --> pdb=" O TYR n 35 " (cutoff:3.500A) Processing helix chain 'n' and resid 77 through 88 removed outlier: 3.583A pdb=" N LEU n 81 " --> pdb=" O THR n 77 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU n 84 " --> pdb=" O GLU n 80 " (cutoff:3.500A) Processing helix chain 'n' and resid 123 through 133 removed outlier: 3.999A pdb=" N ASP n 131 " --> pdb=" O GLU n 127 " (cutoff:3.500A) Processing helix chain 'n' and resid 168 through 173 Processing helix chain 'n' and resid 174 through 177 removed outlier: 3.550A pdb=" N LEU n 177 " --> pdb=" O SER n 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 174 through 177' Processing helix chain 'n' and resid 211 through 222 removed outlier: 3.598A pdb=" N LEU n 215 " --> pdb=" O THR n 211 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER n 216 " --> pdb=" O ALA n 212 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL n 217 " --> pdb=" O PRO n 213 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER n 220 " --> pdb=" O SER n 216 " (cutoff:3.500A) Processing helix chain 't' and resid 79 through 91 removed outlier: 3.553A pdb=" N LYS t 83 " --> pdb=" O GLU t 79 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS t 88 " --> pdb=" O ALA t 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR t 89 " --> pdb=" O LEU t 85 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN t 90 " --> pdb=" O ALA t 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 42 removed outlier: 3.579A pdb=" N ALA v 37 " --> pdb=" O ASN v 33 " (cutoff:3.500A) Processing helix chain 'v' and resid 52 through 59 Processing helix chain 'z' and resid 380 through 387 removed outlier: 3.967A pdb=" N ARG z 384 " --> pdb=" O ALA z 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET z 385 " --> pdb=" O ALA z 381 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER z 387 " --> pdb=" O ARG z 383 " (cutoff:3.500A) Processing helix chain 'z' and resid 390 through 405 removed outlier: 3.847A pdb=" N LYS z 395 " --> pdb=" O GLU z 391 " (cutoff:3.500A) Processing helix chain 'z' and resid 405 through 417 Processing sheet with id=AA1, first strand: chain 'B' and resid 71 through 77 removed outlier: 4.177A pdb=" N GLN B 47 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 62 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL B 45 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG B 64 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLY B 43 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113 removed outlier: 5.612A pdb=" N ILE B 136 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG B 149 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 138 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.134A pdb=" N VAL C 158 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR C 103 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C 93 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR C 95 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.134A pdb=" N VAL C 158 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 84 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 356 through 359 removed outlier: 6.645A pdb=" N LEU C 356 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP C 59 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 335 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL C 220 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA C 217 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE C 278 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ALA C 219 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR C 276 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE C 282 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS C 325 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 284 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 72 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL C 57 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU C 74 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR C 55 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL C 76 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET C 53 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 78 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AA8, first strand: chain 'D' and resid 15 through 21 removed outlier: 5.958A pdb=" N ASN D 18 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 8 " --> pdb=" O ASN D 18 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL D 151 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU D 150 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 64 removed outlier: 3.521A pdb=" N GLU D 63 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 186 through 187 Processing sheet with id=AB2, first strand: chain 'E' and resid 46 through 49 removed outlier: 3.763A pdb=" N ALA E 66 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS E 16 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 130 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 6 through 11 Processing sheet with id=AB4, first strand: chain 'F' and resid 33 through 37 removed outlier: 3.565A pdb=" N ILE F 24 " --> pdb=" O LYS F 21 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.383A pdb=" N ARG F 91 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL F 181 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL F 93 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE F 179 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 100 through 105 removed outlier: 4.093A pdb=" N GLU F 113 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 77 through 79 removed outlier: 4.294A pdb=" N THR G 38 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL G 39 " --> pdb=" O THR G 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 177 through 179 removed outlier: 3.513A pdb=" N LEU H 150 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'q' and resid 35 through 37 removed outlier: 3.732A pdb=" N PHE q 136 " --> pdb=" O LEU q 52 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS q 49 " --> pdb=" O SER q 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'q' and resid 58 through 61 removed outlier: 5.922A pdb=" N ILE q 99 " --> pdb=" O PRO q 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'q' and resid 191 through 192 Processing sheet with id=AC3, first strand: chain 'J' and resid 5 through 9 removed outlier: 6.060A pdb=" N VAL J 6 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL J 35 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE J 8 " --> pdb=" O VAL J 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AC5, first strand: chain 'K' and resid 57 through 59 Processing sheet with id=AC6, first strand: chain 'K' and resid 123 through 125 removed outlier: 3.644A pdb=" N ILE K 124 " --> pdb=" O ALA Z 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AC8, first strand: chain 'L' and resid 22 through 25 removed outlier: 6.966A pdb=" N MET L 59 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL L 39 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N MET L 57 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA L 99 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY L 100 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN L 24 " --> pdb=" O GLY L 100 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ILE L 102 " --> pdb=" O ASN L 24 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 85 through 86 Processing sheet with id=AD1, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.469A pdb=" N SER L 133 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N GLY L 116 " --> pdb=" O SER L 133 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL L 135 " --> pdb=" O GLY L 116 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 14 through 15 Processing sheet with id=AD3, first strand: chain 'M' and resid 19 through 23 removed outlier: 5.390A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.943A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 72 through 73 Processing sheet with id=AD6, first strand: chain 'N' and resid 101 through 103 removed outlier: 3.523A pdb=" N ALA N 127 " --> pdb=" O GLU N 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 37 through 39 removed outlier: 4.246A pdb=" N ILE O 61 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TYR O 127 " --> pdb=" O ASN O 122 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN O 122 " --> pdb=" O TYR O 127 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR O 129 " --> pdb=" O TRP O 120 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP O 120 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU O 131 " --> pdb=" O SER O 118 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER O 118 " --> pdb=" O GLU O 131 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE O 133 " --> pdb=" O LEU O 116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 72 through 79 removed outlier: 5.388A pdb=" N VAL P 74 " --> pdb=" O SER P 66 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER P 66 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA P 76 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL P 53 " --> pdb=" O ASP P 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 120 through 122 removed outlier: 6.141A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 22 through 23 Processing sheet with id=AE2, first strand: chain 'S' and resid 56 through 63 removed outlier: 6.449A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 87 through 94 removed outlier: 6.593A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 39 through 41 removed outlier: 8.475A pdb=" N GLY T 62 " --> pdb=" O ASN T 77 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N ASN T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL T 64 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN T 66 " --> pdb=" O GLY T 73 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER T 71 " --> pdb=" O THR T 68 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 139 through 141 Processing sheet with id=AE6, first strand: chain 'U' and resid 14 through 22 removed outlier: 4.085A pdb=" N TYR U 21 " --> pdb=" O SER U 144 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N SER U 144 " --> pdb=" O TYR U 21 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR U 151 " --> pdb=" O VAL U 114 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL U 114 " --> pdb=" O THR U 151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 58 through 59 Processing sheet with id=AE8, first strand: chain 'U' and resid 128 through 130 Processing sheet with id=AE9, first strand: chain 'V' and resid 54 through 58 removed outlier: 3.651A pdb=" N THR V 64 " --> pdb=" O THR V 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS V 13 " --> pdb=" O SER V 67 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TYR V 103 " --> pdb=" O THR V 14 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR V 16 " --> pdb=" O TYR V 103 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU V 105 " --> pdb=" O THR V 16 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ASP V 18 " --> pdb=" O LEU V 105 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N PHE V 107 " --> pdb=" O ASP V 18 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU V 102 " --> pdb=" O THR V 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 63 through 66 removed outlier: 3.538A pdb=" N GLN W 65 " --> pdb=" O GLN W 85 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS W 120 " --> pdb=" O VAL W 86 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS W 121 " --> pdb=" O THR W 112 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR W 112 " --> pdb=" O LYS W 121 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR W 123 " --> pdb=" O VAL W 110 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL W 110 " --> pdb=" O TYR W 123 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG W 125 " --> pdb=" O LEU W 108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 32 through 34 Processing sheet with id=AF3, first strand: chain 'X' and resid 55 through 58 removed outlier: 7.075A pdb=" N GLU X 55 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 69 through 74 removed outlier: 3.605A pdb=" N LYS X 69 " --> pdb=" O ASP X 83 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN X 81 " --> pdb=" O SER X 71 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL X 73 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA X 79 " --> pdb=" O VAL X 73 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 87 through 88 Processing sheet with id=AF6, first strand: chain 'Y' and resid 69 through 76 removed outlier: 6.738A pdb=" N LYS Y 69 " --> pdb=" O GLU Y 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE Y 71 " --> pdb=" O GLY Y 45 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL Y 75 " --> pdb=" O ALA Y 41 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU Y 42 " --> pdb=" O VAL Y 26 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL Y 24 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE Y 46 " --> pdb=" O LYS Y 22 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS Y 22 " --> pdb=" O ILE Y 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA Y 11 " --> pdb=" O VAL Y 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE Y 25 " --> pdb=" O LYS Y 9 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS Y 9 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL Y 10 " --> pdb=" O THR Y 83 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 205 through 206 removed outlier: 4.612A pdb=" N SER b 113 " --> pdb=" O ARG b 88 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL b 134 " --> pdb=" O GLY b 230 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 153 through 156 Processing sheet with id=AF9, first strand: chain 'c' and resid 23 through 25 removed outlier: 3.546A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 49 through 51 removed outlier: 6.934A pdb=" N ARG d 50 " --> pdb=" O VAL d 93 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU d 94 " --> pdb=" O ARG d 74 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL d 107 " --> pdb=" O GLU d 11 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 75 through 76 Processing sheet with id=AG3, first strand: chain 'f' and resid 9 through 18 removed outlier: 5.793A pdb=" N HIS f 13 " --> pdb=" O LYS f 31 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS f 31 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER f 15 " --> pdb=" O LEU f 29 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL f 27 " --> pdb=" O GLN f 17 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY f 69 " --> pdb=" O ILE f 49 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.635A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL g 35 " --> pdb=" O LYS g 19 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'i' and resid 16 through 18 Processing sheet with id=AG6, first strand: chain 'j' and resid 3 through 4 Processing sheet with id=AG7, first strand: chain 'j' and resid 3 through 4 removed outlier: 5.090A pdb=" N THR j 22 " --> pdb=" O ARG j 46 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA j 23 " --> pdb=" O ASN j 76 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'l' and resid 7 through 12 removed outlier: 3.653A pdb=" N LYS l 19 " --> pdb=" O CYS l 12 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'l' and resid 67 through 70 removed outlier: 4.485A pdb=" N VAL l 68 " --> pdb=" O LEU l 85 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'm' and resid 47 through 49 Processing sheet with id=AH2, first strand: chain 'n' and resid 4 through 5 Processing sheet with id=AH3, first strand: chain 'n' and resid 24 through 26 Processing sheet with id=AH4, first strand: chain 'n' and resid 69 through 72 Processing sheet with id=AH5, first strand: chain 'n' and resid 108 through 109 removed outlier: 3.614A pdb=" N PHE n 138 " --> pdb=" O ALA n 115 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'n' and resid 152 through 153 Processing sheet with id=AH7, first strand: chain 't' and resid 102 through 103 Processing sheet with id=AH8, first strand: chain 'v' and resid 4 through 5 removed outlier: 3.849A pdb=" N GLU v 4 " --> pdb=" O ILE v 13 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'v' and resid 19 through 22 1449 hydrogen bonds defined for protein. 4038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2223 hydrogen bonds 3590 hydrogen bond angles 0 basepair planarities 924 basepair parallelities 1881 stacking parallelities Total time for adding SS restraints: 181.31 Time building geometry restraints manager: 48.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 14433 1.32 - 1.44: 55109 1.44 - 1.56: 57158 1.56 - 1.69: 6875 1.69 - 1.81: 165 Bond restraints: 133740 Sorted by residual: bond pdb=" CA ASP K 27 " pdb=" C ASP K 27 " ideal model delta sigma weight residual 1.522 1.445 0.076 1.72e-02 3.38e+03 1.97e+01 bond pdb=" C LEU P 83 " pdb=" N PRO P 84 " ideal model delta sigma weight residual 1.336 1.376 -0.041 1.08e-02 8.57e+03 1.41e+01 bond pdb=" CA ALA i 53 " pdb=" C ALA i 53 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.80e-02 3.09e+03 1.40e+01 bond pdb=" CA LYS D 191 " pdb=" C LYS D 191 " ideal model delta sigma weight residual 1.522 1.462 0.060 1.72e-02 3.38e+03 1.22e+01 bond pdb=" N ILE B 238 " pdb=" CA ILE B 238 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.19e-02 7.06e+03 9.80e+00 ... (remaining 133735 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.59: 18033 105.59 - 113.44: 80602 113.44 - 121.29: 63966 121.29 - 129.14: 31986 129.14 - 136.99: 2796 Bond angle restraints: 197383 Sorted by residual: angle pdb=" C PRO C 18 " pdb=" CA PRO C 18 " pdb=" CB PRO C 18 " ideal model delta sigma weight residual 111.56 128.95 -17.39 1.65e+00 3.67e-01 1.11e+02 angle pdb=" CA PRO C 18 " pdb=" N PRO C 18 " pdb=" CD PRO C 18 " ideal model delta sigma weight residual 112.00 98.54 13.46 1.40e+00 5.10e-01 9.25e+01 angle pdb=" N VAL n 193 " pdb=" CA VAL n 193 " pdb=" C VAL n 193 " ideal model delta sigma weight residual 113.71 106.99 6.72 9.50e-01 1.11e+00 5.00e+01 angle pdb=" N VAL D 42 " pdb=" CA VAL D 42 " pdb=" C VAL D 42 " ideal model delta sigma weight residual 113.42 105.45 7.97 1.17e+00 7.31e-01 4.64e+01 angle pdb=" N ILE B 238 " pdb=" CA ILE B 238 " pdb=" C ILE B 238 " ideal model delta sigma weight residual 110.53 116.64 -6.11 9.40e-01 1.13e+00 4.22e+01 ... (remaining 197378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 76041 35.94 - 71.87: 7894 71.87 - 107.81: 864 107.81 - 143.74: 22 143.74 - 179.68: 50 Dihedral angle restraints: 84871 sinusoidal: 66487 harmonic: 18384 Sorted by residual: dihedral pdb=" O4' U A3306 " pdb=" C1' U A3306 " pdb=" N1 U A3306 " pdb=" C2 U A3306 " ideal model delta sinusoidal sigma weight residual 200.00 29.98 170.02 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U A1269 " pdb=" C1' U A1269 " pdb=" N1 U A1269 " pdb=" C2 U A1269 " ideal model delta sinusoidal sigma weight residual 200.00 32.19 167.81 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' U A1081 " pdb=" C1' U A1081 " pdb=" N1 U A1081 " pdb=" C2 U A1081 " ideal model delta sinusoidal sigma weight residual 200.00 32.76 167.24 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 84868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 24376 0.133 - 0.266: 413 0.266 - 0.398: 22 0.398 - 0.531: 2 0.531 - 0.664: 1 Chirality restraints: 24814 Sorted by residual: chirality pdb=" CB ILE D 148 " pdb=" CA ILE D 148 " pdb=" CG1 ILE D 148 " pdb=" CG2 ILE D 148 " both_signs ideal model delta sigma weight residual False 2.64 1.98 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA PRO C 18 " pdb=" N PRO C 18 " pdb=" C PRO C 18 " pdb=" CB PRO C 18 " both_signs ideal model delta sigma weight residual False 2.72 2.21 0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CB VAL q 197 " pdb=" CA VAL q 197 " pdb=" CG1 VAL q 197 " pdb=" CG2 VAL q 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 24811 not shown) Planarity restraints: 12218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 17 " -0.074 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO C 18 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 62 " 0.029 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR O 62 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR O 62 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR O 62 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR O 62 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR O 62 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR O 62 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR O 62 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN L 104 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO L 105 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO L 105 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 105 " 0.045 5.00e-02 4.00e+02 ... (remaining 12215 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 858 2.52 - 3.12: 82714 3.12 - 3.71: 219693 3.71 - 4.31: 334214 4.31 - 4.90: 477336 Nonbonded interactions: 1114815 Sorted by model distance: nonbonded pdb=" O LYS C 50 " pdb=" O ARG C 332 " model vdw 1.931 3.040 nonbonded pdb=" OP1 U A3304 " pdb=" NH2 ARG C 332 " model vdw 2.026 2.520 nonbonded pdb=" O2' G A2177 " pdb=" O LEU B 126 " model vdw 2.046 2.440 nonbonded pdb=" O2' G A2945 " pdb=" OP2 C A2948 " model vdw 2.202 2.440 nonbonded pdb=" OP1 A A 929 " pdb=" OG SER D 61 " model vdw 2.226 2.440 ... (remaining 1114810 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=1.00 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 13.630 Check model and map are aligned: 1.310 Set scattering table: 0.820 Process input model: 413.000 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.270 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: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 436.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 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 : 0.010 0.095 133740 Z= 0.588 Angle : 0.939 17.391 197383 Z= 0.492 Chirality : 0.051 0.664 24814 Planarity : 0.006 0.106 12218 Dihedral : 22.670 179.677 73025 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.10 % Favored : 92.83 % Rotamer: Outliers : 1.29 % Allowed : 10.98 % Favored : 87.73 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.08), residues: 6278 helix: -4.43 (0.05), residues: 1907 sheet: -2.41 (0.16), residues: 904 loop : -2.51 (0.09), residues: 3467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 122 HIS 0.018 0.002 HIS C 3 PHE 0.024 0.003 PHE E 127 TYR 0.061 0.003 TYR O 62 ARG 0.014 0.001 ARG g 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1083 time to evaluate : 6.029 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG R 151 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 75 ILE cc_start: 0.8661 (mp) cc_final: 0.8420 (mt) REVERT: B 144 ASN cc_start: 0.8535 (t0) cc_final: 0.8191 (t0) REVERT: B 237 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9089 (mt) REVERT: C 97 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7674 (mtt180) REVERT: C 302 LYS cc_start: 0.7774 (mttm) cc_final: 0.7460 (mtmm) REVERT: D 237 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: D 288 ARG cc_start: 0.8471 (tmm160) cc_final: 0.8206 (ttp80) REVERT: D 346 LYS cc_start: 0.6471 (tptt) cc_final: 0.6232 (tptp) REVERT: E 85 LYS cc_start: 0.6897 (pttt) cc_final: 0.5865 (tmtt) REVERT: E 117 ASP cc_start: 0.6177 (t70) cc_final: 0.5896 (t70) REVERT: F 1 MET cc_start: 0.5666 (mtm) cc_final: 0.5367 (mtm) REVERT: F 3 TYR cc_start: 0.7980 (m-80) cc_final: 0.7683 (m-10) REVERT: H 61 GLN cc_start: 0.8462 (mt0) cc_final: 0.8195 (mp10) REVERT: H 226 TYR cc_start: 0.8683 (t80) cc_final: 0.8284 (t80) REVERT: q 45 GLU cc_start: 0.6326 (tt0) cc_final: 0.6005 (mm-30) REVERT: q 82 ARG cc_start: 0.6731 (ttp80) cc_final: 0.6317 (tpp80) REVERT: q 153 ARG cc_start: 0.6859 (ttp80) cc_final: 0.6620 (ttt-90) REVERT: K 79 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8748 (mt-10) REVERT: L 40 LYS cc_start: 0.8596 (mmtp) cc_final: 0.8341 (mmtm) REVERT: L 108 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7232 (mm-30) REVERT: M 114 ASP cc_start: 0.8774 (t0) cc_final: 0.8573 (t0) REVERT: N 105 LEU cc_start: 0.9484 (tp) cc_final: 0.9212 (tp) REVERT: O 122 ASN cc_start: 0.8669 (t0) cc_final: 0.8463 (t0) REVERT: O 131 GLU cc_start: 0.8010 (pt0) cc_final: 0.7721 (pt0) REVERT: P 45 ASN cc_start: 0.8685 (t0) cc_final: 0.8450 (t0) REVERT: P 57 ASN cc_start: 0.8802 (m110) cc_final: 0.8572 (m110) REVERT: T 13 TYR cc_start: 0.8875 (m-80) cc_final: 0.8554 (m-80) REVERT: T 156 TYR cc_start: 0.7740 (t80) cc_final: 0.7490 (t80) REVERT: U 64 ASN cc_start: 0.9075 (p0) cc_final: 0.8807 (p0) REVERT: U 124 LYS cc_start: 0.8566 (mttt) cc_final: 0.8332 (mttp) REVERT: V 52 ASN cc_start: 0.6354 (OUTLIER) cc_final: 0.5983 (m-40) REVERT: Y 72 ILE cc_start: 0.9175 (mm) cc_final: 0.8925 (mm) REVERT: Y 108 GLU cc_start: 0.7744 (mp0) cc_final: 0.7418 (mp0) REVERT: Z 102 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7325 (tm-30) REVERT: b 33 ARG cc_start: 0.7101 (ttp-170) cc_final: 0.6644 (ttp-170) REVERT: b 52 GLN cc_start: 0.8727 (tp40) cc_final: 0.8506 (tp40) REVERT: d 47 ASP cc_start: 0.8351 (m-30) cc_final: 0.8109 (m-30) REVERT: f 54 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7538 (ttp-170) REVERT: f 106 ASN cc_start: 0.8105 (t0) cc_final: 0.7827 (t0) REVERT: g 95 ILE cc_start: 0.9434 (mm) cc_final: 0.9223 (mm) REVERT: i 20 ASN cc_start: 0.8433 (m-40) cc_final: 0.8197 (t0) REVERT: k 37 TYR cc_start: 0.8353 (p90) cc_final: 0.7933 (p90) REVERT: l 32 LYS cc_start: 0.7085 (mmtt) cc_final: 0.6405 (mmmt) REVERT: m 24 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7671 (mtm110) REVERT: m 45 LYS cc_start: 0.8428 (tttp) cc_final: 0.8022 (ttpt) REVERT: n 16 PHE cc_start: 0.8498 (m-80) cc_final: 0.7912 (m-10) REVERT: n 127 GLU cc_start: 0.6334 (mm-30) cc_final: 0.5990 (tp30) REVERT: n 140 GLN cc_start: 0.7228 (pp30) cc_final: 0.6966 (pp30) REVERT: z 385 MET cc_start: 0.3811 (mmm) cc_final: 0.3373 (mpp) outliers start: 69 outliers final: 39 residues processed: 1140 average time/residue: 1.1758 time to fit residues: 2256.5204 Evaluate side-chains 955 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 913 time to evaluate : 5.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 18 PRO Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 151 ARG Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 52 ASN Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain z residue 424 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 809 optimal weight: 7.9990 chunk 726 optimal weight: 6.9990 chunk 403 optimal weight: 0.8980 chunk 248 optimal weight: 20.0000 chunk 490 optimal weight: 6.9990 chunk 388 optimal weight: 3.9990 chunk 751 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 457 optimal weight: 7.9990 chunk 559 optimal weight: 1.9990 chunk 870 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 215 ASN C 177 HIS ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS D 291 ASN F 51 GLN F 58 HIS F 162 GLN G 97 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 59 GLN H 240 ASN ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN J 121 GLN K 19 GLN L 4 ASN M 56 GLN N 64 GLN N 74 ASN O 123 GLN P 32 GLN P 39 GLN P 206 GLN Q 15 HIS Q 126 GLN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN U 34 GLN V 88 GLN V 101 ASN b 104 GLN b 146 GLN e 52 GLN f 24 ASN f 26 ASN f 106 ASN g 11 ASN g 18 ASN g 83 ASN ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 28 HIS k 25 GLN l 59 HIS n 145 ASN n 170 GLN n 187 ASN t 90 ASN z 393 GLN z 407 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 133740 Z= 0.304 Angle : 0.629 10.361 197383 Z= 0.325 Chirality : 0.039 0.273 24814 Planarity : 0.005 0.160 12218 Dihedral : 23.293 179.048 60346 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 3.26 % Allowed : 15.27 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -3.52 (0.09), residues: 6278 helix: -2.75 (0.09), residues: 1984 sheet: -2.02 (0.16), residues: 929 loop : -2.14 (0.09), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 200 HIS 0.010 0.001 HIS F 64 PHE 0.042 0.002 PHE b 229 TYR 0.025 0.002 TYR D 194 ARG 0.006 0.000 ARG L 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1015 time to evaluate : 5.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG R 151 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 69 TYR cc_start: 0.8089 (t80) cc_final: 0.7630 (t80) REVERT: B 75 ILE cc_start: 0.8646 (mp) cc_final: 0.8357 (mt) REVERT: C 97 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7699 (mtt180) REVERT: C 137 TYR cc_start: 0.6649 (m-10) cc_final: 0.6356 (m-80) REVERT: C 302 LYS cc_start: 0.7784 (mttm) cc_final: 0.7479 (mtmm) REVERT: C 318 LYS cc_start: 0.7638 (pptt) cc_final: 0.7387 (pptt) REVERT: D 288 ARG cc_start: 0.8506 (tmm160) cc_final: 0.8284 (ttp80) REVERT: D 346 LYS cc_start: 0.6396 (tptt) cc_final: 0.6189 (tptp) REVERT: E 85 LYS cc_start: 0.6829 (pttt) cc_final: 0.5999 (tmtt) REVERT: F 1 MET cc_start: 0.5610 (mtm) cc_final: 0.5341 (mtm) REVERT: F 3 TYR cc_start: 0.7925 (m-80) cc_final: 0.7425 (m-10) REVERT: H 61 GLN cc_start: 0.8210 (mt0) cc_final: 0.7925 (mp10) REVERT: H 157 VAL cc_start: 0.7526 (OUTLIER) cc_final: 0.7313 (m) REVERT: q 57 LEU cc_start: 0.7675 (tp) cc_final: 0.7322 (tt) REVERT: q 82 ARG cc_start: 0.6765 (ttp80) cc_final: 0.6229 (tpp80) REVERT: q 153 ARG cc_start: 0.6952 (ttp80) cc_final: 0.6653 (ttt-90) REVERT: L 28 ASN cc_start: 0.8672 (p0) cc_final: 0.8459 (p0) REVERT: L 108 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7172 (mm-30) REVERT: L 110 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7651 (tptp) REVERT: L 128 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.7530 (mmm-85) REVERT: M 114 ASP cc_start: 0.8735 (t0) cc_final: 0.8440 (t0) REVERT: P 45 ASN cc_start: 0.8699 (t0) cc_final: 0.8485 (t0) REVERT: P 185 PHE cc_start: 0.7982 (t80) cc_final: 0.7763 (t80) REVERT: T 106 LEU cc_start: 0.9381 (mt) cc_final: 0.9056 (mp) REVERT: T 156 TYR cc_start: 0.7751 (t80) cc_final: 0.7461 (t80) REVERT: V 28 PHE cc_start: 0.7924 (t80) cc_final: 0.7582 (t80) REVERT: V 52 ASN cc_start: 0.6260 (OUTLIER) cc_final: 0.5973 (m-40) REVERT: V 83 TYR cc_start: 0.8360 (t80) cc_final: 0.8114 (t80) REVERT: Y 72 ILE cc_start: 0.9291 (mm) cc_final: 0.8900 (mm) REVERT: Z 102 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7231 (tm-30) REVERT: b 30 ARG cc_start: 0.6417 (mmm-85) cc_final: 0.6199 (mmm-85) REVERT: b 52 GLN cc_start: 0.8731 (tp40) cc_final: 0.8334 (tp40) REVERT: f 54 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7534 (ttp-170) REVERT: f 106 ASN cc_start: 0.7975 (t0) cc_final: 0.7556 (t0) REVERT: g 95 ILE cc_start: 0.9350 (mm) cc_final: 0.9142 (mm) REVERT: i 20 ASN cc_start: 0.8384 (m-40) cc_final: 0.8107 (t0) REVERT: k 33 ASN cc_start: 0.8471 (t0) cc_final: 0.8231 (t0) REVERT: k 35 ILE cc_start: 0.8929 (mp) cc_final: 0.8619 (mt) REVERT: k 37 TYR cc_start: 0.8374 (p90) cc_final: 0.7999 (p90) REVERT: l 32 LYS cc_start: 0.7061 (mmtt) cc_final: 0.6398 (mmmt) REVERT: m 45 LYS cc_start: 0.8271 (tttp) cc_final: 0.7920 (ttpt) REVERT: n 16 PHE cc_start: 0.8506 (m-10) cc_final: 0.8004 (m-10) REVERT: n 127 GLU cc_start: 0.6447 (mm-30) cc_final: 0.6164 (tp30) outliers start: 174 outliers final: 122 residues processed: 1114 average time/residue: 1.0362 time to fit residues: 1984.6288 Evaluate side-chains 1051 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 927 time to evaluate : 5.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 194 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain q residue 44 ASP Chi-restraints excluded: chain q residue 56 GLU Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 151 ARG Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 28 SER Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 52 ASN Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 97 ILE Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 51 ILE Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 61 MET Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 49 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 18 ASN Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 25 GLN Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 38 ASP Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 56 THR Chi-restraints excluded: chain m residue 82 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 118 HIS Chi-restraints excluded: chain n residue 125 THR Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain z residue 404 LEU Chi-restraints excluded: chain z residue 407 ASN Chi-restraints excluded: chain z residue 424 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 483 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 724 optimal weight: 0.0970 chunk 593 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 872 optimal weight: 1.9990 chunk 942 optimal weight: 10.0000 chunk 776 optimal weight: 1.9990 chunk 865 optimal weight: 3.9990 chunk 297 optimal weight: 30.0000 chunk 699 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 194 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN F 51 GLN G 80 ASN G 97 ASN G 138 GLN H 28 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN M 56 GLN M 62 GLN M 126 GLN P 90 HIS ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 GLN V 88 GLN V 101 ASN b 104 GLN b 146 GLN e 52 GLN g 11 ASN ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 25 GLN l 38 GLN z 407 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 133740 Z= 0.192 Angle : 0.536 10.171 197383 Z= 0.277 Chirality : 0.034 0.276 24814 Planarity : 0.004 0.151 12218 Dihedral : 23.129 179.740 60323 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 3.40 % Allowed : 17.17 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.10), residues: 6278 helix: -1.75 (0.11), residues: 2006 sheet: -1.70 (0.16), residues: 948 loop : -1.85 (0.10), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 200 HIS 0.006 0.001 HIS F 64 PHE 0.035 0.001 PHE b 229 TYR 0.018 0.001 TYR V 78 ARG 0.041 0.000 ARG n 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 997 time to evaluate : 5.904 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: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 69 TYR cc_start: 0.7948 (t80) cc_final: 0.7529 (t80) REVERT: B 75 ILE cc_start: 0.8665 (mp) cc_final: 0.8388 (mt) REVERT: B 88 ILE cc_start: 0.9470 (mm) cc_final: 0.9265 (mt) REVERT: B 194 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8671 (t0) REVERT: C 97 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7602 (mtt180) REVERT: C 302 LYS cc_start: 0.7762 (mttm) cc_final: 0.7459 (mtmm) REVERT: D 288 ARG cc_start: 0.8481 (tmm160) cc_final: 0.8166 (ttp80) REVERT: E 78 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7424 (mt-10) REVERT: E 85 LYS cc_start: 0.6981 (pttt) cc_final: 0.6144 (tmtt) REVERT: E 89 TYR cc_start: 0.7033 (m-80) cc_final: 0.6806 (m-80) REVERT: F 1 MET cc_start: 0.5679 (mtm) cc_final: 0.5429 (mtm) REVERT: q 51 HIS cc_start: 0.8433 (m170) cc_final: 0.7639 (m-70) REVERT: q 153 ARG cc_start: 0.7042 (ttp80) cc_final: 0.6675 (ttt-90) REVERT: q 207 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: K 79 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8590 (mt-10) REVERT: L 28 ASN cc_start: 0.8651 (p0) cc_final: 0.8447 (p0) REVERT: L 59 MET cc_start: 0.8640 (mmm) cc_final: 0.8426 (mmm) REVERT: M 121 MET cc_start: 0.8090 (ppp) cc_final: 0.7890 (ppp) REVERT: M 132 LYS cc_start: 0.7501 (mmtt) cc_final: 0.6661 (ttpt) REVERT: O 127 TYR cc_start: 0.8820 (m-80) cc_final: 0.8498 (m-80) REVERT: O 131 GLU cc_start: 0.7766 (pt0) cc_final: 0.7547 (pt0) REVERT: P 45 ASN cc_start: 0.8631 (t0) cc_final: 0.8394 (t0) REVERT: P 208 MET cc_start: 0.6850 (mtp) cc_final: 0.6649 (mtp) REVERT: R 7 GLN cc_start: 0.8492 (mp10) cc_final: 0.8253 (mm-40) REVERT: R 68 GLN cc_start: 0.8284 (tp40) cc_final: 0.7825 (tp40) REVERT: S 41 TYR cc_start: 0.9074 (t80) cc_final: 0.8828 (t80) REVERT: V 36 TYR cc_start: 0.8935 (t80) cc_final: 0.8706 (t80) REVERT: W 131 ASP cc_start: 0.7453 (t70) cc_final: 0.7208 (t0) REVERT: Y 18 TYR cc_start: 0.8605 (m-80) cc_final: 0.8357 (m-80) REVERT: Y 108 GLU cc_start: 0.7690 (mp0) cc_final: 0.7485 (mp0) REVERT: Z 64 GLU cc_start: 0.8142 (tp30) cc_final: 0.7730 (tp30) REVERT: Z 102 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7142 (tm-30) REVERT: b 52 GLN cc_start: 0.8612 (tp40) cc_final: 0.8262 (tp40) REVERT: f 54 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7413 (ttp-170) REVERT: f 106 ASN cc_start: 0.7850 (t0) cc_final: 0.7162 (t0) REVERT: g 54 ILE cc_start: 0.9321 (mm) cc_final: 0.9098 (mt) REVERT: i 11 ARG cc_start: 0.8359 (mtp85) cc_final: 0.7942 (mtt90) REVERT: k 35 ILE cc_start: 0.8905 (mp) cc_final: 0.8632 (mt) REVERT: l 32 LYS cc_start: 0.7019 (mmtt) cc_final: 0.6363 (mmmt) REVERT: m 24 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7623 (mtm110) REVERT: m 45 LYS cc_start: 0.8282 (tttp) cc_final: 0.7809 (ttpt) REVERT: n 1 MET cc_start: 0.4035 (ttm) cc_final: 0.3742 (ttp) REVERT: n 127 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6240 (tp30) outliers start: 181 outliers final: 126 residues processed: 1103 average time/residue: 1.0737 time to fit residues: 2043.4255 Evaluate side-chains 1052 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 924 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain q residue 56 GLU Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 118 GLU Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain V residue 52 ASN Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 97 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 51 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 49 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 13 LYS Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 38 ASP Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 56 THR Chi-restraints excluded: chain n residue 59 ILE Chi-restraints excluded: chain n residue 118 HIS Chi-restraints excluded: chain n residue 137 VAL Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain n residue 177 LEU Chi-restraints excluded: chain n residue 181 LEU Chi-restraints excluded: chain n residue 211 THR Chi-restraints excluded: chain z residue 379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 861 optimal weight: 9.9990 chunk 655 optimal weight: 0.7980 chunk 452 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 chunk 416 optimal weight: 10.0000 chunk 585 optimal weight: 10.0000 chunk 875 optimal weight: 0.6980 chunk 926 optimal weight: 0.0030 chunk 457 optimal weight: 0.0030 chunk 829 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 overall best weight: 1.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN G 97 ASN G 138 GLN G 167 ASN H 28 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN L 47 ASN L 132 ASN M 62 GLN M 126 GLN P 90 HIS ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN U 121 GLN V 88 GLN V 101 ASN Y 57 HIS Z 68 GLN b 104 GLN b 146 GLN b 209 ASN c 36 GLN g 61 GLN ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 25 GLN l 38 GLN m 34 HIS z 393 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 133740 Z= 0.159 Angle : 0.503 10.072 197383 Z= 0.259 Chirality : 0.032 0.255 24814 Planarity : 0.004 0.147 12218 Dihedral : 23.006 179.797 60316 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 3.64 % Allowed : 18.26 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 6278 helix: -1.12 (0.11), residues: 1998 sheet: -1.46 (0.16), residues: 946 loop : -1.62 (0.10), residues: 3334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP i 49 HIS 0.008 0.001 HIS v 59 PHE 0.032 0.001 PHE b 229 TYR 0.018 0.001 TYR D 194 ARG 0.011 0.000 ARG P 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 983 time to evaluate : 5.875 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 69 TYR cc_start: 0.7869 (t80) cc_final: 0.7464 (t80) REVERT: B 75 ILE cc_start: 0.8698 (mp) cc_final: 0.8423 (mt) REVERT: B 140 ASN cc_start: 0.7790 (t0) cc_final: 0.7449 (t0) REVERT: B 144 ASN cc_start: 0.8589 (t0) cc_final: 0.8353 (t0) REVERT: C 97 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7638 (mtt180) REVERT: C 302 LYS cc_start: 0.7786 (mttm) cc_final: 0.7488 (mtmm) REVERT: D 288 ARG cc_start: 0.8453 (tmm160) cc_final: 0.8149 (ttp80) REVERT: E 78 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7221 (mt-10) REVERT: E 85 LYS cc_start: 0.7092 (pttt) cc_final: 0.6170 (tmtt) REVERT: F 1 MET cc_start: 0.5741 (mtm) cc_final: 0.5480 (mtm) REVERT: F 8 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8228 (mm-40) REVERT: F 31 ARG cc_start: 0.7340 (ptm-80) cc_final: 0.6797 (ptm-80) REVERT: F 41 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8687 (tp) REVERT: F 160 ASP cc_start: 0.8236 (m-30) cc_final: 0.7807 (m-30) REVERT: q 17 TYR cc_start: 0.8850 (t80) cc_final: 0.8569 (t80) REVERT: q 51 HIS cc_start: 0.8389 (m170) cc_final: 0.7630 (m-70) REVERT: q 82 ARG cc_start: 0.6963 (ttp-170) cc_final: 0.6124 (ttt180) REVERT: q 153 ARG cc_start: 0.7071 (ttp80) cc_final: 0.6717 (ttt-90) REVERT: K 79 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8541 (mt-10) REVERT: L 108 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7423 (mm-30) REVERT: M 132 LYS cc_start: 0.7412 (mmtt) cc_final: 0.6614 (ttpt) REVERT: O 127 TYR cc_start: 0.8789 (m-80) cc_final: 0.8466 (m-80) REVERT: P 45 ASN cc_start: 0.8554 (t0) cc_final: 0.8303 (t0) REVERT: Q 22 ASP cc_start: 0.7320 (t0) cc_final: 0.6993 (t0) REVERT: R 7 GLN cc_start: 0.8478 (mp10) cc_final: 0.8249 (mm-40) REVERT: S 30 PHE cc_start: 0.8420 (m-80) cc_final: 0.8176 (m-80) REVERT: T 13 TYR cc_start: 0.8737 (m-80) cc_final: 0.8521 (m-80) REVERT: U 64 ASN cc_start: 0.8865 (p0) cc_final: 0.8476 (p0) REVERT: Y 18 TYR cc_start: 0.8494 (m-80) cc_final: 0.8279 (m-80) REVERT: Y 88 ASP cc_start: 0.7336 (p0) cc_final: 0.6778 (p0) REVERT: Y 106 GLN cc_start: 0.7552 (tp40) cc_final: 0.7016 (tp40) REVERT: Y 108 GLU cc_start: 0.7674 (mp0) cc_final: 0.7281 (mp0) REVERT: b 52 GLN cc_start: 0.8585 (tp40) cc_final: 0.8228 (tp40) REVERT: f 106 ASN cc_start: 0.7815 (t0) cc_final: 0.7142 (t0) REVERT: g 54 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9023 (mt) REVERT: i 11 ARG cc_start: 0.8328 (mtp85) cc_final: 0.7958 (mtt90) REVERT: k 35 ILE cc_start: 0.8841 (mp) cc_final: 0.8607 (mt) REVERT: k 36 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8050 (mmm-85) REVERT: k 37 TYR cc_start: 0.8308 (p90) cc_final: 0.7946 (p90) REVERT: l 8 ARG cc_start: 0.8202 (ptm160) cc_final: 0.7905 (ptm-80) REVERT: m 24 ARG cc_start: 0.7832 (ttm110) cc_final: 0.7575 (mtm110) REVERT: n 127 GLU cc_start: 0.6391 (mm-30) cc_final: 0.6139 (tp30) REVERT: z 385 MET cc_start: 0.3777 (mmm) cc_final: 0.3266 (mpp) REVERT: z 398 MET cc_start: 0.7278 (tpp) cc_final: 0.6928 (ttt) outliers start: 194 outliers final: 133 residues processed: 1094 average time/residue: 1.0781 time to fit residues: 2040.0662 Evaluate side-chains 1054 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 918 time to evaluate : 5.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain q residue 56 GLU Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 129 ASP Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 97 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 51 ILE Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 49 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 36 ARG Chi-restraints excluded: chain l residue 13 LYS Chi-restraints excluded: chain l residue 35 LEU Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 38 ASP Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 46 ILE Chi-restraints excluded: chain n residue 56 THR Chi-restraints excluded: chain n residue 59 ILE Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 118 HIS Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain n residue 177 LEU Chi-restraints excluded: chain n residue 181 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 211 THR Chi-restraints excluded: chain t residue 95 VAL Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain z residue 379 THR Chi-restraints excluded: chain z residue 390 THR Chi-restraints excluded: chain z residue 404 LEU Chi-restraints excluded: chain z residue 424 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 772 optimal weight: 0.0020 chunk 526 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 690 optimal weight: 0.0270 chunk 382 optimal weight: 8.9990 chunk 791 optimal weight: 4.9990 chunk 640 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 473 optimal weight: 5.9990 chunk 832 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 overall best weight: 3.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN F 51 GLN G 80 ASN G 97 ASN H 28 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN M 56 GLN M 62 GLN P 90 HIS R 27 ASN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN U 120 ASN U 121 GLN V 49 ASN V 52 ASN V 88 GLN V 101 ASN b 81 HIS b 104 GLN b 146 GLN g 11 ASN g 18 ASN ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 25 GLN ** k 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN v 59 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 133740 Z= 0.241 Angle : 0.542 23.912 197383 Z= 0.277 Chirality : 0.034 0.256 24814 Planarity : 0.004 0.193 12218 Dihedral : 22.977 179.914 60310 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 4.18 % Allowed : 18.67 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.10), residues: 6278 helix: -0.94 (0.11), residues: 2012 sheet: -1.41 (0.16), residues: 944 loop : -1.56 (0.10), residues: 3322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 200 HIS 0.006 0.001 HIS v 59 PHE 0.034 0.001 PHE b 229 TYR 0.023 0.001 TYR D 194 ARG 0.006 0.000 ARG P 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 926 time to evaluate : 6.016 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. REVERT: B 69 TYR cc_start: 0.7721 (t80) cc_final: 0.7308 (t80) REVERT: B 75 ILE cc_start: 0.8691 (mp) cc_final: 0.8419 (mt) REVERT: B 140 ASN cc_start: 0.7831 (t0) cc_final: 0.7497 (t0) REVERT: B 144 ASN cc_start: 0.8659 (t0) cc_final: 0.8356 (t0) REVERT: C 97 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7593 (mtt180) REVERT: C 302 LYS cc_start: 0.7791 (mttm) cc_final: 0.7488 (mtmm) REVERT: D 288 ARG cc_start: 0.8434 (tmm160) cc_final: 0.8219 (ttp80) REVERT: D 311 HIS cc_start: 0.8758 (t70) cc_final: 0.8548 (t70) REVERT: E 78 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7086 (mt-10) REVERT: E 80 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6494 (tt) REVERT: E 85 LYS cc_start: 0.7118 (pttt) cc_final: 0.6316 (tmtt) REVERT: E 157 GLU cc_start: 0.7803 (pp20) cc_final: 0.7445 (pp20) REVERT: F 1 MET cc_start: 0.5762 (mtm) cc_final: 0.5531 (mtm) REVERT: F 3 TYR cc_start: 0.7909 (m-80) cc_final: 0.7514 (m-10) REVERT: F 41 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8672 (tp) REVERT: H 191 ASN cc_start: 0.8537 (p0) cc_final: 0.8331 (p0) REVERT: q 17 TYR cc_start: 0.8850 (t80) cc_final: 0.8548 (t80) REVERT: q 51 HIS cc_start: 0.8424 (m170) cc_final: 0.7883 (m90) REVERT: q 57 LEU cc_start: 0.7424 (tp) cc_final: 0.7058 (tt) REVERT: q 82 ARG cc_start: 0.6996 (ttp-170) cc_final: 0.5926 (tpp80) REVERT: q 113 GLN cc_start: 0.5143 (OUTLIER) cc_final: 0.3992 (pm20) REVERT: q 153 ARG cc_start: 0.7030 (ttp80) cc_final: 0.6671 (ttt-90) REVERT: q 207 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7597 (tp30) REVERT: L 28 ASN cc_start: 0.8680 (p0) cc_final: 0.8467 (p0) REVERT: M 132 LYS cc_start: 0.7474 (mmtt) cc_final: 0.6639 (ttpt) REVERT: P 45 ASN cc_start: 0.8611 (t0) cc_final: 0.8375 (t0) REVERT: R 7 GLN cc_start: 0.8534 (mp10) cc_final: 0.8274 (mm-40) REVERT: T 13 TYR cc_start: 0.8779 (m-80) cc_final: 0.8570 (m-80) REVERT: Y 88 ASP cc_start: 0.7634 (p0) cc_final: 0.7388 (p0) REVERT: Y 108 GLU cc_start: 0.7622 (mp0) cc_final: 0.7396 (mp0) REVERT: Y 119 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8060 (mm-30) REVERT: b 52 GLN cc_start: 0.8640 (tp40) cc_final: 0.8244 (tp40) REVERT: f 49 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8485 (mt) REVERT: f 106 ASN cc_start: 0.7934 (t0) cc_final: 0.7296 (t0) REVERT: g 18 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8514 (t0) REVERT: g 54 ILE cc_start: 0.9303 (mm) cc_final: 0.9069 (mt) REVERT: i 11 ARG cc_start: 0.8473 (mtp85) cc_final: 0.7970 (mtt90) REVERT: i 20 ASN cc_start: 0.8590 (t0) cc_final: 0.8155 (t0) REVERT: k 36 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8055 (mmm-85) REVERT: k 37 TYR cc_start: 0.8369 (p90) cc_final: 0.8017 (p90) REVERT: l 32 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6315 (mmmt) REVERT: m 24 ARG cc_start: 0.7807 (ttm110) cc_final: 0.7550 (mtm110) REVERT: n 32 GLU cc_start: 0.4081 (OUTLIER) cc_final: 0.3626 (pm20) REVERT: n 127 GLU cc_start: 0.6375 (mm-30) cc_final: 0.6118 (tp30) REVERT: n 197 MET cc_start: 0.7200 (ppp) cc_final: 0.6915 (ppp) REVERT: z 385 MET cc_start: 0.3879 (mmm) cc_final: 0.3299 (mpp) REVERT: z 398 MET cc_start: 0.7343 (tpp) cc_final: 0.7076 (ttt) outliers start: 223 outliers final: 180 residues processed: 1062 average time/residue: 1.1296 time to fit residues: 2081.1766 Evaluate side-chains 1092 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 904 time to evaluate : 5.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain q residue 56 GLU Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 113 GLN Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 169 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 28 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 118 GLU Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 97 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 51 ILE Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 49 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 71 HIS Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 18 ASN Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 94 ILE Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 25 GLN Chi-restraints excluded: chain k residue 36 ARG Chi-restraints excluded: chain l residue 13 LYS Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 35 LEU Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 38 ASP Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 56 THR Chi-restraints excluded: chain m residue 82 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 32 GLU Chi-restraints excluded: chain n residue 46 ILE Chi-restraints excluded: chain n residue 56 THR Chi-restraints excluded: chain n residue 59 ILE Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain n residue 118 HIS Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain n residue 177 LEU Chi-restraints excluded: chain n residue 181 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 211 THR Chi-restraints excluded: chain t residue 95 VAL Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain z residue 379 THR Chi-restraints excluded: chain z residue 404 LEU Chi-restraints excluded: chain z residue 424 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 311 optimal weight: 10.0000 chunk 834 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 544 optimal weight: 0.7980 chunk 228 optimal weight: 50.0000 chunk 927 optimal weight: 30.0000 chunk 770 optimal weight: 9.9990 chunk 429 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 487 optimal weight: 20.0000 overall best weight: 8.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN H 28 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 HIS P 90 HIS R 27 ASN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 HIS T 98 HIS U 121 GLN V 49 ASN V 88 GLN Y 106 GLN ** Y 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 GLN b 146 GLN e 31 ASN g 18 ASN ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN l 82 GLN n 82 GLN n 86 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.133 133740 Z= 0.567 Angle : 0.759 17.091 197383 Z= 0.381 Chirality : 0.045 0.277 24814 Planarity : 0.006 0.171 12218 Dihedral : 23.131 179.957 60310 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.22 % Favored : 91.75 % Rotamer: Outliers : 4.92 % Allowed : 19.53 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.10), residues: 6278 helix: -1.26 (0.11), residues: 2010 sheet: -1.61 (0.16), residues: 945 loop : -1.77 (0.10), residues: 3323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 122 HIS 0.011 0.002 HIS C 243 PHE 0.039 0.002 PHE b 229 TYR 0.036 0.002 TYR D 194 ARG 0.009 0.001 ARG E 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 889 time to evaluate : 5.962 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS O 204 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. REVERT: B 75 ILE cc_start: 0.8637 (mp) cc_final: 0.8403 (mt) REVERT: C 97 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7691 (mtt180) REVERT: C 302 LYS cc_start: 0.7844 (mttm) cc_final: 0.7531 (mtmm) REVERT: D 288 ARG cc_start: 0.8466 (tmm160) cc_final: 0.8201 (ttp80) REVERT: E 78 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7132 (mt-10) REVERT: E 85 LYS cc_start: 0.7096 (pttt) cc_final: 0.6255 (tmtt) REVERT: E 157 GLU cc_start: 0.8054 (pp20) cc_final: 0.7724 (pp20) REVERT: F 1 MET cc_start: 0.5747 (mtm) cc_final: 0.5530 (mtm) REVERT: F 3 TYR cc_start: 0.8022 (m-80) cc_final: 0.7548 (m-10) REVERT: q 51 HIS cc_start: 0.8440 (m170) cc_final: 0.7600 (m-70) REVERT: q 82 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.5999 (tpp80) REVERT: q 153 ARG cc_start: 0.7108 (ttp80) cc_final: 0.6675 (ttt-90) REVERT: q 207 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: K 165 SER cc_start: 0.8449 (p) cc_final: 0.8054 (p) REVERT: L 28 ASN cc_start: 0.8813 (p0) cc_final: 0.8582 (p0) REVERT: L 110 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7979 (tptt) REVERT: P 45 ASN cc_start: 0.8784 (t0) cc_final: 0.8537 (t0) REVERT: P 57 ASN cc_start: 0.8555 (m-40) cc_final: 0.8301 (m110) REVERT: Q 22 ASP cc_start: 0.7611 (t0) cc_final: 0.7333 (t0) REVERT: S 30 PHE cc_start: 0.8542 (m-80) cc_final: 0.8150 (m-80) REVERT: S 132 THR cc_start: 0.9159 (m) cc_final: 0.8712 (p) REVERT: T 13 TYR cc_start: 0.8840 (m-80) cc_final: 0.8611 (m-80) REVERT: T 156 TYR cc_start: 0.7831 (t80) cc_final: 0.7587 (t80) REVERT: U 64 ASN cc_start: 0.9013 (p0) cc_final: 0.8579 (p0) REVERT: Y 108 GLU cc_start: 0.7448 (mp0) cc_final: 0.7181 (mp0) REVERT: Z 64 GLU cc_start: 0.8170 (tp30) cc_final: 0.7920 (tp30) REVERT: b 52 GLN cc_start: 0.8776 (tp40) cc_final: 0.8322 (tp40) REVERT: f 106 ASN cc_start: 0.8172 (t0) cc_final: 0.7542 (t0) REVERT: g 18 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8881 (t0) REVERT: i 11 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8067 (mtt90) REVERT: i 20 ASN cc_start: 0.8813 (t0) cc_final: 0.8350 (t0) REVERT: k 36 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8277 (mmm-85) REVERT: k 37 TYR cc_start: 0.8518 (p90) cc_final: 0.8251 (p90) REVERT: l 32 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6495 (mmmt) REVERT: m 24 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7563 (mtm110) REVERT: m 45 LYS cc_start: 0.8229 (tttp) cc_final: 0.8022 (ttpt) REVERT: z 398 MET cc_start: 0.7283 (tpp) cc_final: 0.6624 (tmm) outliers start: 262 outliers final: 213 residues processed: 1054 average time/residue: 1.0536 time to fit residues: 1932.8124 Evaluate side-chains 1083 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 867 time to evaluate : 5.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 194 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 97 ASN Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain q residue 35 ASP Chi-restraints excluded: chain q residue 56 GLU Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 169 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 28 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 118 GLU Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 97 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 51 ILE Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 49 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 71 HIS Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 18 ASN Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 94 ILE Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 36 ARG Chi-restraints excluded: chain l residue 20 HIS Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 35 LEU Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 38 ASP Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 56 THR Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 59 CYS Chi-restraints excluded: chain m residue 82 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 46 ILE Chi-restraints excluded: chain n residue 56 THR Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain n residue 125 THR Chi-restraints excluded: chain n residue 137 VAL Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain n residue 177 LEU Chi-restraints excluded: chain n residue 181 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 211 THR Chi-restraints excluded: chain t residue 95 VAL Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain z residue 404 LEU Chi-restraints excluded: chain z residue 411 THR Chi-restraints excluded: chain z residue 424 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 894 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 528 optimal weight: 3.9990 chunk 677 optimal weight: 0.9980 chunk 524 optimal weight: 5.9990 chunk 781 optimal weight: 2.9990 chunk 518 optimal weight: 0.6980 chunk 924 optimal weight: 7.9990 chunk 578 optimal weight: 0.9990 chunk 563 optimal weight: 0.8980 chunk 426 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN H 28 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN M 62 GLN P 57 ASN P 90 HIS R 27 ASN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 GLN V 49 ASN V 88 GLN W 111 ASN b 104 GLN b 146 GLN c 36 GLN e 31 ASN g 18 ASN ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 25 GLN l 38 GLN n 82 GLN n 86 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 133740 Z= 0.142 Angle : 0.524 12.936 197383 Z= 0.270 Chirality : 0.034 0.278 24814 Planarity : 0.004 0.160 12218 Dihedral : 23.040 179.906 60308 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 2.95 % Allowed : 21.71 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.10), residues: 6278 helix: -0.66 (0.12), residues: 1991 sheet: -1.29 (0.17), residues: 924 loop : -1.50 (0.10), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 83 HIS 0.004 0.001 HIS C 280 PHE 0.033 0.001 PHE b 229 TYR 0.025 0.001 TYR V 36 ARG 0.008 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 943 time to evaluate : 5.324 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. REVERT: B 69 TYR cc_start: 0.7542 (t80) cc_final: 0.7061 (t80) REVERT: B 140 ASN cc_start: 0.7782 (t0) cc_final: 0.7458 (t0) REVERT: B 144 ASN cc_start: 0.8687 (t0) cc_final: 0.8373 (t0) REVERT: C 97 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7579 (mtt180) REVERT: C 214 MET cc_start: 0.7875 (mtp) cc_final: 0.7659 (mtp) REVERT: C 302 LYS cc_start: 0.7774 (mttm) cc_final: 0.7482 (mtmm) REVERT: C 308 MET cc_start: 0.8550 (mmm) cc_final: 0.7636 (mtt) REVERT: E 78 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7176 (mt-10) REVERT: E 85 LYS cc_start: 0.6980 (pttt) cc_final: 0.6147 (tmtt) REVERT: E 157 GLU cc_start: 0.7887 (pp20) cc_final: 0.7490 (pp20) REVERT: F 1 MET cc_start: 0.5829 (mtm) cc_final: 0.5616 (mtm) REVERT: F 3 TYR cc_start: 0.7931 (m-80) cc_final: 0.7536 (m-10) REVERT: F 31 ARG cc_start: 0.7421 (ptm-80) cc_final: 0.6817 (ptm-80) REVERT: F 41 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8713 (tp) REVERT: F 160 ASP cc_start: 0.7704 (m-30) cc_final: 0.7355 (m-30) REVERT: H 38 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: H 64 ILE cc_start: 0.9115 (mt) cc_final: 0.8622 (tt) REVERT: q 51 HIS cc_start: 0.8387 (m170) cc_final: 0.7647 (m-70) REVERT: q 82 ARG cc_start: 0.6884 (ttp-170) cc_final: 0.6122 (ttt180) REVERT: q 113 GLN cc_start: 0.5509 (OUTLIER) cc_final: 0.3869 (pm20) REVERT: q 153 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6622 (ttt-90) REVERT: K 79 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8466 (mt-10) REVERT: L 28 ASN cc_start: 0.8759 (p0) cc_final: 0.8504 (p0) REVERT: L 59 MET cc_start: 0.8625 (mmm) cc_final: 0.8280 (mmm) REVERT: M 70 PHE cc_start: 0.8209 (p90) cc_final: 0.7929 (p90) REVERT: M 132 LYS cc_start: 0.7420 (mmtt) cc_final: 0.6636 (ttpt) REVERT: O 127 TYR cc_start: 0.8793 (m-80) cc_final: 0.8494 (m-80) REVERT: P 45 ASN cc_start: 0.8619 (t0) cc_final: 0.8401 (t0) REVERT: Q 22 ASP cc_start: 0.7362 (t0) cc_final: 0.7053 (t0) REVERT: R 7 GLN cc_start: 0.8553 (mp10) cc_final: 0.8314 (mm-40) REVERT: R 38 ARG cc_start: 0.8990 (ttm-80) cc_final: 0.8630 (ttm-80) REVERT: R 72 GLU cc_start: 0.7778 (mp0) cc_final: 0.7532 (mp0) REVERT: S 1 MET cc_start: 0.4738 (tpp) cc_final: 0.4427 (tpt) REVERT: T 156 TYR cc_start: 0.7830 (t80) cc_final: 0.7600 (t80) REVERT: U 64 ASN cc_start: 0.8839 (p0) cc_final: 0.8436 (p0) REVERT: b 52 GLN cc_start: 0.8681 (tp40) cc_final: 0.8391 (tp40) REVERT: f 54 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7598 (ttm170) REVERT: g 96 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7529 (mm-30) REVERT: i 11 ARG cc_start: 0.8363 (mtp85) cc_final: 0.7956 (mtt90) REVERT: k 36 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7873 (mmm-85) REVERT: k 37 TYR cc_start: 0.8351 (p90) cc_final: 0.8090 (p90) REVERT: l 8 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7930 (ptm-80) REVERT: l 32 LYS cc_start: 0.7020 (mmtt) cc_final: 0.6387 (mmmt) REVERT: m 24 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7612 (mtm110) REVERT: z 385 MET cc_start: 0.4014 (mmm) cc_final: 0.3293 (mpp) REVERT: z 398 MET cc_start: 0.7249 (tpp) cc_final: 0.6964 (ttt) outliers start: 157 outliers final: 124 residues processed: 1038 average time/residue: 1.0483 time to fit residues: 1885.2541 Evaluate side-chains 1034 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 906 time to evaluate : 5.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain q residue 35 ASP Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 113 GLN Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 129 ASP Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 71 HIS Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 25 GLN Chi-restraints excluded: chain k residue 36 ARG Chi-restraints excluded: chain l residue 13 LYS Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 35 LEU Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 118 HIS Chi-restraints excluded: chain n residue 177 LEU Chi-restraints excluded: chain n residue 181 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 211 THR Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain v residue 54 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 571 optimal weight: 0.2980 chunk 369 optimal weight: 0.6980 chunk 552 optimal weight: 0.9980 chunk 278 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 587 optimal weight: 1.9990 chunk 629 optimal weight: 10.0000 chunk 456 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 726 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN H 28 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN ** L 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN N 28 HIS P 90 HIS R 27 ASN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN S 114 HIS U 121 GLN V 88 GLN b 104 GLN b 146 GLN g 18 ASN g 61 GLN ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 ASN j 10 GLN k 25 GLN l 38 GLN m 25 GLN n 82 GLN n 86 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 133740 Z= 0.166 Angle : 0.512 26.948 197383 Z= 0.262 Chirality : 0.032 0.272 24814 Planarity : 0.004 0.200 12218 Dihedral : 22.951 179.695 60308 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 3.49 % Allowed : 21.48 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.10), residues: 6278 helix: -0.46 (0.12), residues: 2002 sheet: -1.25 (0.17), residues: 947 loop : -1.41 (0.10), residues: 3329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP k 26 HIS 0.005 0.001 HIS D 311 PHE 0.031 0.001 PHE b 229 TYR 0.028 0.001 TYR V 36 ARG 0.009 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 910 time to evaluate : 5.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. REVERT: B 69 TYR cc_start: 0.7514 (t80) cc_final: 0.7030 (t80) REVERT: B 75 ILE cc_start: 0.8710 (mp) cc_final: 0.8436 (mt) REVERT: B 144 ASN cc_start: 0.8663 (t0) cc_final: 0.8339 (t0) REVERT: C 97 ARG cc_start: 0.8129 (mtm-85) cc_final: 0.7595 (mtt180) REVERT: C 302 LYS cc_start: 0.7825 (mttm) cc_final: 0.7471 (mtmm) REVERT: C 308 MET cc_start: 0.8538 (mmm) cc_final: 0.7655 (mtt) REVERT: C 380 MET cc_start: 0.6597 (mmm) cc_final: 0.5755 (mmt) REVERT: D 311 HIS cc_start: 0.8713 (t70) cc_final: 0.8502 (t-90) REVERT: E 78 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7136 (mt-10) REVERT: E 157 GLU cc_start: 0.7920 (pp20) cc_final: 0.7527 (pp20) REVERT: F 1 MET cc_start: 0.5828 (mtm) cc_final: 0.5571 (mtm) REVERT: F 31 ARG cc_start: 0.7434 (ptm-80) cc_final: 0.6827 (ptm-80) REVERT: F 41 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8718 (tp) REVERT: F 63 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7717 (pttt) REVERT: F 69 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6990 (tmt170) REVERT: F 160 ASP cc_start: 0.7816 (m-30) cc_final: 0.7461 (m-30) REVERT: H 38 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: q 17 TYR cc_start: 0.8845 (t80) cc_final: 0.8541 (t80) REVERT: q 51 HIS cc_start: 0.8394 (m170) cc_final: 0.7628 (m-70) REVERT: q 57 LEU cc_start: 0.7357 (tp) cc_final: 0.6976 (tt) REVERT: q 65 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7296 (tt) REVERT: q 82 ARG cc_start: 0.6951 (ttp-170) cc_final: 0.6139 (ttt180) REVERT: q 113 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.3948 (pm20) REVERT: q 153 ARG cc_start: 0.7095 (ttp80) cc_final: 0.6586 (ttt-90) REVERT: K 67 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8447 (ptt90) REVERT: L 28 ASN cc_start: 0.8804 (p0) cc_final: 0.8559 (p0) REVERT: L 59 MET cc_start: 0.8637 (mmm) cc_final: 0.8314 (mmm) REVERT: L 110 LYS cc_start: 0.7920 (tptp) cc_final: 0.7610 (tptp) REVERT: M 132 LYS cc_start: 0.7384 (mmtt) cc_final: 0.6640 (ttpt) REVERT: N 109 TYR cc_start: 0.8975 (m-80) cc_final: 0.8647 (m-80) REVERT: O 127 TYR cc_start: 0.8799 (m-80) cc_final: 0.8497 (m-80) REVERT: P 45 ASN cc_start: 0.8609 (t0) cc_final: 0.8368 (t0) REVERT: P 216 GLU cc_start: 0.6853 (tp30) cc_final: 0.6387 (pp20) REVERT: Q 22 ASP cc_start: 0.7379 (t0) cc_final: 0.7047 (t0) REVERT: R 7 GLN cc_start: 0.8544 (mp10) cc_final: 0.8310 (mm-40) REVERT: R 38 ARG cc_start: 0.8986 (ttm-80) cc_final: 0.8616 (ttm-80) REVERT: R 72 GLU cc_start: 0.7759 (mp0) cc_final: 0.7540 (mp0) REVERT: T 13 TYR cc_start: 0.8768 (m-80) cc_final: 0.8509 (m-80) REVERT: U 64 ASN cc_start: 0.8837 (p0) cc_final: 0.8434 (p0) REVERT: Z 64 GLU cc_start: 0.8179 (tp30) cc_final: 0.7804 (tp30) REVERT: b 30 ARG cc_start: 0.6264 (ttp80) cc_final: 0.5995 (tmt170) REVERT: b 52 GLN cc_start: 0.8703 (tp40) cc_final: 0.8380 (tp40) REVERT: i 11 ARG cc_start: 0.8321 (mtp85) cc_final: 0.7922 (mtt90) REVERT: k 36 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7840 (mmm-85) REVERT: k 37 TYR cc_start: 0.8310 (p90) cc_final: 0.8011 (p90) REVERT: m 24 ARG cc_start: 0.7712 (ttm110) cc_final: 0.7469 (mtm110) REVERT: n 172 GLU cc_start: 0.6923 (pt0) cc_final: 0.5767 (mp0) REVERT: z 385 MET cc_start: 0.3858 (mmm) cc_final: 0.3297 (mpp) REVERT: z 398 MET cc_start: 0.7204 (tpp) cc_final: 0.6943 (ttt) outliers start: 186 outliers final: 157 residues processed: 1030 average time/residue: 1.0802 time to fit residues: 1919.2454 Evaluate side-chains 1063 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 898 time to evaluate : 5.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain q residue 35 ASP Chi-restraints excluded: chain q residue 56 GLU Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 113 GLN Chi-restraints excluded: chain q residue 147 VAL Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 129 ASP Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 49 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 71 HIS Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 18 ASN Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 94 ILE Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 25 GLN Chi-restraints excluded: chain k residue 36 ARG Chi-restraints excluded: chain l residue 13 LYS Chi-restraints excluded: chain l residue 20 HIS Chi-restraints excluded: chain l residue 35 LEU Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 38 ASP Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 82 THR Chi-restraints excluded: chain m residue 89 MET Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 59 ILE Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain n residue 118 HIS Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain n residue 177 LEU Chi-restraints excluded: chain n residue 181 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 211 THR Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain z residue 404 LEU Chi-restraints excluded: chain z residue 424 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 840 optimal weight: 1.9990 chunk 885 optimal weight: 5.9990 chunk 807 optimal weight: 6.9990 chunk 861 optimal weight: 0.8980 chunk 518 optimal weight: 0.9980 chunk 375 optimal weight: 1.9990 chunk 676 optimal weight: 0.7980 chunk 264 optimal weight: 20.0000 chunk 778 optimal weight: 6.9990 chunk 814 optimal weight: 8.9990 chunk 858 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN H 28 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN M 62 GLN P 57 ASN P 90 HIS R 27 ASN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 GLN V 88 GLN ** a 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 GLN b 146 GLN d 43 HIS ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 ASN j 10 GLN ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN m 25 GLN n 82 GLN n 86 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 133740 Z= 0.130 Angle : 0.502 21.879 197383 Z= 0.257 Chirality : 0.032 0.273 24814 Planarity : 0.004 0.184 12218 Dihedral : 22.955 179.921 60308 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 3.10 % Allowed : 22.12 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.10), residues: 6278 helix: -0.34 (0.12), residues: 2007 sheet: -1.13 (0.17), residues: 937 loop : -1.35 (0.11), residues: 3334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP i 49 HIS 0.005 0.001 HIS F 64 PHE 0.037 0.001 PHE S 30 TYR 0.025 0.001 TYR V 36 ARG 0.013 0.000 ARG Q 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 920 time to evaluate : 5.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. REVERT: B 69 TYR cc_start: 0.7444 (t80) cc_final: 0.6986 (t80) REVERT: B 75 ILE cc_start: 0.8746 (mp) cc_final: 0.8521 (mt) REVERT: B 144 ASN cc_start: 0.8661 (t0) cc_final: 0.8286 (t0) REVERT: C 97 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7590 (mtt180) REVERT: C 302 LYS cc_start: 0.7820 (mttm) cc_final: 0.7486 (mtmm) REVERT: D 311 HIS cc_start: 0.8726 (t70) cc_final: 0.8444 (t-90) REVERT: E 78 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7122 (mt-10) REVERT: E 157 GLU cc_start: 0.7879 (pp20) cc_final: 0.7546 (pm20) REVERT: F 1 MET cc_start: 0.5827 (mtm) cc_final: 0.5572 (mtm) REVERT: F 31 ARG cc_start: 0.7379 (ptm-80) cc_final: 0.6834 (ptm-80) REVERT: F 41 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8736 (tp) REVERT: F 63 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7699 (pttt) REVERT: F 69 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6999 (tmt170) REVERT: F 160 ASP cc_start: 0.7792 (m-30) cc_final: 0.7432 (m-30) REVERT: H 38 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: q 17 TYR cc_start: 0.8837 (t80) cc_final: 0.8567 (t80) REVERT: q 51 HIS cc_start: 0.8366 (m170) cc_final: 0.7583 (m-70) REVERT: q 65 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7289 (tt) REVERT: q 82 ARG cc_start: 0.6995 (ttp-170) cc_final: 0.6099 (ttt180) REVERT: q 113 GLN cc_start: 0.5197 (OUTLIER) cc_final: 0.3963 (pm20) REVERT: q 153 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6599 (ttt-90) REVERT: K 67 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8433 (ptt90) REVERT: K 79 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8576 (mt-10) REVERT: L 28 ASN cc_start: 0.8799 (p0) cc_final: 0.8550 (p0) REVERT: L 59 MET cc_start: 0.8627 (mmm) cc_final: 0.8300 (mmm) REVERT: L 128 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.7882 (mtp180) REVERT: M 132 LYS cc_start: 0.7330 (mmtt) cc_final: 0.6615 (ttpt) REVERT: N 109 TYR cc_start: 0.8986 (m-80) cc_final: 0.8656 (m-80) REVERT: O 127 TYR cc_start: 0.8786 (m-80) cc_final: 0.8489 (m-80) REVERT: P 45 ASN cc_start: 0.8570 (t0) cc_final: 0.8331 (t0) REVERT: P 216 GLU cc_start: 0.6798 (tp30) cc_final: 0.6426 (pp20) REVERT: R 7 GLN cc_start: 0.8539 (mp10) cc_final: 0.8304 (mm-40) REVERT: R 38 ARG cc_start: 0.8964 (ttm-80) cc_final: 0.8608 (ttm-80) REVERT: T 5 HIS cc_start: 0.9055 (m-70) cc_final: 0.8820 (m90) REVERT: T 13 TYR cc_start: 0.8756 (m-80) cc_final: 0.8492 (m-80) REVERT: U 64 ASN cc_start: 0.8795 (p0) cc_final: 0.8400 (p0) REVERT: Z 64 GLU cc_start: 0.8172 (tp30) cc_final: 0.7789 (tp30) REVERT: b 30 ARG cc_start: 0.6244 (ttp80) cc_final: 0.5971 (tmt170) REVERT: b 52 GLN cc_start: 0.8706 (tp40) cc_final: 0.8425 (tp40) REVERT: i 11 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7898 (mtt90) REVERT: k 36 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7837 (mtp85) REVERT: k 37 TYR cc_start: 0.8296 (p90) cc_final: 0.8012 (p90) REVERT: l 8 ARG cc_start: 0.8160 (ptm160) cc_final: 0.7838 (ptm-80) REVERT: m 24 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7480 (mtm110) REVERT: n 1 MET cc_start: 0.3270 (mtt) cc_final: 0.2994 (mtt) REVERT: z 385 MET cc_start: 0.3829 (mmm) cc_final: 0.3280 (mpp) REVERT: z 398 MET cc_start: 0.7255 (tpp) cc_final: 0.7032 (ttt) outliers start: 165 outliers final: 143 residues processed: 1026 average time/residue: 1.0912 time to fit residues: 1935.5738 Evaluate side-chains 1048 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 897 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain q residue 35 ASP Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 113 GLN Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 129 ASP Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 49 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 71 HIS Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 36 ARG Chi-restraints excluded: chain l residue 13 LYS Chi-restraints excluded: chain l residue 35 LEU Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 38 ASP Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 56 THR Chi-restraints excluded: chain n residue 59 ILE Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain n residue 118 HIS Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain n residue 177 LEU Chi-restraints excluded: chain n residue 181 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 211 THR Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain z residue 404 LEU Chi-restraints excluded: chain z residue 411 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 565 optimal weight: 7.9990 chunk 910 optimal weight: 6.9990 chunk 555 optimal weight: 3.9990 chunk 432 optimal weight: 10.0000 chunk 633 optimal weight: 9.9990 chunk 955 optimal weight: 10.0000 chunk 879 optimal weight: 9.9990 chunk 760 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 587 optimal weight: 3.9990 chunk 466 optimal weight: 9.9990 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 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN H 28 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 HIS P 57 ASN P 90 HIS Q 158 HIS R 27 ASN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 HIS U 121 GLN V 88 GLN W 111 ASN ** a 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 146 GLN c 36 GLN e 31 ASN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 ASN j 10 GLN k 25 GLN m 25 GLN v 58 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 133740 Z= 0.468 Angle : 0.688 20.612 197383 Z= 0.347 Chirality : 0.041 0.271 24814 Planarity : 0.005 0.178 12218 Dihedral : 23.007 179.910 60308 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.73 % Favored : 92.24 % Rotamer: Outliers : 3.79 % Allowed : 21.43 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.10), residues: 6278 helix: -0.72 (0.12), residues: 2011 sheet: -1.38 (0.16), residues: 951 loop : -1.54 (0.10), residues: 3316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 122 HIS 0.011 0.002 HIS C 243 PHE 0.048 0.002 PHE S 30 TYR 0.031 0.002 TYR D 194 ARG 0.012 0.001 ARG Q 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12556 Ramachandran restraints generated. 6278 Oldfield, 0 Emsley, 6278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 883 time to evaluate : 6.010 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. REVERT: B 69 TYR cc_start: 0.7597 (t80) cc_final: 0.7181 (t80) REVERT: B 75 ILE cc_start: 0.8677 (mp) cc_final: 0.8433 (mt) REVERT: C 97 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7623 (mtt180) REVERT: C 302 LYS cc_start: 0.7890 (mttm) cc_final: 0.7503 (mtmm) REVERT: E 78 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7336 (mt-10) REVERT: E 85 LYS cc_start: 0.7012 (pttt) cc_final: 0.6239 (tmtt) REVERT: E 157 GLU cc_start: 0.7942 (pp20) cc_final: 0.7588 (pp20) REVERT: F 1 MET cc_start: 0.5773 (mtm) cc_final: 0.5523 (mtm) REVERT: F 3 TYR cc_start: 0.8006 (m-80) cc_final: 0.7560 (m-10) REVERT: F 63 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7844 (pttt) REVERT: F 160 ASP cc_start: 0.8136 (m-30) cc_final: 0.7905 (m-30) REVERT: H 134 TYR cc_start: 0.8839 (p90) cc_final: 0.8623 (p90) REVERT: q 51 HIS cc_start: 0.8488 (m170) cc_final: 0.7880 (m90) REVERT: q 57 LEU cc_start: 0.7388 (tp) cc_final: 0.6939 (tt) REVERT: q 82 ARG cc_start: 0.7056 (ttp-170) cc_final: 0.6259 (ttt180) REVERT: q 113 GLN cc_start: 0.5589 (OUTLIER) cc_final: 0.3655 (pm20) REVERT: q 153 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6642 (ttt-90) REVERT: q 207 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7568 (tp30) REVERT: J 38 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: K 67 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8781 (ptt90) REVERT: K 139 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8870 (mm) REVERT: L 28 ASN cc_start: 0.8842 (p0) cc_final: 0.8574 (p0) REVERT: N 92 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7944 (mmtm) REVERT: P 45 ASN cc_start: 0.8703 (t0) cc_final: 0.8458 (t0) REVERT: Q 22 ASP cc_start: 0.7591 (t0) cc_final: 0.7288 (t0) REVERT: R 7 GLN cc_start: 0.8602 (mp10) cc_final: 0.8336 (mm-40) REVERT: S 132 THR cc_start: 0.9157 (m) cc_final: 0.8726 (p) REVERT: U 64 ASN cc_start: 0.8970 (p0) cc_final: 0.8557 (p0) REVERT: b 30 ARG cc_start: 0.6224 (ttp80) cc_final: 0.5971 (tmt170) REVERT: b 52 GLN cc_start: 0.8744 (tp40) cc_final: 0.8317 (tp40) REVERT: f 54 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7756 (ttm170) REVERT: i 11 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8047 (mtt90) REVERT: k 36 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8091 (mmm-85) REVERT: k 37 TYR cc_start: 0.8418 (p90) cc_final: 0.8133 (p90) REVERT: l 32 LYS cc_start: 0.7114 (mmtt) cc_final: 0.6480 (mmmt) REVERT: m 24 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7537 (mtm110) REVERT: n 16 PHE cc_start: 0.8518 (m-10) cc_final: 0.7879 (m-10) REVERT: n 172 GLU cc_start: 0.7124 (pt0) cc_final: 0.5843 (mp0) REVERT: z 385 MET cc_start: 0.4122 (mmm) cc_final: 0.3485 (mpp) REVERT: z 398 MET cc_start: 0.7227 (tpp) cc_final: 0.6650 (tmm) outliers start: 202 outliers final: 169 residues processed: 1017 average time/residue: 1.0579 time to fit residues: 1864.4129 Evaluate side-chains 1048 residues out of total 5331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 872 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 97 ASN Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain q residue 35 ASP Chi-restraints excluded: chain q residue 56 GLU Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 113 GLN Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 117 ASN Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 129 ASP Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 49 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 71 HIS Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 94 ILE Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 25 GLN Chi-restraints excluded: chain k residue 36 ARG Chi-restraints excluded: chain l residue 20 HIS Chi-restraints excluded: chain l residue 35 LEU Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 56 THR Chi-restraints excluded: chain m residue 82 THR Chi-restraints excluded: chain m residue 89 MET Chi-restraints excluded: chain m residue 90 VAL Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 56 THR Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain n residue 177 LEU Chi-restraints excluded: chain n residue 181 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 211 THR Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain z residue 404 LEU Chi-restraints excluded: chain z residue 411 THR Chi-restraints excluded: chain z residue 424 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 604 optimal weight: 1.9990 chunk 810 optimal weight: 0.7980 chunk 233 optimal weight: 20.0000 chunk 701 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 762 optimal weight: 7.9990 chunk 318 optimal weight: 6.9990 chunk 782 optimal weight: 1.9990 chunk 96 optimal weight: 50.0000 chunk 140 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN F 8 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN ** L 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN P 90 HIS Q 158 HIS ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 GLN V 88 GLN ** a 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 ASN j 10 GLN k 25 GLN l 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.081528 restraints weight = 237309.956| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.24 r_work: 0.2785 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.275 133740 Z= 0.386 Angle : 0.722 59.199 197383 Z= 0.376 Chirality : 0.038 0.980 24814 Planarity : 0.005 0.175 12218 Dihedral : 23.010 179.906 60308 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.74 % Favored : 92.23 % Rotamer: Outliers : 3.53 % Allowed : 21.84 % Favored : 74.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.10), residues: 6278 helix: -0.72 (0.12), residues: 2011 sheet: -1.38 (0.16), residues: 949 loop : -1.54 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 122 HIS 0.010 0.001 HIS C 243 PHE 0.043 0.002 PHE S 30 TYR 0.028 0.002 TYR D 194 ARG 0.010 0.001 ARG Q 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29899.00 seconds wall clock time: 524 minutes 2.27 seconds (31442.27 seconds total)