Starting phenix.real_space_refine on Sat Mar 2 10:21:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jce_6550/03_2024/3jce_6550_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jce_6550/03_2024/3jce_6550.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jce_6550/03_2024/3jce_6550_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jce_6550/03_2024/3jce_6550_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jce_6550/03_2024/3jce_6550_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jce_6550/03_2024/3jce_6550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jce_6550/03_2024/3jce_6550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jce_6550/03_2024/3jce_6550_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jce_6550/03_2024/3jce_6550_updated.pdb" } resolution = 3.2 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= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4800 5.49 5 Mg 1 5.21 5 S 173 5.16 5 C 77913 2.51 5 N 28607 2.21 5 O 42523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "e PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 124": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n ASP 33": "OD1" <-> "OD2" Residue "n ASP 38": "OD1" <-> "OD2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "W ARG 76": "NH1" <-> "NH2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 5": "NH1" <-> "NH2" Residue "x ARG 23": "NH1" <-> "NH2" Residue "x ARG 48": "NH1" <-> "NH2" Residue "x ARG 50": "NH1" <-> "NH2" Residue "x ARG 90": "NH1" <-> "NH2" Residue "x ARG 142": "NH1" <-> "NH2" Residue "x ARG 160": "NH1" <-> "NH2" Residue "x ARG 175": "NH1" <-> "NH2" Residue "x ARG 178": "NH1" <-> "NH2" Residue "x ARG 211": "NH1" <-> "NH2" Residue "x ARG 218": "NH1" <-> "NH2" Residue "x ARG 236": "NH1" <-> "NH2" Residue "x ARG 247": "NH1" <-> "NH2" Residue "x ARG 278": "NH1" <-> "NH2" Residue "x ARG 311": "NH1" <-> "NH2" Residue "x TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 339": "NH1" <-> "NH2" Residue "x GLU 349": "OE1" <-> "OE2" Residue "x ARG 354": "NH1" <-> "NH2" Residue "x ARG 357": "NH1" <-> "NH2" Residue "x ARG 379": "NH1" <-> "NH2" Residue "x ARG 400": "NH1" <-> "NH2" Residue "x ARG 426": "NH1" <-> "NH2" Residue "x TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 457": "NH1" <-> "NH2" Residue "x ARG 463": "NH1" <-> "NH2" Residue "x ARG 474": "NH1" <-> "NH2" Residue "x ARG 482": "NH1" <-> "NH2" Residue "x ARG 491": "NH1" <-> "NH2" Residue "x ARG 501": "NH1" <-> "NH2" Residue "x ARG 507": "NH1" <-> "NH2" Residue "x ARG 509": "NH1" <-> "NH2" Residue "x ARG 521": "NH1" <-> "NH2" Residue "x ARG 539": "NH1" <-> "NH2" Residue "x ARG 546": "NH1" <-> "NH2" Residue "x TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 560": "NH1" <-> "NH2" Residue "x ARG 574": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 154017 Number of models: 1 Model: "" Number of chains: 59 Chain: "a" Number of atoms: 32895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32895 Classifications: {'RNA': 1533} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 77, 'rna3p_pur': 762, 'rna3p_pyr': 582} Link IDs: {'rna2p': 189, 'rna3p': 1343} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "f" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 4, 'TRANS': 92} Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1733 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 225} Chain: "A" Number of atoms: 62320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62320 Classifications: {'RNA': 2903} Modifications used: {'rna2p_pur': 275, 'rna2p_pyr': 149, 'rna3p_pur': 1399, 'rna3p_pyr': 1080} Link IDs: {'rna2p': 424, 'rna3p': 2478} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2076 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 17, 'TRANS': 252} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 166} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 144} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "6" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1633 Classifications: {'RNA': 75, 'peptide': 1} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 30, 'rna3p_pyr': 35} Link IDs: {'rna2p': 10, 'rna3p': 64, None: 1} Not linked: pdbres=" C 6 75 " pdbres="F3O 6 76 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Chain: "7" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 320 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "8" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 31, 'rna3p_pyr': 35} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "x" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4573 Classifications: {'peptide': 586} Link IDs: {'CIS': 10, 'PTRANS': 24, 'TRANS': 551} Chain breaks: 1 Chain: "9" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 66} Chain: "x" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 57.07, per 1000 atoms: 0.37 Number of scatterers: 154017 At special positions: 0 Unit cell: (261.36, 232.32, 266.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 173 16.00 P 4800 15.00 Mg 1 11.99 O 42523 8.00 N 28607 7.00 C 77913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 69.01 Conformation dependent library (CDL) restraints added in 7.6 seconds 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12034 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 199 helices and 73 sheets defined 37.9% alpha, 17.5% beta 1183 base pairs and 2413 stacking pairs defined. Time for finding SS restraints: 78.26 Creating SS restraints... Processing helix chain 'c' and resid 6 through 13 removed outlier: 4.110A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLY c 13 " --> pdb=" O GLY c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.555A pdb=" N LYS c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.716A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.191A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU c 87 " --> pdb=" O ASP c 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG c 88 " --> pdb=" O VAL c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 3.909A pdb=" N ASP c 112 " --> pdb=" O LYS c 108 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 removed outlier: 3.919A pdb=" N GLN c 123 " --> pdb=" O SER c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 4.218A pdb=" N ALA c 137 " --> pdb=" O ALA c 133 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY c 145 " --> pdb=" O ALA c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.073A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.942A pdb=" N LYS d 60 " --> pdb=" O ARG d 56 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL d 61 " --> pdb=" O GLU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 83 removed outlier: 3.662A pdb=" N LEU d 82 " --> pdb=" O GLU d 78 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 3.614A pdb=" N ASN d 89 " --> pdb=" O ASN d 85 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU d 91 " --> pdb=" O GLY d 87 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA d 92 " --> pdb=" O GLU d 88 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 110 through 121 Processing helix chain 'd' and resid 152 through 166 removed outlier: 6.749A pdb=" N LYS d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA d 157 " --> pdb=" O SER d 153 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU d 160 " --> pdb=" O LYS d 156 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN d 164 " --> pdb=" O GLU d 160 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.998A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 3.998A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR d 204 " --> pdb=" O ILE d 200 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.697A pdb=" N GLN e 61 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS e 62 " --> pdb=" O ALA e 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS e 66 " --> pdb=" O LYS e 62 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 6.221A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 148 removed outlier: 3.830A pdb=" N ARG e 138 " --> pdb=" O ILE e 134 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU e 145 " --> pdb=" O ILE e 141 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN e 146 " --> pdb=" O ASP e 142 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASN e 148 " --> pdb=" O LEU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 157 removed outlier: 3.561A pdb=" N VAL e 153 " --> pdb=" O SER e 149 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS e 156 " --> pdb=" O MET e 152 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 33 removed outlier: 4.629A pdb=" N GLY f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR f 26 " --> pdb=" O ILE f 22 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA f 27 " --> pdb=" O GLU f 23 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 4.267A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU f 74 " --> pdb=" O VAL f 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU f 75 " --> pdb=" O ILE f 71 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.505A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN g 28 " --> pdb=" O ALA g 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.554A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE g 42 " --> pdb=" O THR g 38 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER g 45 " --> pdb=" O SER g 41 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 5.692A pdb=" N ALA g 61 " --> pdb=" O SER g 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE g 62 " --> pdb=" O GLU g 58 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA g 65 " --> pdb=" O ALA g 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN g 68 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG g 70 " --> pdb=" O LEU g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.846A pdb=" N ASN g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA g 98 " --> pdb=" O VAL g 94 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL g 105 " --> pdb=" O MET g 101 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS g 110 " --> pdb=" O GLU g 106 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.652A pdb=" N ALA g 128 " --> pdb=" O LEU g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 150 removed outlier: 3.647A pdb=" N ARG g 138 " --> pdb=" O ALA g 134 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.643A pdb=" N LEU h 11 " --> pdb=" O ILE h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 39 removed outlier: 3.611A pdb=" N PHE i 39 " --> pdb=" O LEU i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 56 removed outlier: 4.592A pdb=" N MET i 46 " --> pdb=" O GLU i 42 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL i 48 " --> pdb=" O ALA i 44 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix removed outlier: 3.545A pdb=" N LEU i 54 " --> pdb=" O GLN i 50 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 87 removed outlier: 3.669A pdb=" N GLN i 75 " --> pdb=" O GLY i 71 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA i 76 " --> pdb=" O ILE i 72 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 102 removed outlier: 4.154A pdb=" N ARG i 95 " --> pdb=" O ASP i 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER i 96 " --> pdb=" O GLU i 92 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU i 97 " --> pdb=" O SER i 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU i 98 " --> pdb=" O LEU i 94 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG i 99 " --> pdb=" O ARG i 95 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.351A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU j 24 " --> pdb=" O GLN j 20 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.783A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 4.311A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 59 removed outlier: 3.890A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 59' Processing helix chain 'k' and resid 60 through 75 removed outlier: 3.505A pdb=" N ASP k 72 " --> pdb=" O GLU k 68 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL k 74 " --> pdb=" O CYS k 70 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 5.009A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 removed outlier: 3.629A pdb=" N ARG l 9 " --> pdb=" O ASN l 5 " (cutoff:3.500A) Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.962A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.852A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.527A pdb=" N ALA m 35 " --> pdb=" O LYS m 31 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA m 36 " --> pdb=" O ALA m 32 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.729A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N SER m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.731A pdb=" N ASP m 54 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR m 55 " --> pdb=" O GLY m 51 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.558A pdb=" N MET m 75 " --> pdb=" O ARG m 71 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS m 78 " --> pdb=" O SER m 74 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU m 80 " --> pdb=" O SER m 76 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 21 removed outlier: 3.648A pdb=" N LYS n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA n 8 " --> pdb=" O GLN n 4 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP n 18 " --> pdb=" O VAL n 14 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS n 19 " --> pdb=" O ALA n 15 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE n 21 " --> pdb=" O ALA n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 23 through 35 removed outlier: 4.031A pdb=" N LEU n 27 " --> pdb=" O LYS n 23 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA n 29 " --> pdb=" O ALA n 25 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL n 34 " --> pdb=" O ILE n 30 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASN n 35 " --> pdb=" O ILE n 31 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 49 removed outlier: 4.345A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.643A pdb=" N ALA n 87 " --> pdb=" O LYS n 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET n 89 " --> pdb=" O ARG n 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 57 removed outlier: 5.937A pdb=" N SER n 55 " --> pdb=" O PRO n 52 " (cutoff:3.500A) Proline residue: n 57 - end of helix Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.924A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA o 44 " --> pdb=" O GLN o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.977A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU o 66 " --> pdb=" O GLN o 62 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR o 69 " --> pdb=" O LYS o 65 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.679A pdb=" N GLU o 83 " --> pdb=" O THR o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.907A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY p 64 " --> pdb=" O TRP p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.757A pdb=" N LEU r 29 " --> pdb=" O ASP r 25 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN r 31 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.903A pdb=" N ARG r 53 " --> pdb=" O ALA r 49 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG r 63 " --> pdb=" O ILE r 59 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 4.626A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.558A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 7 through 41 removed outlier: 4.376A pdb=" N ALA t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE t 12 " --> pdb=" O LYS t 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU t 15 " --> pdb=" O ALA t 11 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS t 19 " --> pdb=" O GLU t 15 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL t 35 " --> pdb=" O PHE t 31 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR t 36 " --> pdb=" O ILE t 32 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 4.065A pdb=" N ALA t 50 " --> pdb=" O ALA t 46 " (cutoff:3.500A) Proline residue: t 56 - end of helix removed outlier: 3.845A pdb=" N GLN t 61 " --> pdb=" O ILE t 57 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.504A pdb=" N ARG t 74 " --> pdb=" O ASN t 70 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR t 80 " --> pdb=" O LYS t 76 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN t 84 " --> pdb=" O THR t 80 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS t 85 " --> pdb=" O ALA t 81 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA t 87 " --> pdb=" O ILE t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 18 through 24 removed outlier: 3.678A pdb=" N GLU u 24 " --> pdb=" O LYS u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 25 through 34 removed outlier: 3.835A pdb=" N GLU u 31 " --> pdb=" O GLY u 27 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG u 34 " --> pdb=" O ALA u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 53 removed outlier: 4.106A pdb=" N THR u 42 " --> pdb=" O TYR u 38 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N THR u 43 " --> pdb=" O GLU u 39 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS u 46 " --> pdb=" O THR u 42 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER u 51 " --> pdb=" O ARG u 47 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL u 53 " --> pdb=" O LYS u 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 31 removed outlier: 3.548A pdb=" N ILE b 30 " --> pdb=" O MET b 26 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE b 31 " --> pdb=" O LYS b 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 26 through 31' Processing helix chain 'b' and resid 41 through 63 removed outlier: 3.681A pdb=" N THR b 45 " --> pdb=" O ASN b 41 " (cutoff:3.500A) Proline residue: b 47 - end of helix removed outlier: 3.797A pdb=" N ALA b 54 " --> pdb=" O ASN b 50 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS b 58 " --> pdb=" O ALA b 54 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE b 59 " --> pdb=" O GLU b 55 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA b 60 " --> pdb=" O LEU b 56 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER b 61 " --> pdb=" O ASN b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 87 removed outlier: 3.770A pdb=" N LYS b 80 " --> pdb=" O SER b 76 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP b 81 " --> pdb=" O GLU b 77 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA b 82 " --> pdb=" O ALA b 78 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA b 83 " --> pdb=" O VAL b 79 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU b 84 " --> pdb=" O LYS b 80 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 4.914A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU b 113 " --> pdb=" O SER b 109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS b 114 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 4.192A pdb=" N LEU b 134 " --> pdb=" O LYS b 130 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU b 140 " --> pdb=" O ARG b 136 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU b 141 " --> pdb=" O THR b 137 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 169 removed outlier: 3.901A pdb=" N GLU b 168 " --> pdb=" O ASP b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 179 removed outlier: 4.355A pdb=" N GLU b 174 " --> pdb=" O ILE b 170 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 4.689A pdb=" N ALA b 215 " --> pdb=" O LEU b 211 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA b 218 " --> pdb=" O GLY b 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR b 219 " --> pdb=" O ALA b 215 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU b 222 " --> pdb=" O ALA b 218 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 153 removed outlier: 6.547A pdb=" N ASP b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 18 removed outlier: 3.611A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 removed outlier: 3.687A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS 2 16 " --> pdb=" O ARG 2 12 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 24 removed outlier: 3.502A pdb=" N ALA 2 23 " --> pdb=" O ARG 2 19 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 removed outlier: 3.530A pdb=" N ARG 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 removed outlier: 3.528A pdb=" N ALA 3 10 " --> pdb=" O VAL 3 6 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.867A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.935A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE 3 58 " --> pdb=" O LEU 3 54 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA 3 59 " --> pdb=" O GLY 3 55 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS 3 60 " --> pdb=" O LEU 3 56 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '5' and resid 5 through 16 removed outlier: 4.106A pdb=" N ILE 5 11 " --> pdb=" O ARG 5 7 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG 5 12 " --> pdb=" O MET 5 8 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 34 removed outlier: 4.225A pdb=" N ILE 5 27 " --> pdb=" O ILE 5 23 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA 5 28 " --> pdb=" O ASN 5 24 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU 5 32 " --> pdb=" O ALA 5 28 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 5 33 " --> pdb=" O LEU 5 29 " (cutoff:3.500A) Processing helix chain '5' and resid 81 through 90 removed outlier: 4.016A pdb=" N ALA 5 87 " --> pdb=" O ASN 5 83 " (cutoff:3.500A) Processing helix chain '5' and resid 101 through 106 removed outlier: 4.891A pdb=" N LYS 5 105 " --> pdb=" O ALA 5 101 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS 5 106 " --> pdb=" O ASP 5 102 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 101 through 106' Processing helix chain '5' and resid 120 through 126 removed outlier: 4.736A pdb=" N VAL 5 124 " --> pdb=" O ALA 5 120 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY 5 125 " --> pdb=" O MET 5 121 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN 5 126 " --> pdb=" O ARG 5 122 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 120 through 126' Processing helix chain '5' and resid 149 through 159 removed outlier: 6.117A pdb=" N VAL 5 153 " --> pdb=" O VAL 5 149 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS 5 154 " --> pdb=" O ALA 5 150 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN 5 155 " --> pdb=" O GLU 5 151 " (cutoff:3.500A) Processing helix chain '5' and resid 181 through 200 removed outlier: 4.089A pdb=" N ASN 5 188 " --> pdb=" O LYS 5 184 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU 5 190 " --> pdb=" O LYS 5 186 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA 5 191 " --> pdb=" O GLU 5 187 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL 5 194 " --> pdb=" O GLU 5 190 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA 5 195 " --> pdb=" O ALA 5 191 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU 5 196 " --> pdb=" O LEU 5 192 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS 5 197 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA 5 199 " --> pdb=" O ALA 5 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 16 removed outlier: 3.640A pdb=" N ARG C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 16' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.518A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Proline residue: C 135 - end of helix No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.895A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 4.297A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.062A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'C' and resid 196 through 201 removed outlier: 5.168A pdb=" N HIS C 199 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.687A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.965A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 4.800A pdb=" N PHE D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 103' Processing helix chain 'D' and resid 120 through 126 removed outlier: 4.810A pdb=" N TRP D 125 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN D 126 " --> pdb=" O THR D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 126' Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.756A pdb=" N GLN E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.577A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.784A pdb=" N GLN E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.751A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.859A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 removed outlier: 4.260A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 20 removed outlier: 4.475A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.561A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 60 removed outlier: 3.735A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.693A pdb=" N PHE F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.687A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.226A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 7 removed outlier: 4.420A pdb=" N LYS G 5 " --> pdb=" O SER G 1 " (cutoff:3.500A) Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 removed outlier: 3.662A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU G 80 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.808A pdb=" N GLY G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 4.047A pdb=" N ARG H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 51 removed outlier: 3.918A pdb=" N PHE H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU H 48 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 63 removed outlier: 5.359A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 73 removed outlier: 7.271A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 removed outlier: 5.963A pdb=" N ALA H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 101 through 106' Processing helix chain 'H' and resid 92 through 99 removed outlier: 3.936A pdb=" N GLY H 95 " --> pdb=" O GLY H 92 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG H 97 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP H 98 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE H 99 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 6.506A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 3.837A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 3.635A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.428A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.644A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 5.533A pdb=" N ALA J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.520A pdb=" N ASP J 71 " --> pdb=" O ASN J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 4.212A pdb=" N ARG J 96 " --> pdb=" O MET J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.942A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY J 107 " --> pdb=" O ILE J 103 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.143A pdb=" N ALA J 117 " --> pdb=" O PRO J 113 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 3.906A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 112 through 119' Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.562A pdb=" N ARG L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix No H-bonds generated for 'chain 'L' and resid 56 through 62' Processing helix chain 'L' and resid 68 through 75 removed outlier: 5.835A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 86 removed outlier: 4.193A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.462A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.652A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.533A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG M 50 " --> pdb=" O ILE M 46 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.893A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.815A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU N 28 " --> pdb=" O MET N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 58 removed outlier: 3.511A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.692A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.707A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.905A pdb=" N LYS N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 20 removed outlier: 5.492A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.536A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 63' Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.511A pdb=" N GLY O 75 " --> pdb=" O ALA O 71 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 4.659A pdb=" N LEU O 106 " --> pdb=" O ARG O 102 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA O 107 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG O 111 " --> pdb=" O ALA O 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.752A pdb=" N LYS P 5 " --> pdb=" O SER P 1 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 103 removed outlier: 4.748A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 6.074A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.267A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 removed outlier: 4.273A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 60 removed outlier: 4.225A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE Q 56 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU Q 59 " --> pdb=" O GLN Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 removed outlier: 3.528A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 removed outlier: 4.863A pdb=" N SER Q 86 " --> pdb=" O LEU Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 101 removed outlier: 4.586A pdb=" N ASP Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE Q 97 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 removed outlier: 3.580A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 5.150A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 4.214A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR S 39 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.544A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.884A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 4 through 9 removed outlier: 3.715A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 4 through 9' Processing helix chain 'T' and resid 18 through 28 removed outlier: 4.604A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 5.087A pdb=" N ILE T 43 " --> pdb=" O THR T 39 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.949A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.580A pdb=" N ARG V 18 " --> pdb=" O LYS V 14 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.661A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.441A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 44 removed outlier: 6.600A pdb=" N LYS W 43 " --> pdb=" O GLN W 39 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE W 44 " --> pdb=" O ARG W 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 39 through 44' Processing helix chain 'X' and resid 51 through 62 removed outlier: 6.031A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 removed outlier: 3.865A pdb=" N LEU X 70 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA X 72 " --> pdb=" O ALA X 68 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ARG X 73 " --> pdb=" O GLU X 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 7 removed outlier: 4.822A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 4.130A pdb=" N GLU Y 13 " --> pdb=" O LYS Y 9 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 61 removed outlier: 3.616A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP Y 49 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS Y 54 " --> pdb=" O VAL Y 50 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU Y 57 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS Y 60 " --> pdb=" O LEU Y 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.582A pdb=" N ALA Z 21 " --> pdb=" O PRO Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.527A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain 'x' and resid 16 through 28 removed outlier: 4.217A pdb=" N SER x 21 " --> pdb=" O LYS x 17 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG x 23 " --> pdb=" O THR x 19 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS x 28 " --> pdb=" O ILE x 24 " (cutoff:3.500A) Processing helix chain 'x' and resid 44 through 51 removed outlier: 3.572A pdb=" N ARG x 48 " --> pdb=" O MET x 44 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG x 50 " --> pdb=" O LEU x 46 " (cutoff:3.500A) Processing helix chain 'x' and resid 84 through 96 removed outlier: 3.634A pdb=" N ARG x 90 " --> pdb=" O TYR x 86 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER x 91 " --> pdb=" O GLU x 87 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA x 93 " --> pdb=" O SER x 89 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA x 94 " --> pdb=" O ARG x 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS x 95 " --> pdb=" O SER x 91 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU x 96 " --> pdb=" O LEU x 92 " (cutoff:3.500A) Processing helix chain 'x' and resid 109 through 123 removed outlier: 3.559A pdb=" N LEU x 113 " --> pdb=" O GLU x 109 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS x 116 " --> pdb=" O THR x 112 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU x 121 " --> pdb=" O TYR x 117 " (cutoff:3.500A) Processing helix chain 'x' and resid 139 through 151 removed outlier: 3.760A pdb=" N ALA x 144 " --> pdb=" O PRO x 140 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU x 145 " --> pdb=" O GLU x 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU x 146 " --> pdb=" O ARG x 142 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU x 148 " --> pdb=" O ALA x 144 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP x 149 " --> pdb=" O GLU x 145 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE x 150 " --> pdb=" O GLU x 146 " (cutoff:3.500A) Processing helix chain 'x' and resid 172 through 181 removed outlier: 3.657A pdb=" N ARG x 178 " --> pdb=" O GLU x 174 " (cutoff:3.500A) Proline residue: x 181 - end of helix Processing helix chain 'x' and resid 303 through 322 removed outlier: 3.976A pdb=" N TYR x 307 " --> pdb=" O SER x 303 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU x 308 " --> pdb=" O SER x 304 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA x 309 " --> pdb=" O ASP x 305 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU x 314 " --> pdb=" O PHE x 310 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY x 315 " --> pdb=" O ARG x 311 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU x 319 " --> pdb=" O GLY x 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN x 320 " --> pdb=" O LYS x 316 " (cutoff:3.500A) Processing helix chain 'x' and resid 344 through 358 removed outlier: 3.582A pdb=" N GLU x 353 " --> pdb=" O GLU x 349 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU x 356 " --> pdb=" O GLN x 352 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU x 358 " --> pdb=" O ARG x 354 " (cutoff:3.500A) Processing helix chain 'x' and resid 392 through 397 removed outlier: 5.686A pdb=" N TYR x 397 " --> pdb=" O VAL x 393 " (cutoff:3.500A) Processing helix chain 'x' and resid 411 through 426 removed outlier: 3.625A pdb=" N LEU x 415 " --> pdb=" O PRO x 411 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY x 416 " --> pdb=" O GLN x 412 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASN x 417 " --> pdb=" O ALA x 413 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR x 420 " --> pdb=" O GLY x 416 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU x 421 " --> pdb=" O ASN x 417 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU x 424 " --> pdb=" O THR x 420 " (cutoff:3.500A) Processing helix chain 'x' and resid 446 through 452 removed outlier: 4.175A pdb=" N LEU x 452 " --> pdb=" O ALA x 448 " (cutoff:3.500A) Processing helix chain 'x' and resid 453 through 463 removed outlier: 3.520A pdb=" N ARG x 457 " --> pdb=" O ASP x 453 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU x 458 " --> pdb=" O PHE x 454 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG x 463 " --> pdb=" O LYS x 459 " (cutoff:3.500A) Processing helix chain 'x' and resid 500 through 519 removed outlier: 4.117A pdb=" N GLN x 505 " --> pdb=" O ARG x 501 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASN x 506 " --> pdb=" O ASP x 502 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL x 512 " --> pdb=" O GLY x 508 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU x 513 " --> pdb=" O ARG x 509 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET x 515 " --> pdb=" O LEU x 511 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP x 517 " --> pdb=" O GLU x 513 " (cutoff:3.500A) Processing helix chain 'x' and resid 557 through 579 removed outlier: 4.079A pdb=" N LYS x 561 " --> pdb=" O ASP x 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS x 563 " --> pdb=" O SER x 559 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU x 564 " --> pdb=" O ARG x 560 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS x 567 " --> pdb=" O LYS x 563 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS x 572 " --> pdb=" O GLN x 568 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG x 574 " --> pdb=" O GLU x 570 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN x 577 " --> pdb=" O LYS x 573 " (cutoff:3.500A) Processing helix chain 'x' and resid 585 through 590 removed outlier: 3.596A pdb=" N LEU x 589 " --> pdb=" O GLN x 585 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA x 590 " --> pdb=" O GLU x 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 585 through 590' Processing helix chain 'x' and resid 166 through 171 removed outlier: 6.612A pdb=" N VAL x 169 " --> pdb=" O GLY x 166 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN x 170 " --> pdb=" O VAL x 167 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP x 171 " --> pdb=" O GLY x 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 166 through 171' Processing sheet with id= 1, first strand: chain 'c' and resid 53 through 59 removed outlier: 4.006A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU c 58 " --> pdb=" O ARG c 65 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE c 64 " --> pdb=" O PRO c 98 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN c 100 " --> pdb=" O ILE c 64 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL c 66 " --> pdb=" O GLN c 100 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN c 102 " --> pdb=" O VAL c 66 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 164 through 170 removed outlier: 5.735A pdb=" N ARG c 164 " --> pdb=" O GLY c 155 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL c 153 " --> pdb=" O GLU c 166 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS c 199 " --> pdb=" O GLU c 152 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN c 185 " --> pdb=" O VAL c 200 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'd' and resid 141 through 145 removed outlier: 4.138A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N MET d 178 " --> pdb=" O ILE d 145 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'e' and resid 11 through 16 removed outlier: 4.238A pdb=" N GLN e 12 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS e 14 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL e 38 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 83 through 88 removed outlier: 7.366A pdb=" N HIS e 83 " --> pdb=" O PRO e 98 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 33 through 41 removed outlier: 5.354A pdb=" N GLY e 51 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR e 37 " --> pdb=" O GLY e 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY e 49 " --> pdb=" O THR e 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL e 39 " --> pdb=" O GLY e 47 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ARG e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'f' and resid 38 through 43 removed outlier: 4.066A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET f 90 " --> pdb=" O GLU f 5 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'g' and resid 73 through 77 Processing sheet with id= 9, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.417A pdb=" N ALA h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU h 61 " --> pdb=" O VAL h 25 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU h 58 " --> pdb=" O GLU h 52 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU h 52 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU h 60 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'h' and resid 102 through 106 removed outlier: 7.034A pdb=" N VAL h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'i' and resid 5 through 11 removed outlier: 3.939A pdb=" N GLY i 10 " --> pdb=" O ALA i 17 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'j' and resid 39 through 42 removed outlier: 5.960A pdb=" N ILE j 40 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'k' and resid 42 through 45 removed outlier: 3.802A pdb=" N THR k 33 " --> pdb=" O HIS k 22 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE k 23 " --> pdb=" O MET k 85 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL k 84 " --> pdb=" O THR k 108 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'l' and resid 29 through 33 removed outlier: 3.536A pdb=" N ILE l 80 " --> pdb=" O GLY l 32 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.537A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.328A pdb=" N PHE p 16 " --> pdb=" O HIS p 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'q' and resid 7 through 11 removed outlier: 3.692A pdb=" N VAL q 59 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'q' and resid 19 through 30 removed outlier: 4.636A pdb=" N LYS q 19 " --> pdb=" O ASP q 48 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP q 48 " --> pdb=" O LYS q 19 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 's' and resid 30 through 34 removed outlier: 3.594A pdb=" N THR s 33 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE s 49 " --> pdb=" O VAL s 60 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'b' and resid 88 through 92 removed outlier: 5.935A pdb=" N PHE b 89 " --> pdb=" O ILE b 66 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU b 67 " --> pdb=" O ALA b 159 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE b 161 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL b 69 " --> pdb=" O PHE b 161 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE b 185 " --> pdb=" O VAL b 162 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA b 184 " --> pdb=" O PHE b 197 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '1' and resid 7 through 12 removed outlier: 6.415A pdb=" N HIS 1 18 " --> pdb=" O SER 1 12 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '1' and resid 34 through 38 removed outlier: 3.573A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '4' and resid 14 through 19 removed outlier: 5.764A pdb=" N ILE 4 26 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN 4 35 " --> pdb=" O VAL 4 25 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS 4 33 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '5' and resid 44 through 47 removed outlier: 4.011A pdb=" N SER 5 213 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN 5 47 " --> pdb=" O LYS 5 211 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS 5 211 " --> pdb=" O ASN 5 47 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '5' and resid 60 through 64 removed outlier: 4.003A pdb=" N TYR 5 163 " --> pdb=" O GLY 5 61 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR 5 63 " --> pdb=" O VAL 5 161 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '5' and resid 75 through 79 removed outlier: 4.662A pdb=" N ALA 5 76 " --> pdb=" O VAL 5 113 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE 5 115 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 32 through 35 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'C' and resid 75 through 78 removed outlier: 4.770A pdb=" N LEU C 94 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 137 through 141 removed outlier: 4.189A pdb=" N SER C 138 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 90 through 95 removed outlier: 6.281A pdb=" N ARG C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 3 through 9 removed outlier: 4.524A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS D 204 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 10 through 16 removed outlier: 3.802A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL D 26 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP D 181 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 188 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 32 through 35 removed outlier: 6.642A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.990A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 1 through 4 removed outlier: 5.881A pdb=" N LEU E 3 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'E' and resid 44 through 47 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.786A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N MET E 188 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS E 185 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL E 187 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE E 149 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 148 " --> pdb=" O ASP E 168 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.655A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR F 34 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR F 154 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 151 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE F 155 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR F 157 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLY F 125 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'G' and resid 14 through 18 removed outlier: 5.615A pdb=" N LYS G 26 " --> pdb=" O ASP G 15 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 40 through 44 removed outlier: 3.860A pdb=" N GLY G 52 " --> pdb=" O GLU G 41 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'G' and resid 93 through 98 removed outlier: 3.533A pdb=" N SER G 105 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN G 103 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU G 104 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 112 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'G' and resid 120 through 124 removed outlier: 3.573A pdb=" N LYS G 133 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU G 132 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS G 84 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'H' and resid 17 through 20 removed outlier: 4.359A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.803A pdb=" N VAL I 60 " --> pdb=" O ALA I 6 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL I 57 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR I 59 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER I 65 " --> pdb=" O TYR I 61 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 46, first strand: chain 'J' and resid 74 through 77 removed outlier: 4.356A pdb=" N TYR J 74 " --> pdb=" O ALA J 87 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'K' and resid 5 through 9 removed outlier: 5.150A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS K 21 " --> pdb=" O THR K 6 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE K 22 " --> pdb=" O LYS K 40 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'M' and resid 62 through 66 removed outlier: 6.132A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG M 66 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL M 36 " --> pdb=" O LYS M 127 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.743A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.554A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA O 37 " --> pdb=" O ALA O 51 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP O 93 " --> pdb=" O LEU O 26 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'P' and resid 37 through 44 removed outlier: 3.791A pdb=" N VAL P 27 " --> pdb=" O PHE P 42 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY P 44 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS P 86 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER P 84 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'P' and resid 56 through 63 removed outlier: 8.134A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL P 69 " --> pdb=" O LYS P 62 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.672A pdb=" N VAL R 4 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LEU R 39 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE R 41 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN R 43 " --> pdb=" O GLU R 45 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.144A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE R 98 " --> pdb=" O GLN R 18 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU R 62 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'R' and resid 68 through 78 No H-bonds generated for sheet with id= 55 Processing sheet with id= 56, first strand: chain 'S' and resid 4 through 8 removed outlier: 3.557A pdb=" N ILE S 103 " --> pdb=" O HIS S 7 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.586A pdb=" N HIS T 15 " --> pdb=" O VAL T 31 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE T 30 " --> pdb=" O VAL T 85 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU T 32 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'U' and resid 39 through 44 removed outlier: 4.534A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.333A pdb=" N GLY U 83 " --> pdb=" O ARG U 93 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG U 93 " --> pdb=" O GLY U 83 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS U 91 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'V' and resid 6 through 9 removed outlier: 4.006A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA V 94 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL V 72 " --> pdb=" O ALA V 94 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE V 70 " --> pdb=" O ILE V 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE V 63 " --> pdb=" O ILE V 70 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'V' and resid 2 through 5 Processing sheet with id= 62, first strand: chain 'W' and resid 65 through 70 removed outlier: 6.275A pdb=" N SER W 80 " --> pdb=" O LYS W 67 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE W 78 " --> pdb=" O GLU W 69 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'X' and resid 11 through 17 removed outlier: 6.645A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Z' and resid 32 through 38 removed outlier: 6.657A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR Z 9 " --> pdb=" O MET Z 53 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'x' and resid 7 through 11 removed outlier: 3.734A pdb=" N LEU x 99 " --> pdb=" O SER x 8 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA x 98 " --> pdb=" O GLU x 125 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL x 159 " --> pdb=" O PRO x 128 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU x 130 " --> pdb=" O VAL x 159 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'x' and resid 56 through 62 removed outlier: 3.930A pdb=" N GLN x 57 " --> pdb=" O ASP x 77 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP x 77 " --> pdb=" O GLN x 57 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'x' and resid 197 through 201 removed outlier: 4.629A pdb=" N ASP x 197 " --> pdb=" O LEU x 209 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU x 209 " --> pdb=" O ASP x 197 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER x 208 " --> pdb=" O LEU x 258 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'x' and resid 229 through 234 removed outlier: 4.353A pdb=" N ASP x 221 " --> pdb=" O ALA x 234 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR x 273 " --> pdb=" O MET x 226 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'x' and resid 295 through 300 Processing sheet with id= 70, first strand: chain 'x' and resid 381 through 385 removed outlier: 8.245A pdb=" N VAL x 371 " --> pdb=" O PRO x 402 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU x 373 " --> pdb=" O ARG x 400 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR x 443 " --> pdb=" O CYS x 406 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET x 408 " --> pdb=" O LEU x 441 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR x 442 " --> pdb=" O THR x 430 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU x 444 " --> pdb=" O VAL x 428 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL x 428 " --> pdb=" O GLU x 444 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'x' and resid 496 through 499 removed outlier: 3.963A pdb=" N LEU x 497 " --> pdb=" O VAL x 483 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE x 524 " --> pdb=" O GLN x 544 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLN x 544 " --> pdb=" O PHE x 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL x 542 " --> pdb=" O ILE x 526 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'x' and resid 404 through 410 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'x' and resid 431 through 435 removed outlier: 3.771A pdb=" N ASN x 431 " --> pdb=" O THR x 442 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL x 433 " --> pdb=" O ALA x 440 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA x 440 " --> pdb=" O VAL x 433 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS x 435 " --> pdb=" O GLN x 438 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN x 438 " --> pdb=" O HIS x 435 " (cutoff:3.500A) 1528 hydrogen bonds defined for protein. 4512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2801 hydrogen bonds 4394 hydrogen bond angles 0 basepair planarities 1183 basepair parallelities 2413 stacking parallelities Total time for adding SS restraints: 211.72 Time building geometry restraints manager: 74.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 26810 1.33 - 1.45: 69567 1.45 - 1.58: 60807 1.58 - 1.71: 9561 1.71 - 1.83: 308 Bond restraints: 167053 Sorted by residual: bond pdb=" C4' F3O 6 76 " pdb=" C3' F3O 6 76 " ideal model delta sigma weight residual 1.258 1.514 -0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" C2' F3O 6 76 " pdb=" C1' F3O 6 76 " ideal model delta sigma weight residual 1.290 1.517 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" N3B GNP x 701 " pdb=" PG GNP x 701 " ideal model delta sigma weight residual 1.801 1.580 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C4' F3O 6 76 " pdb=" O4' F3O 6 76 " ideal model delta sigma weight residual 1.607 1.426 0.181 2.00e-02 2.50e+03 8.23e+01 bond pdb=" O3A GNP x 701 " pdb=" PB GNP x 701 " ideal model delta sigma weight residual 1.687 1.514 0.173 2.00e-02 2.50e+03 7.50e+01 ... (remaining 167048 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.73: 25133 105.73 - 113.65: 106136 113.65 - 121.58: 78037 121.58 - 129.51: 36498 129.51 - 137.44: 3539 Bond angle restraints: 249343 Sorted by residual: angle pdb=" C LYS M 71 " pdb=" N PRO M 72 " pdb=" CA PRO M 72 " ideal model delta sigma weight residual 119.05 130.97 -11.92 1.11e+00 8.12e-01 1.15e+02 angle pdb=" C ARG p 14 " pdb=" N PRO p 15 " pdb=" CA PRO p 15 " ideal model delta sigma weight residual 119.78 130.81 -11.03 1.03e+00 9.43e-01 1.15e+02 angle pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.78 130.50 -10.72 1.03e+00 9.43e-01 1.08e+02 angle pdb=" C LEU M 124 " pdb=" N PRO M 125 " pdb=" CA PRO M 125 " ideal model delta sigma weight residual 119.28 130.70 -11.42 1.10e+00 8.26e-01 1.08e+02 angle pdb=" N LYS W 71 " pdb=" CA LYS W 71 " pdb=" C LYS W 71 " ideal model delta sigma weight residual 108.75 117.95 -9.20 9.60e-01 1.09e+00 9.19e+01 ... (remaining 249338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 94986 35.54 - 71.08: 10584 71.08 - 106.61: 1357 106.61 - 142.15: 28 142.15 - 177.69: 32 Dihedral angle restraints: 106987 sinusoidal: 88327 harmonic: 18660 Sorted by residual: dihedral pdb=" O4' C 7 21 " pdb=" C1' C 7 21 " pdb=" N1 C 7 21 " pdb=" C2 C 7 21 " ideal model delta sinusoidal sigma weight residual -160.00 9.39 -169.39 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' C 6 75 " pdb=" C1' C 6 75 " pdb=" N1 C 6 75 " pdb=" C2 C 6 75 " ideal model delta sinusoidal sigma weight residual 200.00 33.18 166.82 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' C A2160 " pdb=" C1' C A2160 " pdb=" N1 C A2160 " pdb=" C2 C A2160 " ideal model delta sinusoidal sigma weight residual 200.00 37.25 162.75 1 1.50e+01 4.44e-03 8.34e+01 ... (remaining 106984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 26359 0.049 - 0.097: 4747 0.097 - 0.146: 618 0.146 - 0.195: 76 0.195 - 0.243: 23 Chirality restraints: 31823 Sorted by residual: chirality pdb=" C1' A A 752 " pdb=" O4' A A 752 " pdb=" C2' A A 752 " pdb=" N9 A A 752 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' A A1395 " pdb=" O4' A A1395 " pdb=" C2' A A1395 " pdb=" N9 A A1395 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C3' A A 119 " pdb=" C4' A A 119 " pdb=" O3' A A 119 " pdb=" C2' A A 119 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 31820 not shown) Planarity restraints: 13784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 212 " 0.031 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP C 212 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP C 212 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 212 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 212 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 212 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 212 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 212 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 212 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR x 241 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO x 242 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO x 242 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO x 242 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 151 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO D 152 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " -0.044 5.00e-02 4.00e+02 ... (remaining 13781 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 11 1.87 - 2.62: 5016 2.62 - 3.38: 203781 3.38 - 4.14: 476625 4.14 - 4.90: 715969 Nonbonded interactions: 1401402 Sorted by model distance: nonbonded pdb=" O ALA n 29 " pdb=" OD1 ASP n 33 " model vdw 1.106 3.040 nonbonded pdb=" CD1 PHE n 21 " pdb=" CB ALA n 25 " model vdw 1.175 3.760 nonbonded pdb=" O ARG n 41 " pdb=" N ASN n 43 " model vdw 1.277 2.520 nonbonded pdb=" CD2 HIS x 12 " pdb=" CG GLU x 109 " model vdw 1.396 3.660 nonbonded pdb=" CD2 HIS x 12 " pdb=" CB GLU x 109 " model vdw 1.504 3.660 ... (remaining 1401397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '6' and resid 1 through 75) selection = (chain '9' and resid 1 through 75) } 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: 1.730 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: 0.140 Extract box with map and model: 13.030 Check model and map are aligned: 1.640 Set scattering table: 1.070 Process input model: 526.490 Find NCS groups from input model: 3.050 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 550.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.256 167053 Z= 0.476 Angle : 0.878 20.376 249343 Z= 0.545 Chirality : 0.038 0.243 31823 Planarity : 0.004 0.080 13784 Dihedral : 22.678 177.688 94944 Min Nonbonded Distance : 1.106 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 4.81 % Allowed : 10.35 % Favored : 84.83 % Rotamer: Outliers : 0.47 % Allowed : 1.07 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.93 (0.10), residues: 6442 helix: -3.80 (0.06), residues: 1752 sheet: -4.05 (0.12), residues: 993 loop : -0.15 (0.12), residues: 3697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP C 212 HIS 0.018 0.002 HIS M 13 PHE 0.031 0.003 PHE E 85 TYR 0.039 0.003 TYR C 102 ARG 0.015 0.001 ARG m 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 712 time to evaluate : 6.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 105 MET cc_start: 0.0692 (mtt) cc_final: 0.0428 (ptt) REVERT: i 57 MET cc_start: -0.2226 (ptm) cc_final: -0.4309 (tmm) REVERT: k 85 MET cc_start: -0.3394 (mtt) cc_final: -0.3948 (mtp) REVERT: n 47 LYS cc_start: -0.1811 (OUTLIER) cc_final: -0.2366 (mmtm) REVERT: 2 1 MET cc_start: -0.2282 (tpt) cc_final: -0.3283 (mtt) REVERT: 5 218 MET cc_start: 0.0742 (ttm) cc_final: 0.0384 (ttt) REVERT: C 180 MET cc_start: -0.0666 (mmm) cc_final: -0.1881 (mmm) REVERT: C 200 MET cc_start: 0.0147 (ttp) cc_final: -0.1405 (tmm) REVERT: E 199 MET cc_start: -0.2785 (ttp) cc_final: -0.3418 (tpp) REVERT: K 1 MET cc_start: 0.1001 (mtp) cc_final: 0.0121 (ttt) REVERT: L 55 MET cc_start: -0.0341 (tpp) cc_final: -0.1794 (mmt) REVERT: O 10 ARG cc_start: 0.1354 (mtm180) cc_final: 0.0524 (tpt170) REVERT: S 1 MET cc_start: 0.0761 (mmp) cc_final: -0.2286 (tmm) REVERT: T 69 ARG cc_start: -0.1955 (OUTLIER) cc_final: -0.2957 (mpp-170) REVERT: X 55 MET cc_start: -0.2681 (mtp) cc_final: -0.4094 (mtt) REVERT: Y 1 MET cc_start: -0.1761 (ttt) cc_final: -0.3040 (tmm) REVERT: Z 46 MET cc_start: -0.0864 (mtt) cc_final: -0.1145 (mtt) REVERT: x 323 SER cc_start: -0.3057 (OUTLIER) cc_final: -0.3358 (p) REVERT: x 349 GLU cc_start: 0.1421 (OUTLIER) cc_final: 0.0719 (tp30) REVERT: x 408 MET cc_start: -0.2427 (mtm) cc_final: -0.3933 (tpt) outliers start: 25 outliers final: 5 residues processed: 736 average time/residue: 1.5457 time to fit residues: 1878.3514 Evaluate side-chains 375 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 366 time to evaluate : 6.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 33 ASP Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 39 GLU Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain x residue 323 SER Chi-restraints excluded: chain x residue 349 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 935 optimal weight: 3.9990 chunk 839 optimal weight: 9.9990 chunk 465 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 566 optimal weight: 10.0000 chunk 448 optimal weight: 9.9990 chunk 868 optimal weight: 2.9990 chunk 336 optimal weight: 0.1980 chunk 528 optimal weight: 9.9990 chunk 646 optimal weight: 9.9990 chunk 1006 optimal weight: 6.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 71 GLN ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 ASN f 55 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 5 GLN j 56 HIS k 22 HIS l 5 ASN l 75 GLN ** n 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN o 35 GLN o 50 HIS p 26 ASN p 59 HIS q 9 GLN q 45 HIS r 52 GLN b 119 GLN 0 4 GLN 0 5 ASN 5 58 ASN ** 5 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 110 ASN 5 188 ASN 5 234 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 199 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 150 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 115 GLN E 165 HIS F 4 HIS F 62 GLN G 103 ASN G 110 HIS G 138 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN L 54 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 40 GLN Q 36 GLN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS U 44 HIS U 73 ASN X 16 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN ** x 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 81 HIS x 266 HIS x 294 GLN x 352 GLN x 407 HIS x 500 HIS x 523 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0793 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 167053 Z= 0.271 Angle : 0.840 14.681 249343 Z= 0.420 Chirality : 0.042 0.486 31823 Planarity : 0.007 0.085 13784 Dihedral : 23.611 179.816 82184 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 1.75 % Allowed : 8.49 % Favored : 89.75 % Rotamer: Outliers : 2.54 % Allowed : 6.65 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.10), residues: 6442 helix: -2.07 (0.10), residues: 1872 sheet: -3.39 (0.13), residues: 1073 loop : -1.19 (0.11), residues: 3497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 212 HIS 0.026 0.003 HIS m 14 PHE 0.069 0.003 PHE n 21 TYR 0.048 0.003 TYR x 326 ARG 0.027 0.001 ARG O 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 430 time to evaluate : 6.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 20 ARG cc_start: 0.3493 (ppt170) cc_final: 0.2960 (pmt-80) REVERT: h 14 ILE cc_start: 0.4393 (OUTLIER) cc_final: 0.3952 (tt) REVERT: h 96 MET cc_start: -0.2166 (mtt) cc_final: -0.2432 (mmm) REVERT: i 57 MET cc_start: -0.1558 (ptm) cc_final: -0.1925 (ttp) REVERT: b 15 PHE cc_start: 0.1904 (m-10) cc_final: 0.1663 (m-10) REVERT: 2 1 MET cc_start: -0.1748 (tpt) cc_final: -0.2686 (mtt) REVERT: 4 11 CYS cc_start: 0.0099 (OUTLIER) cc_final: -0.0630 (t) REVERT: 5 137 MET cc_start: -0.3338 (mmt) cc_final: -0.4194 (mtt) REVERT: C 89 ASN cc_start: 0.1140 (m-40) cc_final: 0.0908 (m-40) REVERT: C 180 MET cc_start: -0.1289 (mmm) cc_final: -0.2337 (mmm) REVERT: C 200 MET cc_start: -0.0231 (ttp) cc_final: -0.0677 (tmm) REVERT: E 117 ARG cc_start: 0.4451 (mtt180) cc_final: 0.3678 (mmt180) REVERT: E 141 MET cc_start: -0.0424 (ttt) cc_final: -0.0798 (ttt) REVERT: E 188 MET cc_start: 0.1552 (tpp) cc_final: 0.1059 (tpt) REVERT: I 116 MET cc_start: 0.1762 (mtp) cc_final: 0.1543 (mtt) REVERT: I 135 MET cc_start: 0.0906 (ttt) cc_final: 0.0461 (mtt) REVERT: J 114 LEU cc_start: 0.1788 (OUTLIER) cc_final: 0.1088 (mm) REVERT: K 1 MET cc_start: 0.1825 (mtp) cc_final: 0.0731 (ttt) REVERT: M 1 MET cc_start: -0.3015 (mmm) cc_final: -0.3238 (mmm) REVERT: N 3 HIS cc_start: 0.2158 (m-70) cc_final: 0.1839 (m170) REVERT: O 10 ARG cc_start: 0.2148 (mtm180) cc_final: -0.0299 (mmp-170) REVERT: S 1 MET cc_start: 0.0260 (mmp) cc_final: -0.3942 (ptm) REVERT: X 55 MET cc_start: -0.2706 (mtp) cc_final: -0.4573 (mtt) REVERT: Y 1 MET cc_start: -0.1995 (ttt) cc_final: -0.2863 (tmm) outliers start: 136 outliers final: 64 residues processed: 522 average time/residue: 1.3890 time to fit residues: 1245.5207 Evaluate side-chains 396 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 329 time to evaluate : 5.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 150 LYS Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 55 THR Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 33 ASP Chi-restraints excluded: chain n residue 39 GLU Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 71 HIS Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain u residue 39 GLU Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 44 HIS Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain x residue 171 ASP Chi-restraints excluded: chain x residue 240 PHE Chi-restraints excluded: chain x residue 338 PHE Chi-restraints excluded: chain x residue 348 MET Chi-restraints excluded: chain x residue 397 TYR Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 548 ASN Chi-restraints excluded: chain x residue 589 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 559 optimal weight: 9.9990 chunk 312 optimal weight: 0.9990 chunk 837 optimal weight: 0.0870 chunk 685 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 chunk 1007 optimal weight: 20.0000 chunk 1088 optimal weight: 7.9990 chunk 897 optimal weight: 2.9990 chunk 999 optimal weight: 9.9990 chunk 343 optimal weight: 5.9990 chunk 808 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 ASN h 16 ASN i 50 GLN j 58 ASN l 75 GLN ** n 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN ** p 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 61 GLN ** 5 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 160 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS J 77 HIS K 5 GLN L 35 HIS ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS Y 41 HIS ** x 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 429 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0848 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 167053 Z= 0.171 Angle : 0.617 14.524 249343 Z= 0.320 Chirality : 0.034 0.284 31823 Planarity : 0.005 0.077 13784 Dihedral : 23.368 179.817 82170 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 1.47 % Allowed : 9.69 % Favored : 88.84 % Rotamer: Outliers : 2.54 % Allowed : 9.06 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.10), residues: 6442 helix: -1.27 (0.11), residues: 1908 sheet: -2.95 (0.14), residues: 1002 loop : -1.42 (0.10), residues: 3532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP b 22 HIS 0.025 0.002 HIS 3 30 PHE 0.034 0.002 PHE b 49 TYR 0.038 0.002 TYR x 397 ARG 0.020 0.001 ARG h 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 363 time to evaluate : 6.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 20 ARG cc_start: 0.3765 (ppt170) cc_final: 0.3050 (pmt-80) REVERT: g 101 MET cc_start: -0.1507 (mtt) cc_final: -0.1797 (ttm) REVERT: h 96 MET cc_start: -0.1325 (mtt) cc_final: -0.2489 (mmm) REVERT: b 15 PHE cc_start: 0.2362 (m-10) cc_final: 0.2123 (m-10) REVERT: b 26 MET cc_start: 0.0125 (mmt) cc_final: -0.0159 (mtt) REVERT: 2 1 MET cc_start: -0.1576 (tpt) cc_final: -0.2755 (mtt) REVERT: 4 11 CYS cc_start: -0.0243 (OUTLIER) cc_final: -0.1491 (t) REVERT: C 89 ASN cc_start: 0.1501 (m-40) cc_final: 0.1224 (m-40) REVERT: C 180 MET cc_start: -0.1329 (mmm) cc_final: -0.2105 (mmm) REVERT: C 200 MET cc_start: 0.0069 (ttp) cc_final: -0.1061 (tmm) REVERT: E 117 ARG cc_start: 0.4590 (mtt180) cc_final: 0.3849 (mmt180) REVERT: E 141 MET cc_start: 0.0703 (ttt) cc_final: 0.0200 (ttt) REVERT: I 135 MET cc_start: 0.0222 (ttt) cc_final: -0.0250 (mtt) REVERT: K 1 MET cc_start: 0.1982 (mtp) cc_final: -0.0182 (tpt) REVERT: M 82 MET cc_start: 0.0844 (mmp) cc_final: 0.0181 (mmp) REVERT: M 105 MET cc_start: -0.0295 (mmm) cc_final: -0.0530 (mmm) REVERT: O 10 ARG cc_start: 0.2082 (mtm180) cc_final: -0.0056 (mmp-170) REVERT: R 40 MET cc_start: 0.0311 (mpp) cc_final: -0.1442 (mmt) REVERT: S 1 MET cc_start: 0.0633 (mmp) cc_final: -0.4027 (ptm) REVERT: X 55 MET cc_start: -0.2312 (mtp) cc_final: -0.3500 (mtt) REVERT: Y 1 MET cc_start: -0.1966 (ttt) cc_final: -0.2806 (tmm) REVERT: Z 46 MET cc_start: -0.0796 (mtt) cc_final: -0.1188 (mtt) outliers start: 136 outliers final: 71 residues processed: 456 average time/residue: 1.3567 time to fit residues: 1079.3034 Evaluate side-chains 395 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 323 time to evaluate : 5.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 33 ASP Chi-restraints excluded: chain n residue 39 GLU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain p residue 60 TRP Chi-restraints excluded: chain q residue 45 HIS Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain b residue 199 ILE Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain M residue 97 GLN Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 92 TRP Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain x residue 71 TYR Chi-restraints excluded: chain x residue 240 PHE Chi-restraints excluded: chain x residue 241 THR Chi-restraints excluded: chain x residue 338 PHE Chi-restraints excluded: chain x residue 340 CYS Chi-restraints excluded: chain x residue 348 MET Chi-restraints excluded: chain x residue 548 ASN Chi-restraints excluded: chain x residue 589 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 995 optimal weight: 7.9990 chunk 757 optimal weight: 20.0000 chunk 523 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 481 optimal weight: 10.0000 chunk 676 optimal weight: 20.0000 chunk 1011 optimal weight: 9.9990 chunk 1070 optimal weight: 0.6980 chunk 528 optimal weight: 9.9990 chunk 958 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 97 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN g 86 GLN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN o 28 GLN q 9 GLN ** q 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS C 57 HIS C 116 GLN C 142 ASN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 164 GLN E 41 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN Q 13 HIS ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 HIS ** x 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 320 ASN x 347 HIS ** x 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1457 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 167053 Z= 0.340 Angle : 0.964 35.309 249343 Z= 0.476 Chirality : 0.045 0.564 31823 Planarity : 0.008 0.156 13784 Dihedral : 23.939 179.585 82166 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 34.00 Ramachandran Plot: Outliers : 1.46 % Allowed : 9.45 % Favored : 89.09 % Rotamer: Outliers : 3.98 % Allowed : 9.88 % Favored : 86.14 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.10), residues: 6442 helix: -1.57 (0.11), residues: 1867 sheet: -2.87 (0.14), residues: 1037 loop : -1.82 (0.10), residues: 3538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.005 TRP b 22 HIS 0.044 0.003 HIS x 347 PHE 0.082 0.004 PHE d 107 TYR 0.059 0.004 TYR x 63 ARG 0.024 0.001 ARG h 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 387 time to evaluate : 6.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 147 MET cc_start: 0.0977 (OUTLIER) cc_final: 0.0476 (ptm) REVERT: m 81 MET cc_start: -0.1747 (OUTLIER) cc_final: -0.1963 (ptt) REVERT: t 28 MET cc_start: -0.0744 (ptm) cc_final: -0.1214 (ptp) REVERT: 2 1 MET cc_start: -0.0894 (tpt) cc_final: -0.2983 (mmm) REVERT: 2 22 MET cc_start: 0.2306 (mtt) cc_final: 0.1977 (mtm) REVERT: 5 137 MET cc_start: -0.3233 (mmt) cc_final: -0.4310 (tpp) REVERT: C 145 MET cc_start: 0.1860 (ttm) cc_final: 0.1658 (ttm) REVERT: C 180 MET cc_start: -0.1462 (mmm) cc_final: -0.2012 (mmm) REVERT: C 200 MET cc_start: -0.0048 (ttp) cc_final: -0.1175 (tmm) REVERT: E 117 ARG cc_start: 0.4747 (mtt180) cc_final: 0.4247 (mmt180) REVERT: E 141 MET cc_start: 0.0993 (ttt) cc_final: 0.0513 (ttt) REVERT: E 188 MET cc_start: 0.1065 (tpp) cc_final: -0.0567 (tpt) REVERT: F 129 MET cc_start: -0.0239 (tpt) cc_final: -0.0721 (mmt) REVERT: H 1 MET cc_start: 0.3880 (ptm) cc_final: 0.2977 (ppp) REVERT: J 41 LYS cc_start: 0.0558 (OUTLIER) cc_final: -0.0035 (tttm) REVERT: K 1 MET cc_start: 0.1785 (mtp) cc_final: 0.0373 (tpt) REVERT: M 82 MET cc_start: 0.0908 (mmp) cc_final: 0.0114 (mmp) REVERT: N 20 MET cc_start: 0.4043 (mmm) cc_final: 0.3715 (mmp) REVERT: N 33 ILE cc_start: -0.1292 (OUTLIER) cc_final: -0.1776 (pt) REVERT: O 10 ARG cc_start: 0.2144 (mtm180) cc_final: -0.0328 (mmp-170) REVERT: S 1 MET cc_start: 0.0372 (mmp) cc_final: -0.3326 (ptm) REVERT: T 24 MET cc_start: -0.2438 (ttp) cc_final: -0.2923 (ttt) REVERT: x 113 LEU cc_start: 0.4355 (OUTLIER) cc_final: 0.4068 (mt) REVERT: x 116 CYS cc_start: -0.0468 (OUTLIER) cc_final: -0.1092 (m) REVERT: x 120 MET cc_start: 0.0649 (OUTLIER) cc_final: 0.0325 (mmt) REVERT: x 432 MET cc_start: -0.1852 (ptt) cc_final: -0.2342 (ptt) REVERT: x 567 LYS cc_start: 0.2714 (OUTLIER) cc_final: 0.2184 (pttp) REVERT: x 589 LEU cc_start: -0.1462 (OUTLIER) cc_final: -0.1800 (pp) outliers start: 213 outliers final: 104 residues processed: 542 average time/residue: 1.3529 time to fit residues: 1286.2427 Evaluate side-chains 450 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 337 time to evaluate : 6.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain d residue 105 MET Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 71 MET Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain m residue 81 MET Chi-restraints excluded: chain n residue 33 ASP Chi-restraints excluded: chain n residue 39 GLU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 45 HIS Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain u residue 32 VAL Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 22 TRP Chi-restraints excluded: chain b residue 132 GLU Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain 0 residue 39 ARG Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 48 LEU Chi-restraints excluded: chain 5 residue 83 ASN Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 181 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 103 TYR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain x residue 63 TYR Chi-restraints excluded: chain x residue 71 TYR Chi-restraints excluded: chain x residue 113 LEU Chi-restraints excluded: chain x residue 116 CYS Chi-restraints excluded: chain x residue 120 MET Chi-restraints excluded: chain x residue 122 MET Chi-restraints excluded: chain x residue 171 ASP Chi-restraints excluded: chain x residue 240 PHE Chi-restraints excluded: chain x residue 241 THR Chi-restraints excluded: chain x residue 248 THR Chi-restraints excluded: chain x residue 340 CYS Chi-restraints excluded: chain x residue 400 ARG Chi-restraints excluded: chain x residue 465 TYR Chi-restraints excluded: chain x residue 567 LYS Chi-restraints excluded: chain x residue 589 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 891 optimal weight: 6.9990 chunk 607 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 797 optimal weight: 6.9990 chunk 441 optimal weight: 10.0000 chunk 913 optimal weight: 8.9990 chunk 740 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 546 optimal weight: 10.0000 chunk 961 optimal weight: 1.9990 chunk 270 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 71 GLN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 52 GLN ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 HIS ** q 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN t 52 ASN ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 133 ASN D 49 GLN G 87 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS J 135 GLN L 35 HIS ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1732 moved from start: 0.9052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 167053 Z= 0.329 Angle : 0.978 19.631 249343 Z= 0.490 Chirality : 0.048 0.866 31823 Planarity : 0.008 0.102 13784 Dihedral : 24.614 179.491 82163 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 35.72 Ramachandran Plot: Outliers : 1.43 % Allowed : 11.30 % Favored : 87.27 % Rotamer: Outliers : 3.98 % Allowed : 12.69 % Favored : 83.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.26 % Twisted Proline : 0.45 % Twisted General : 0.14 % 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: -3.18 (0.09), residues: 6442 helix: -1.74 (0.11), residues: 1845 sheet: -2.74 (0.14), residues: 1033 loop : -2.11 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.006 TRP G 61 HIS 0.039 0.003 HIS m 12 PHE 0.065 0.004 PHE 2 5 TYR 0.045 0.004 TYR x 63 ARG 0.022 0.001 ARG h 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 416 time to evaluate : 6.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 48 LEU cc_start: 0.1658 (OUTLIER) cc_final: 0.1104 (mt) REVERT: d 69 GLU cc_start: 0.2202 (mm-30) cc_final: 0.1802 (tp30) REVERT: f 88 MET cc_start: -0.0653 (mtt) cc_final: -0.0948 (mtt) REVERT: i 57 MET cc_start: -0.1602 (ttp) cc_final: -0.1949 (tmm) REVERT: j 19 ASP cc_start: 0.4990 (OUTLIER) cc_final: 0.4674 (p0) REVERT: n 65 ARG cc_start: 0.0802 (OUTLIER) cc_final: -0.0519 (ptt180) REVERT: n 71 HIS cc_start: 0.2754 (OUTLIER) cc_final: 0.2128 (m170) REVERT: b 19 THR cc_start: 0.2962 (OUTLIER) cc_final: 0.2730 (t) REVERT: 2 1 MET cc_start: -0.0156 (tpt) cc_final: -0.0482 (tpt) REVERT: 5 1 MET cc_start: -0.3325 (OUTLIER) cc_final: -0.5014 (mmm) REVERT: 5 109 MET cc_start: -0.1220 (ppp) cc_final: -0.4239 (ptt) REVERT: C 180 MET cc_start: 0.0479 (mmm) cc_final: -0.0232 (mmm) REVERT: E 100 MET cc_start: -0.0497 (mtt) cc_final: -0.0704 (mtt) REVERT: E 117 ARG cc_start: 0.4943 (mtt180) cc_final: 0.4088 (mmt180) REVERT: E 141 MET cc_start: 0.0478 (ttt) cc_final: 0.0162 (ttt) REVERT: K 1 MET cc_start: 0.1725 (mtp) cc_final: 0.1171 (ttt) REVERT: O 10 ARG cc_start: 0.2799 (mtm180) cc_final: 0.0209 (mmp-170) REVERT: O 98 GLN cc_start: 0.1018 (OUTLIER) cc_final: 0.0646 (mp10) REVERT: R 40 MET cc_start: 0.0242 (mpp) cc_final: -0.1137 (ptp) REVERT: S 1 MET cc_start: 0.0579 (mmp) cc_final: -0.1928 (ppp) REVERT: W 81 ILE cc_start: -0.0600 (OUTLIER) cc_final: -0.0976 (mt) REVERT: Y 1 MET cc_start: 0.0012 (ttt) cc_final: -0.0360 (ttt) REVERT: x 223 VAL cc_start: -0.1519 (OUTLIER) cc_final: -0.1961 (t) REVERT: x 408 MET cc_start: 0.0381 (ptp) cc_final: -0.0014 (ptp) REVERT: x 410 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.3717 (pp) REVERT: x 432 MET cc_start: -0.1672 (ptt) cc_final: -0.2090 (ptt) REVERT: x 465 TYR cc_start: 0.1409 (OUTLIER) cc_final: 0.0975 (m-80) REVERT: x 589 LEU cc_start: -0.2285 (OUTLIER) cc_final: -0.2755 (pp) outliers start: 213 outliers final: 115 residues processed: 575 average time/residue: 1.3722 time to fit residues: 1377.9353 Evaluate side-chains 489 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 362 time to evaluate : 6.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 150 LYS Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 71 MET Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 27 LEU Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 33 ASP Chi-restraints excluded: chain n residue 39 GLU Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 71 HIS Chi-restraints excluded: chain n residue 74 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain p residue 60 TRP Chi-restraints excluded: chain q residue 45 HIS Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain u residue 32 VAL Chi-restraints excluded: chain u residue 53 VAL Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 22 TRP Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 132 GLU Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 48 LEU Chi-restraints excluded: chain 5 residue 181 ASP Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 1 SER Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain x residue 71 TYR Chi-restraints excluded: chain x residue 120 MET Chi-restraints excluded: chain x residue 122 MET Chi-restraints excluded: chain x residue 171 ASP Chi-restraints excluded: chain x residue 197 ASP Chi-restraints excluded: chain x residue 223 VAL Chi-restraints excluded: chain x residue 240 PHE Chi-restraints excluded: chain x residue 241 THR Chi-restraints excluded: chain x residue 338 PHE Chi-restraints excluded: chain x residue 348 MET Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 433 VAL Chi-restraints excluded: chain x residue 465 TYR Chi-restraints excluded: chain x residue 589 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 360 optimal weight: 0.9990 chunk 964 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 628 optimal weight: 9.9990 chunk 264 optimal weight: 7.9990 chunk 1072 optimal weight: 4.9990 chunk 889 optimal weight: 10.0000 chunk 496 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 354 optimal weight: 30.0000 chunk 562 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 12 HIS ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 HIS 0 5 ASN ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN M 97 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN X 22 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1879 moved from start: 1.0047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 167053 Z= 0.279 Angle : 0.898 21.970 249343 Z= 0.449 Chirality : 0.045 0.327 31823 Planarity : 0.007 0.111 13784 Dihedral : 24.633 179.964 82163 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 36.35 Ramachandran Plot: Outliers : 1.32 % Allowed : 10.43 % Favored : 88.25 % Rotamer: Outliers : 3.70 % Allowed : 14.07 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.26 % Twisted Proline : 0.45 % Twisted General : 0.13 % 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: -3.06 (0.10), residues: 6442 helix: -1.56 (0.11), residues: 1838 sheet: -2.69 (0.14), residues: 992 loop : -2.09 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP b 22 HIS 0.016 0.002 HIS k 118 PHE 0.029 0.003 PHE C 66 TYR 0.031 0.003 TYR x 397 ARG 0.043 0.001 ARG b 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 393 time to evaluate : 6.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 9 MET cc_start: 0.0291 (OUTLIER) cc_final: -0.0202 (ptt) REVERT: p 18 GLN cc_start: 0.0928 (OUTLIER) cc_final: 0.0672 (mt0) REVERT: s 3 ARG cc_start: 0.3732 (ptp90) cc_final: 0.1233 (mmt180) REVERT: t 28 MET cc_start: -0.0113 (ptm) cc_final: -0.0765 (ptp) REVERT: 2 1 MET cc_start: -0.1351 (tpt) cc_final: -0.1639 (tpt) REVERT: 5 1 MET cc_start: -0.2348 (OUTLIER) cc_final: -0.5649 (mmm) REVERT: 5 109 MET cc_start: -0.1598 (ppp) cc_final: -0.4349 (ptt) REVERT: 5 137 MET cc_start: -0.1912 (mtt) cc_final: -0.2391 (mtt) REVERT: C 180 MET cc_start: 0.0198 (mmm) cc_final: -0.0359 (mmm) REVERT: C 231 HIS cc_start: 0.2039 (OUTLIER) cc_final: 0.1589 (m-70) REVERT: D 11 MET cc_start: 0.0876 (ppp) cc_final: 0.0619 (tmm) REVERT: E 100 MET cc_start: -0.0596 (mtt) cc_final: -0.1211 (mtt) REVERT: E 117 ARG cc_start: 0.5114 (mtt180) cc_final: 0.4092 (mmt180) REVERT: F 95 MET cc_start: 0.0355 (tpp) cc_final: 0.0004 (tpp) REVERT: G 22 VAL cc_start: -0.2136 (OUTLIER) cc_final: -0.2386 (m) REVERT: M 82 MET cc_start: 0.1485 (mmp) cc_final: 0.1020 (mmp) REVERT: M 97 GLN cc_start: 0.2487 (OUTLIER) cc_final: 0.2088 (pt0) REVERT: N 51 LEU cc_start: -0.0935 (OUTLIER) cc_final: -0.1950 (mp) REVERT: O 10 ARG cc_start: 0.2832 (mtm180) cc_final: 0.0834 (mmp-170) REVERT: P 12 MET cc_start: 0.1086 (OUTLIER) cc_final: 0.0619 (mtp) REVERT: S 1 MET cc_start: 0.1296 (mmp) cc_final: -0.1861 (ptm) REVERT: x 432 MET cc_start: -0.1803 (ptt) cc_final: -0.2249 (ptt) REVERT: x 589 LEU cc_start: -0.1956 (OUTLIER) cc_final: -0.2498 (pp) outliers start: 198 outliers final: 119 residues processed: 535 average time/residue: 1.3375 time to fit residues: 1255.4831 Evaluate side-chains 480 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 352 time to evaluate : 6.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 167 TRP Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 71 MET Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 152 MET Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 67 GLU Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 33 ASP Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 45 HIS Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain u residue 53 VAL Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 132 GLU Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 48 LEU Chi-restraints excluded: chain 5 residue 181 ASP Chi-restraints excluded: chain 5 residue 202 THR Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 229 HIS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 97 GLN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 97 PHE Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain x residue 63 TYR Chi-restraints excluded: chain x residue 71 TYR Chi-restraints excluded: chain x residue 116 CYS Chi-restraints excluded: chain x residue 122 MET Chi-restraints excluded: chain x residue 171 ASP Chi-restraints excluded: chain x residue 197 ASP Chi-restraints excluded: chain x residue 240 PHE Chi-restraints excluded: chain x residue 241 THR Chi-restraints excluded: chain x residue 370 VAL Chi-restraints excluded: chain x residue 433 VAL Chi-restraints excluded: chain x residue 589 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 1033 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 610 optimal weight: 9.9990 chunk 782 optimal weight: 0.9980 chunk 606 optimal weight: 10.0000 chunk 902 optimal weight: 0.0170 chunk 598 optimal weight: 20.0000 chunk 1067 optimal weight: 0.0020 chunk 668 optimal weight: 9.9990 chunk 651 optimal weight: 9.9990 chunk 493 optimal weight: 9.9990 overall best weight: 4.2030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 120 HIS ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN ** x 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 593 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1875 moved from start: 1.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 167053 Z= 0.226 Angle : 0.800 18.831 249343 Z= 0.405 Chirality : 0.042 0.320 31823 Planarity : 0.006 0.113 13784 Dihedral : 24.654 179.463 82160 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 31.31 Ramachandran Plot: Outliers : 1.24 % Allowed : 10.51 % Favored : 88.25 % Rotamer: Outliers : 3.48 % Allowed : 15.10 % Favored : 81.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.26 % Twisted Proline : 0.45 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.10), residues: 6442 helix: -1.31 (0.11), residues: 1851 sheet: -2.65 (0.14), residues: 1010 loop : -2.08 (0.10), residues: 3581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP b 22 HIS 0.053 0.002 HIS b 14 PHE 0.042 0.002 PHE R 53 TYR 0.022 0.002 TYR x 397 ARG 0.026 0.001 ARG 1 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 382 time to evaluate : 6.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 9 MET cc_start: 0.0091 (OUTLIER) cc_final: -0.0896 (ptt) REVERT: g 70 ARG cc_start: 0.0401 (OUTLIER) cc_final: -0.0676 (pmt-80) REVERT: i 46 MET cc_start: -0.0211 (ppp) cc_final: -0.0478 (ppp) REVERT: i 57 MET cc_start: 0.0031 (tmm) cc_final: -0.0347 (tmm) REVERT: n 49 GLN cc_start: -0.2031 (OUTLIER) cc_final: -0.5091 (pp30) REVERT: s 3 ARG cc_start: 0.4454 (ptp90) cc_final: 0.1556 (mtt90) REVERT: 1 19 PHE cc_start: 0.4014 (OUTLIER) cc_final: 0.3102 (p90) REVERT: 2 1 MET cc_start: -0.0472 (tpt) cc_final: -0.0797 (tpt) REVERT: 2 22 MET cc_start: 0.1385 (mtt) cc_final: 0.0350 (mtt) REVERT: 5 1 MET cc_start: -0.2669 (OUTLIER) cc_final: -0.5974 (mtp) REVERT: 5 109 MET cc_start: -0.1012 (ppp) cc_final: -0.3910 (ptt) REVERT: C 47 ARG cc_start: 0.3003 (OUTLIER) cc_final: 0.0829 (mmt90) REVERT: C 180 MET cc_start: 0.0019 (mmm) cc_final: -0.0704 (mmm) REVERT: E 1 MET cc_start: 0.2695 (OUTLIER) cc_final: 0.1959 (pmm) REVERT: E 100 MET cc_start: -0.0584 (mtt) cc_final: -0.0810 (mtt) REVERT: E 117 ARG cc_start: 0.4901 (mtt180) cc_final: 0.3981 (mmt180) REVERT: I 126 ARG cc_start: 0.2755 (mmp-170) cc_final: 0.2406 (mmp-170) REVERT: O 10 ARG cc_start: 0.2777 (mtm180) cc_final: 0.0771 (mmp-170) REVERT: P 49 ILE cc_start: 0.3483 (OUTLIER) cc_final: 0.2535 (mp) REVERT: S 1 MET cc_start: 0.0933 (mmp) cc_final: -0.2203 (ptm) REVERT: W 81 ILE cc_start: -0.0405 (OUTLIER) cc_final: -0.0696 (mt) REVERT: x 223 VAL cc_start: -0.0998 (OUTLIER) cc_final: -0.1353 (t) REVERT: x 340 CYS cc_start: -0.2128 (OUTLIER) cc_final: -0.2825 (m) REVERT: x 432 MET cc_start: -0.1576 (ptt) cc_final: -0.1947 (ptt) REVERT: x 589 LEU cc_start: -0.1952 (OUTLIER) cc_final: -0.2489 (pp) outliers start: 186 outliers final: 120 residues processed: 520 average time/residue: 1.3081 time to fit residues: 1193.5467 Evaluate side-chains 486 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 354 time to evaluate : 6.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 150 LYS Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 71 MET Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 67 GLU Chi-restraints excluded: chain g residue 70 ARG Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 33 ASP Chi-restraints excluded: chain n residue 49 GLN Chi-restraints excluded: chain n residue 74 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 45 HIS Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain u residue 53 VAL Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 22 TRP Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 132 GLU Chi-restraints excluded: chain 0 residue 18 HIS Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 48 LEU Chi-restraints excluded: chain 5 residue 181 ASP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain x residue 53 THR Chi-restraints excluded: chain x residue 71 TYR Chi-restraints excluded: chain x residue 116 CYS Chi-restraints excluded: chain x residue 122 MET Chi-restraints excluded: chain x residue 197 ASP Chi-restraints excluded: chain x residue 223 VAL Chi-restraints excluded: chain x residue 240 PHE Chi-restraints excluded: chain x residue 241 THR Chi-restraints excluded: chain x residue 340 CYS Chi-restraints excluded: chain x residue 433 VAL Chi-restraints excluded: chain x residue 465 TYR Chi-restraints excluded: chain x residue 589 LEU Chi-restraints excluded: chain x residue 599 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 660 optimal weight: 20.0000 chunk 426 optimal weight: 20.0000 chunk 637 optimal weight: 50.0000 chunk 321 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 678 optimal weight: 9.9990 chunk 727 optimal weight: 8.9990 chunk 527 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 839 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 HIS ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 110 GLN k 28 ASN m 52 GLN ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 45 HIS ** q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN E 29 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 110 HIS G 114 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS R 86 GLN ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2396 moved from start: 1.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.229 167053 Z= 0.430 Angle : 1.264 35.145 249343 Z= 0.615 Chirality : 0.058 0.727 31823 Planarity : 0.010 0.234 13784 Dihedral : 25.609 179.814 82160 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 57.06 Ramachandran Plot: Outliers : 1.32 % Allowed : 13.35 % Favored : 85.33 % Rotamer: Outliers : 4.09 % Allowed : 15.27 % Favored : 80.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.26 % Twisted Proline : 0.45 % Twisted General : 0.19 % 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: -3.60 (0.09), residues: 6442 helix: -2.19 (0.10), residues: 1797 sheet: -2.76 (0.15), residues: 920 loop : -2.45 (0.09), residues: 3725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP b 22 HIS 0.071 0.005 HIS i 81 PHE 0.075 0.005 PHE b 15 TYR 0.068 0.005 TYR M 103 ARG 0.037 0.002 ARG c 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 420 time to evaluate : 6.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 1 MET cc_start: -0.0244 (OUTLIER) cc_final: -0.0640 (tmm) REVERT: f 9 MET cc_start: -0.0117 (OUTLIER) cc_final: -0.0782 (ptt) REVERT: j 68 ARG cc_start: 0.4813 (OUTLIER) cc_final: 0.4110 (mtp180) REVERT: j 71 LEU cc_start: 0.2810 (tp) cc_final: 0.2509 (tp) REVERT: n 49 GLN cc_start: -0.1794 (OUTLIER) cc_final: -0.3681 (mp10) REVERT: t 28 MET cc_start: 0.0489 (ptm) cc_final: 0.0178 (ptp) REVERT: b 26 MET cc_start: 0.1286 (mtp) cc_final: 0.0836 (mtm) REVERT: b 99 MET cc_start: -0.1333 (ptp) cc_final: -0.1611 (ptp) REVERT: 2 1 MET cc_start: -0.0768 (tpt) cc_final: -0.1041 (tpt) REVERT: 2 22 MET cc_start: 0.1001 (mtt) cc_final: 0.0050 (mtt) REVERT: 5 1 MET cc_start: -0.2141 (mmt) cc_final: -0.5476 (mmt) REVERT: C 47 ARG cc_start: 0.3617 (OUTLIER) cc_final: 0.0939 (mmt90) REVERT: C 180 MET cc_start: 0.0308 (mmm) cc_final: -0.0174 (mmm) REVERT: C 242 HIS cc_start: 0.1443 (OUTLIER) cc_final: 0.1231 (m90) REVERT: E 100 MET cc_start: -0.0462 (mtt) cc_final: -0.1061 (mtt) REVERT: E 117 ARG cc_start: 0.4857 (mtt180) cc_final: 0.3751 (mmt180) REVERT: O 10 ARG cc_start: 0.3593 (mtm180) cc_final: 0.1124 (mmp-170) REVERT: Q 2 ARG cc_start: 0.2947 (ttt-90) cc_final: 0.2485 (ttt-90) REVERT: Q 4 LYS cc_start: -0.0687 (OUTLIER) cc_final: -0.1014 (pttm) REVERT: R 1 MET cc_start: 0.3370 (tpt) cc_final: 0.2632 (tpt) REVERT: S 1 MET cc_start: 0.1475 (mmp) cc_final: 0.0390 (mmp) REVERT: V 46 LYS cc_start: 0.5666 (OUTLIER) cc_final: 0.5431 (tttt) REVERT: x 24 ILE cc_start: -0.2960 (OUTLIER) cc_final: -0.3576 (tt) REVERT: x 308 GLU cc_start: -0.0332 (OUTLIER) cc_final: -0.1589 (tt0) REVERT: x 351 ILE cc_start: -0.0583 (OUTLIER) cc_final: -0.1391 (mm) REVERT: x 432 MET cc_start: -0.1435 (ptt) cc_final: -0.1806 (ptt) REVERT: x 589 LEU cc_start: -0.0717 (OUTLIER) cc_final: -0.1159 (pp) outliers start: 219 outliers final: 136 residues processed: 574 average time/residue: 1.3387 time to fit residues: 1346.5064 Evaluate side-chains 530 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 382 time to evaluate : 8.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 135 LYS Chi-restraints excluded: chain c residue 150 LYS Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain e residue 152 MET Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 4 ARG Chi-restraints excluded: chain g residue 67 GLU Chi-restraints excluded: chain g residue 70 ARG Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 49 GLN Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 74 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain u residue 53 VAL Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 22 TRP Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 59 ILE Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 132 GLU Chi-restraints excluded: chain 0 residue 18 HIS Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 48 LEU Chi-restraints excluded: chain 5 residue 181 ASP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 17 LYS Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 44 HIS Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 80 HIS Chi-restraints excluded: chain W residue 10 ARG Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 71 TYR Chi-restraints excluded: chain x residue 113 LEU Chi-restraints excluded: chain x residue 116 CYS Chi-restraints excluded: chain x residue 120 MET Chi-restraints excluded: chain x residue 172 VAL Chi-restraints excluded: chain x residue 197 ASP Chi-restraints excluded: chain x residue 240 PHE Chi-restraints excluded: chain x residue 241 THR Chi-restraints excluded: chain x residue 308 GLU Chi-restraints excluded: chain x residue 351 ILE Chi-restraints excluded: chain x residue 400 ARG Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 465 TYR Chi-restraints excluded: chain x residue 564 LEU Chi-restraints excluded: chain x residue 589 LEU Chi-restraints excluded: chain x residue 599 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 971 optimal weight: 5.9990 chunk 1023 optimal weight: 20.0000 chunk 933 optimal weight: 4.9990 chunk 995 optimal weight: 3.9990 chunk 1022 optimal weight: 8.9990 chunk 598 optimal weight: 20.0000 chunk 433 optimal weight: 10.0000 chunk 781 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 chunk 899 optimal weight: 3.9990 chunk 941 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 76 GLN ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN ** n 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS D 32 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS J 76 HIS ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 294 GLN ** x 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2152 moved from start: 1.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 167053 Z= 0.223 Angle : 0.859 18.763 249343 Z= 0.432 Chirality : 0.044 0.405 31823 Planarity : 0.006 0.080 13784 Dihedral : 25.261 179.988 82158 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 33.60 Ramachandran Plot: Outliers : 1.16 % Allowed : 11.05 % Favored : 87.78 % Rotamer: Outliers : 2.77 % Allowed : 17.45 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.26 % Twisted Proline : 0.45 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.09), residues: 6442 helix: -1.71 (0.11), residues: 1870 sheet: -2.67 (0.15), residues: 928 loop : -2.34 (0.10), residues: 3644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP b 22 HIS 0.016 0.002 HIS P 76 PHE 0.051 0.003 PHE u 12 TYR 0.030 0.002 TYR c 168 ARG 0.035 0.001 ARG x 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 404 time to evaluate : 6.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 134 MET cc_start: 0.2193 (mtm) cc_final: 0.1437 (mtm) REVERT: d 105 MET cc_start: -0.1508 (ptt) cc_final: -0.1811 (ptt) REVERT: g 70 ARG cc_start: 0.0274 (OUTLIER) cc_final: -0.0148 (pmt-80) REVERT: h 16 ASN cc_start: 0.6207 (p0) cc_final: 0.5820 (p0) REVERT: h 96 MET cc_start: -0.1466 (tpp) cc_final: -0.1775 (tpp) REVERT: i 57 MET cc_start: 0.0631 (tmm) cc_final: 0.0200 (tmm) REVERT: j 68 ARG cc_start: 0.5404 (OUTLIER) cc_final: 0.4394 (mtp180) REVERT: t 28 MET cc_start: 0.0146 (ptm) cc_final: -0.0054 (ttp) REVERT: b 26 MET cc_start: 0.1397 (mtp) cc_final: 0.1033 (mtm) REVERT: 2 1 MET cc_start: -0.1057 (tpt) cc_final: -0.1289 (tpt) REVERT: 2 22 MET cc_start: 0.1356 (mtt) cc_final: 0.0469 (mtt) REVERT: 5 1 MET cc_start: -0.2153 (mmt) cc_final: -0.5483 (mmt) REVERT: C 47 ARG cc_start: 0.2767 (OUTLIER) cc_final: 0.0031 (mmt90) REVERT: C 180 MET cc_start: -0.0057 (mmm) cc_final: -0.0832 (mmm) REVERT: F 16 MET cc_start: -0.0545 (mmp) cc_final: -0.0782 (mmm) REVERT: M 82 MET cc_start: 0.0653 (mmp) cc_final: -0.2024 (tpt) REVERT: N 51 LEU cc_start: -0.1011 (OUTLIER) cc_final: -0.2053 (mp) REVERT: O 10 ARG cc_start: 0.2788 (mtm180) cc_final: 0.0918 (mmp-170) REVERT: R 40 MET cc_start: 0.0408 (pmm) cc_final: -0.0178 (pmm) REVERT: S 1 MET cc_start: 0.0368 (mmp) cc_final: -0.0448 (mmp) REVERT: W 57 THR cc_start: -0.0355 (OUTLIER) cc_final: -0.0805 (m) REVERT: x 308 GLU cc_start: -0.0096 (OUTLIER) cc_final: -0.1237 (tt0) REVERT: x 351 ILE cc_start: -0.0937 (OUTLIER) cc_final: -0.2029 (mm) REVERT: x 432 MET cc_start: -0.2113 (ptt) cc_final: -0.2383 (ptt) REVERT: x 515 MET cc_start: -0.0279 (ptt) cc_final: -0.0553 (ptt) REVERT: x 589 LEU cc_start: -0.0807 (OUTLIER) cc_final: -0.1260 (pp) REVERT: x 599 LYS cc_start: 0.2753 (OUTLIER) cc_final: 0.1999 (pttm) outliers start: 148 outliers final: 105 residues processed: 512 average time/residue: 1.3425 time to fit residues: 1199.4080 Evaluate side-chains 485 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 371 time to evaluate : 6.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 150 LYS Chi-restraints excluded: chain c residue 195 VAL Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 71 MET Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain g residue 70 ARG Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 74 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 45 HIS Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 22 TRP Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 103 TRP Chi-restraints excluded: chain b residue 132 GLU Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 18 HIS Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 48 LEU Chi-restraints excluded: chain 5 residue 181 ASP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 31 TYR Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain x residue 71 TYR Chi-restraints excluded: chain x residue 116 CYS Chi-restraints excluded: chain x residue 197 ASP Chi-restraints excluded: chain x residue 240 PHE Chi-restraints excluded: chain x residue 241 THR Chi-restraints excluded: chain x residue 308 GLU Chi-restraints excluded: chain x residue 351 ILE Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 465 TYR Chi-restraints excluded: chain x residue 589 LEU Chi-restraints excluded: chain x residue 599 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 991 optimal weight: 0.0470 chunk 653 optimal weight: 10.0000 chunk 1052 optimal weight: 2.9990 chunk 642 optimal weight: 50.0000 chunk 499 optimal weight: 9.9990 chunk 731 optimal weight: 9.9990 chunk 1103 optimal weight: 30.0000 chunk 1015 optimal weight: 4.9990 chunk 879 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 678 optimal weight: 9.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 GLN ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 0 5 ASN ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN X 22 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2309 moved from start: 1.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 167053 Z= 0.274 Angle : 0.932 18.346 249343 Z= 0.463 Chirality : 0.047 1.028 31823 Planarity : 0.007 0.126 13784 Dihedral : 25.322 178.437 82158 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 40.56 Ramachandran Plot: Outliers : 1.04 % Allowed : 12.74 % Favored : 86.22 % Rotamer: Outliers : 2.22 % Allowed : 18.14 % Favored : 79.63 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.26 % Twisted Proline : 0.45 % Twisted General : 0.05 % 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: -3.30 (0.09), residues: 6442 helix: -1.60 (0.11), residues: 1854 sheet: -2.67 (0.15), residues: 958 loop : -2.42 (0.10), residues: 3630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP X 38 HIS 0.021 0.002 HIS P 76 PHE 0.048 0.003 PHE u 12 TYR 0.033 0.003 TYR h 65 ARG 0.074 0.001 ARG h 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12884 Ramachandran restraints generated. 6442 Oldfield, 0 Emsley, 6442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 372 time to evaluate : 6.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 4 ARG cc_start: -0.1027 (OUTLIER) cc_final: -0.1755 (ptp-170) REVERT: h 96 MET cc_start: -0.1053 (tpp) cc_final: -0.1770 (tpp) REVERT: t 28 MET cc_start: 0.0258 (ptm) cc_final: 0.0030 (ptp) REVERT: b 26 MET cc_start: 0.1619 (mtp) cc_final: 0.1282 (mtm) REVERT: 2 1 MET cc_start: -0.0800 (tpt) cc_final: -0.1021 (tpt) REVERT: 2 22 MET cc_start: 0.1737 (mtt) cc_final: 0.0968 (mtt) REVERT: C 47 ARG cc_start: 0.2526 (OUTLIER) cc_final: -0.0045 (mmt90) REVERT: C 180 MET cc_start: 0.0056 (mmm) cc_final: -0.0695 (mmm) REVERT: C 220 ARG cc_start: 0.1404 (OUTLIER) cc_final: -0.1118 (mmp-170) REVERT: C 255 LYS cc_start: 0.2975 (OUTLIER) cc_final: 0.2428 (ptpp) REVERT: E 117 ARG cc_start: 0.4810 (mtt180) cc_final: 0.3991 (mmt180) REVERT: N 51 LEU cc_start: -0.1068 (OUTLIER) cc_final: -0.1916 (mp) REVERT: O 10 ARG cc_start: 0.2795 (mtm180) cc_final: 0.0955 (mmp-170) REVERT: S 1 MET cc_start: 0.0970 (mmp) cc_final: 0.0310 (mmp) REVERT: V 46 LYS cc_start: 0.5779 (OUTLIER) cc_final: 0.5570 (tttm) REVERT: Z 46 MET cc_start: 0.1084 (mmt) cc_final: 0.0561 (mmt) REVERT: x 24 ILE cc_start: -0.2618 (OUTLIER) cc_final: -0.3122 (tt) REVERT: x 308 GLU cc_start: 0.0165 (OUTLIER) cc_final: -0.1102 (tt0) REVERT: x 351 ILE cc_start: -0.0739 (OUTLIER) cc_final: -0.1813 (mm) REVERT: x 589 LEU cc_start: -0.1549 (OUTLIER) cc_final: -0.1848 (pp) REVERT: x 599 LYS cc_start: 0.3357 (OUTLIER) cc_final: 0.1377 (ttpt) outliers start: 119 outliers final: 91 residues processed: 463 average time/residue: 1.3614 time to fit residues: 1102.5993 Evaluate side-chains 459 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 357 time to evaluate : 6.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 150 LYS Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain g residue 4 ARG Chi-restraints excluded: chain g residue 70 ARG Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 74 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 45 HIS Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 22 TRP Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 103 TRP Chi-restraints excluded: chain b residue 132 GLU Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 18 HIS Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 48 LEU Chi-restraints excluded: chain 5 residue 181 ASP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 71 TYR Chi-restraints excluded: chain x residue 116 CYS Chi-restraints excluded: chain x residue 197 ASP Chi-restraints excluded: chain x residue 223 VAL Chi-restraints excluded: chain x residue 240 PHE Chi-restraints excluded: chain x residue 241 THR Chi-restraints excluded: chain x residue 308 GLU Chi-restraints excluded: chain x residue 351 ILE Chi-restraints excluded: chain x residue 410 LEU Chi-restraints excluded: chain x residue 465 TYR Chi-restraints excluded: chain x residue 589 LEU Chi-restraints excluded: chain x residue 599 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 538 optimal weight: 10.0000 chunk 698 optimal weight: 10.0000 chunk 936 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 810 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 880 optimal weight: 8.9990 chunk 368 optimal weight: 8.9990 chunk 904 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN ** n 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.129541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.120487 restraints weight = 767104.051| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 3.41 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4078 moved from start: 1.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.197 167053 Z= 0.364 Angle : 1.138 26.139 249343 Z= 0.566 Chirality : 0.054 0.535 31823 Planarity : 0.009 0.212 13784 Dihedral : 26.072 179.173 82158 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 49.53 Ramachandran Plot: Outliers : 1.21 % Allowed : 13.30 % Favored : 85.49 % Rotamer: Outliers : 2.65 % Allowed : 18.01 % Favored : 79.33 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.24 % Twisted Proline : 1.35 % Twisted General : 0.27 % 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: -3.72 (0.09), residues: 6442 helix: -2.13 (0.10), residues: 1823 sheet: -2.86 (0.15), residues: 923 loop : -2.60 (0.09), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.005 TRP M 92 HIS 0.026 0.003 HIS C 242 PHE 0.051 0.004 PHE u 12 TYR 0.037 0.004 TYR R 2 ARG 0.047 0.002 ARG j 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24672.32 seconds wall clock time: 444 minutes 8.30 seconds (26648.30 seconds total)